diff --git a/.gitignore b/.gitignore
index 777fd2ad..34c5f7bb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+# Developer's secret diary
+Notes.md
+
# Cache with transcript/protein pickle files
.gpsea_cache
dev/
diff --git a/docs/cohort-data/CYP21A2.0.1.20.json b/docs/cohort-data/CYP21A2.0.1.20.json
index bb9bc8e2..081709b8 100644
--- a/docs/cohort-data/CYP21A2.0.1.20.json
+++ b/docs/cohort-data/CYP21A2.0.1.20.json
@@ -2,71 +2,78 @@
"members": [
{
"labels": {
- "label": "individual 39",
- "meta_label": "PMID_30968594_individual_39"
+ "label": "individual 10",
+ "meta_label": "PMID_30968594_individual_10"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0008665",
+ "is_present": true,
+ "onset": null
+ },
{
"term_id": "HP:0000953",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0040171",
- "is_present": true
+ "term_id": "HP:0030088",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0003154",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011731",
- "is_present": false
+ "term_id": "HP:0008163",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0000870",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0025133",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [
- {
- "test_term_id": "LOINC:1668-3",
- "test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 69.0,
- "unit": "UCUM:ng/dL"
- },
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 148.0,
+ "test_result": 614.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 190.0,
+ "test_result": 267.1,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 144.8,
+ "test_result": 132.2,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2842-3",
"test_name": "Prolactin [Mass/Vol]",
- "test_result": 73.31,
+ "test_result": 131.28,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2243-4",
"test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 26.89,
+ "test_result": 31.74,
"unit": "UCUM:ng/dL"
}
],
@@ -74,7 +81,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 20.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -82,8 +93,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 32039425,
- "end": 32039426,
+ "start": 32040420,
+ "end": 32040421,
"contig": {
"name": "6",
"genbank_acc": "CM000668.2",
@@ -93,8 +104,8 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -103,50 +114,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_000500.9",
- "hgvs_cdna": "NM_000500.9:c.518T>A",
+ "hgvs_cdna": "NM_000500.9:c.955C>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_000491.4",
- "hgvsp": "NP_000491.4:p.Ile173Asn",
+ "hgvsp": "NP_000491.4:p.Gln319Ter",
"protein_effect_location": {
- "start": 172,
- "end": 173
+ "start": 318,
+ "end": 319
}
},
- {
- "gene_id": "C4B",
- "transcript_id": "NM_001002029.4",
- "hgvs_cdna": null,
- "is_preferred": true,
- "variant_effects": [
- "DOWNSTREAM_GENE_VARIANT"
- ],
- "overlapping_exons": null,
- "protein_id": "NP_001002029.3",
- "hgvsp": null,
- "protein_effect_location": null
- },
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.428T>A",
+ "hgvs_cdna": "NM_001128590.4:c.865C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Ile143Asn",
+ "hgvsp": "NP_001122062.3:p.Gln289Ter",
"protein_effect_location": {
- "start": 142,
- "end": 143
+ "start": 288,
+ "end": 289
}
},
{
@@ -165,37 +163,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.113T>A",
+ "hgvs_cdna": "NM_001368143.2:c.550C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_001355072.1",
- "hgvsp": "NP_001355072.1:p.Ile38Asn",
+ "hgvsp": "NP_001355072.1:p.Gln184Ter",
"protein_effect_location": {
- "start": 37,
- "end": 38
+ "start": 183,
+ "end": 184
}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.113T>A",
+ "hgvs_cdna": "NM_001368144.2:c.550C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_001355073.1",
- "hgvsp": "NP_001355073.1:p.Ile38Asn",
+ "hgvsp": "NP_001355073.1:p.Gln184Ter",
"protein_effect_location": {
- "start": 37,
- "end": 38
+ "start": 183,
+ "end": 184
}
},
{
@@ -228,8 +226,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 39",
- "meta_label": "PMID_30968594_individual_39"
+ "label": "individual 10",
+ "meta_label": "PMID_30968594_individual_10"
}
],
"genotypes": [
@@ -558,8 +556,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 39",
- "meta_label": "PMID_30968594_individual_39"
+ "label": "individual 10",
+ "meta_label": "PMID_30968594_individual_10"
}
],
"genotypes": [
@@ -571,65 +569,79 @@
},
{
"labels": {
- "label": "individual 54",
- "meta_label": "PMID_30968594_individual_54"
+ "label": "individual 11",
+ "meta_label": "PMID_30968594_individual_11"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0008665",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000953",
- "is_present": true
+ "term_id": "HP:0030088",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030087",
- "is_present": false
+ "term_id": "HP:0003154",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011043",
- "is_present": false
+ "term_id": "HP:0011731",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0008163",
- "is_present": true
+ "term_id": "HP:0000870",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000870",
- "is_present": true
+ "term_id": "HP:0008214",
+ "is_present": true,
+ "onset": null
}
],
"measurements": [
{
"test_term_id": "LOINC:1668-3",
"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 50.2,
+ "test_result": 533.7,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 69.0,
+ "test_result": 630.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 56.68,
+ "test_result": 100.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 75.32,
+ "test_result": 284.2,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2842-3",
"test_name": "Prolactin [Mass/Vol]",
- "test_result": 22.87,
+ "test_result": 50.92,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2243-4",
+ "test_name": "Estradiol (E2) [Mass/Vol]",
+ "test_result": 0.01,
"unit": "UCUM:ng/dL"
}
],
@@ -637,7 +649,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 60.875,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -645,8 +661,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 32039425,
- "end": 32039426,
+ "start": 32039806,
+ "end": 32039807,
"contig": {
"name": "6",
"genbank_acc": "CM000668.2",
@@ -666,19 +682,19 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_000500.9",
- "hgvs_cdna": "NM_000500.9:c.518T>A",
+ "hgvs_cdna": "NM_000500.9:c.710T>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 6
],
"protein_id": "NP_000491.4",
- "hgvsp": "NP_000491.4:p.Ile173Asn",
+ "hgvsp": "NP_000491.4:p.Ile237Asn",
"protein_effect_location": {
- "start": 172,
- "end": 173
+ "start": 236,
+ "end": 237
}
},
{
@@ -697,19 +713,19 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.428T>A",
+ "hgvs_cdna": "NM_001128590.4:c.620T>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Ile143Asn",
+ "hgvsp": "NP_001122062.3:p.Ile207Asn",
"protein_effect_location": {
- "start": 142,
- "end": 143
+ "start": 206,
+ "end": 207
}
},
{
@@ -728,37 +744,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.113T>A",
+ "hgvs_cdna": "NM_001368143.2:c.305T>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 6
],
"protein_id": "NP_001355072.1",
- "hgvsp": "NP_001355072.1:p.Ile38Asn",
+ "hgvsp": "NP_001355072.1:p.Ile102Asn",
"protein_effect_location": {
- "start": 37,
- "end": 38
+ "start": 101,
+ "end": 102
}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.113T>A",
+ "hgvs_cdna": "NM_001368144.2:c.305T>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_001355073.1",
- "hgvsp": "NP_001355073.1:p.Ile38Asn",
+ "hgvsp": "NP_001355073.1:p.Ile102Asn",
"protein_effect_location": {
- "start": 37,
- "end": 38
+ "start": 101,
+ "end": 102
}
},
{
@@ -791,385 +807,329 @@
"genotypes": {
"samples": [
{
- "label": "individual 54",
- "meta_label": "PMID_30968594_individual_54"
+ "label": "individual 11",
+ "meta_label": "PMID_30968594_individual_11"
}
],
"genotypes": [
- "HOMOZYGOUS_ALTERNATE"
+ "HETEROZYGOUS"
]
}
- }
- ]
- },
- {
- "labels": {
- "label": "individual 42",
- "meta_label": "PMID_30968594_individual_42"
- },
- "sex": "FEMALE",
- "phenotypes": [
- {
- "term_id": "HP:0001007",
- "is_present": true
- },
- {
- "term_id": "HP:0008665",
- "is_present": true
- },
- {
- "term_id": "HP:0001061",
- "is_present": true
- },
- {
- "term_id": "HP:0030088",
- "is_present": true
- },
- {
- "term_id": "HP:0003154",
- "is_present": true
- },
- {
- "term_id": "HP:0011731",
- "is_present": false
- },
- {
- "term_id": "HP:0000870",
- "is_present": true
- },
- {
- "term_id": "HP:0025133",
- "is_present": false
- }
- ],
- "measurements": [
- {
- "test_term_id": "LOINC:2986-8",
- "test_name": "Testosterone[Mass/Vol]",
- "test_result": 555.0,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2141-0",
- "test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 169.0,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2143-6",
- "test_name": "Cortisol [Mass/Vol]",
- "test_result": 445.7,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2842-3",
- "test_name": "Prolactin [Mass/Vol]",
- "test_result": 26.03,
- "unit": "UCUM:ng/dL"
},
- {
- "test_term_id": "LOINC:2243-4",
- "test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 48.93,
- "unit": "UCUM:ng/dL"
- }
- ],
- "diseases": [
- {
- "term_id": "OMIM:201910",
- "name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
- }
- ],
- "variants": [
{
"variant_info": {
- "variant_coordinates": {
- "region": {
- "start": 32039425,
- "end": 32039426,
- "contig": {
- "name": "6",
- "genbank_acc": "CM000668.2",
- "refseq_name": "NC_000006.12",
- "ucsc_name": "chr6",
- "length": 170805979
- },
- "strand": "POSITIVE"
- },
- "ref": "T",
- "alt": "A",
- "change_length": 0
- },
- "sv_info": null
+ "variant_coordinates": null,
+ "sv_info": {
+ "structural_type": "SO:1000029",
+ "variant_class": "DEL",
+ "gene_id": "HGNC:2600",
+ "gene_symbol": "CYP21A2"
+ }
},
"tx_annotations": [
{
- "gene_id": "CYP21A2",
- "transcript_id": "NM_000500.9",
- "hgvs_cdna": "NM_000500.9:c.518T>A",
- "is_preferred": true,
+ "gene_id": "HGNC:2600",
+ "transcript_id": "NM_001128590.4",
+ "hgvs_cdna": null,
+ "is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "TRANSCRIPT_ABLATION"
],
"overlapping_exons": [
- 4
- ],
- "protein_id": "NP_000491.4",
- "hgvsp": "NP_000491.4:p.Ile173Asn",
- "protein_effect_location": {
- "start": 172,
- "end": 173
- }
- },
- {
- "gene_id": "C4B",
- "transcript_id": "NM_001002029.4",
- "hgvs_cdna": null,
- "is_preferred": true,
- "variant_effects": [
- "DOWNSTREAM_GENE_VARIANT"
+ 0,
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8
],
- "overlapping_exons": null,
- "protein_id": "NP_001002029.3",
+ "protein_id": null,
"hgvsp": null,
"protein_effect_location": null
},
{
- "gene_id": "CYP21A2",
- "transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.428T>A",
+ "gene_id": "HGNC:2600",
+ "transcript_id": "NM_000500.6",
+ "hgvs_cdna": null,
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "TRANSCRIPT_ABLATION"
],
"overlapping_exons": [
- 3
- ],
- "protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Ile143Asn",
- "protein_effect_location": {
- "start": 142,
- "end": 143
- }
- },
- {
- "gene_id": "TNXB",
- "transcript_id": "NM_001365276.2",
- "hgvs_cdna": null,
- "is_preferred": true,
- "variant_effects": [
- "DOWNSTREAM_GENE_VARIANT"
+ 0,
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8,
+ 9
],
- "overlapping_exons": null,
- "protein_id": "NP_001352205.1",
+ "protein_id": null,
"hgvsp": null,
"protein_effect_location": null
},
{
- "gene_id": "CYP21A2",
+ "gene_id": "HGNC:2600",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.113T>A",
+ "hgvs_cdna": null,
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "TRANSCRIPT_ABLATION"
],
"overlapping_exons": [
- 4
+ 0,
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8,
+ 9
],
- "protein_id": "NP_001355072.1",
- "hgvsp": "NP_001355072.1:p.Ile38Asn",
- "protein_effect_location": {
- "start": 37,
- "end": 38
- }
+ "protein_id": null,
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
- "gene_id": "CYP21A2",
- "transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.113T>A",
+ "gene_id": "HGNC:2600",
+ "transcript_id": "NM_001128590.2",
+ "hgvs_cdna": null,
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "TRANSCRIPT_ABLATION"
],
"overlapping_exons": [
- 3
+ 0,
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8
],
- "protein_id": "NP_001355073.1",
- "hgvsp": "NP_001355073.1:p.Ile38Asn",
- "protein_effect_location": {
- "start": 37,
- "end": 38
- }
+ "protein_id": null,
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
- "gene_id": "TNXB",
- "transcript_id": "NM_019105.8",
+ "gene_id": "HGNC:2600",
+ "transcript_id": "NM_001368144.2",
"hgvs_cdna": null,
"is_preferred": false,
"variant_effects": [
- "DOWNSTREAM_GENE_VARIANT"
+ "TRANSCRIPT_ABLATION"
],
- "overlapping_exons": null,
- "protein_id": "NP_061978.6",
+ "overlapping_exons": [
+ 0,
+ 1,
+ 2,
+ 3,
+ 4,
+ 5,
+ 6,
+ 7,
+ 8
+ ],
+ "protein_id": null,
"hgvsp": null,
"protein_effect_location": null
},
{
- "gene_id": "TNXB",
- "transcript_id": "NM_032470.4",
+ "gene_id": "HGNC:2600",
+ "transcript_id": "NM_001128590.1",
"hgvs_cdna": null,
"is_preferred": false,
"variant_effects": [
- "DOWNSTREAM_GENE_VARIANT"
+ "TRANSCRIPT_ABLATION"
],
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@@ -1190,21 +1150,29 @@
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{
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@@ -1722,8 +1652,8 @@
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- "label": "individual 6",
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+ "label": "individual 12",
+ "meta_label": "PMID_30968594_individual_12"
}
],
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@@ -1735,75 +1665,73 @@
},
{
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- "label": "individual 62",
- "meta_label": "PMID_30968594_individual_62"
+ "label": "individual 13",
+ "meta_label": "PMID_30968594_individual_13"
},
- "sex": "FEMALE",
+ "sex": "MALE",
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+ "vital_status": null,
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{
- "term_id": "HP:0000789",
- "is_present": true
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- {
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+ "term_id": "HP:0000953",
+ "is_present": true,
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{
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+ "term_id": "HP:0030087",
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{
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{
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"test_name": "Testosterone[Mass/Vol]",
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},
{
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},
{
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"test_name": "Cortisol [Mass/Vol]",
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},
{
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{
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}
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@@ -1811,7 +1739,11 @@
{
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+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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}
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@@ -1819,8 +1751,8 @@
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@@ -1831,7 +1763,7 @@
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@@ -1840,20 +1772,16 @@
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@@ -1871,20 +1799,16 @@
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@@ -1902,13 +1826,13 @@
{
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@@ -1917,13 +1841,13 @@
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@@ -1959,8 +1883,8 @@
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@@ -1970,318 +1894,134 @@
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@@ -2289,8 +2029,8 @@
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+ "label": "individual 13",
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@@ -2302,25 +2042,84 @@
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{
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+ "label": "individual 14",
+ "meta_label": "PMID_30968594_individual_14"
},
- "sex": "FEMALE",
+ "sex": "MALE",
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+ "vital_status": null,
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+ "term_id": "HP:0010788",
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{
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+ "test_result": 815.2,
+ "unit": "UCUM:ng/dL"
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+ "test_term_id": "LOINC:2986-8",
+ "test_name": "Testosterone[Mass/Vol]",
+ "test_result": 664.0,
+ "unit": "UCUM:ng/dL"
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+ "test_result": 329.7,
+ "unit": "UCUM:ng/dL"
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+ "test_name": "Cortisol [Mass/Vol]",
+ "test_result": 350.9,
+ "unit": "UCUM:ng/dL"
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+ "test_term_id": "LOINC:2842-3",
+ "test_name": "Prolactin [Mass/Vol]",
+ "test_result": 20.17,
+ "unit": "UCUM:ng/dL"
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+ "test_name": "Estradiol (E2) [Mass/Vol]",
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}
],
@@ -2328,7 +2127,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
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}
],
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@@ -2468,8 +2271,8 @@
"genotypes": {
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{
- "label": "individual 35",
- "meta_label": "PMID_30968594_individual_35"
+ "label": "individual 14",
+ "meta_label": "PMID_30968594_individual_14"
}
],
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@@ -2481,71 +2284,24 @@
},
{
"labels": {
- "label": "individual 23",
- "meta_label": "PMID_30968594_individual_23"
+ "label": "individual 15",
+ "meta_label": "PMID_30968594_individual_15"
},
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+ "vital_status": null,
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@@ -2553,7 +2309,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
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}
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@@ -2693,329 +2453,228 @@
"genotypes": {
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{
- "label": "individual 23",
- "meta_label": "PMID_30968594_individual_23"
+ "label": "individual 15",
+ "meta_label": "PMID_30968594_individual_15"
}
],
"genotypes": [
- "HETEROZYGOUS"
+ "HOMOZYGOUS_ALTERNATE"
]
}
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+ "meta_label": "PMID_30968594_individual_16"
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+ "vital_status": null,
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},
{
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{
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{
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+ "overlapping_exons": null,
+ "protein_id": "NP_115859.2",
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}
@@ -3023,12 +2682,12 @@
"genotypes": {
"samples": [
{
- "label": "individual 23",
- "meta_label": "PMID_30968594_individual_23"
+ "label": "individual 16",
+ "meta_label": "PMID_30968594_individual_16"
}
],
"genotypes": [
- "HETEROZYGOUS"
+ "HOMOZYGOUS_ALTERNATE"
]
}
}
@@ -3036,67 +2695,79 @@
},
{
"labels": {
- "label": "individual 58",
- "meta_label": "PMID_30968594_individual_58"
+ "label": "individual 17",
+ "meta_label": "PMID_30968594_individual_17"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0002014",
+ "is_present": true,
+ "onset": null
+ },
{
"term_id": "HP:0040171",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011043",
- "is_present": false
+ "term_id": "HP:0003154",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011731",
- "is_present": false
+ "term_id": "HP:0008163",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0000870",
- "is_present": true
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},
{
- "term_id": "HP:0025133",
- "is_present": false
+ "term_id": "HP:0008214",
+ "is_present": true,
+ "onset": null
}
],
"measurements": [
{
"test_term_id": "LOINC:1668-3",
"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 59.9,
+ "test_result": 824.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 100.0,
+ "test_result": 103.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 28.54,
+ "test_result": 230.7,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 405.2,
+ "test_result": 65.28,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2842-3",
"test_name": "Prolactin [Mass/Vol]",
- "test_result": 61.71,
+ "test_result": 82.23,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2243-4",
"test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 29.81,
+ "test_result": 0.52,
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}
],
@@ -3104,7 +2775,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 17.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -3112,8 +2787,8 @@
"variant_info": {
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"region": {
- "start": 32038513,
- "end": 32038514,
+ "start": 32039080,
+ "end": 32039081,
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@@ -3124,7 +2799,7 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "T",
+ "alt": "G",
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},
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@@ -3133,20 +2808,16 @@
{
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- "hgvs_cdna": "NM_000500.9:c.92C>T",
+ "hgvs_cdna": "NM_000500.9:c.293-13C>G",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
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+ "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000491.4",
- "hgvsp": "NP_000491.4:p.Pro31Leu",
- "protein_effect_location": {
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- "end": 31
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+ "protein_effect_location": null
},
{
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@@ -3164,20 +2835,16 @@
{
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"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.92C>T",
+ "hgvs_cdna": "NM_001128590.4:c.203-13C>G",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
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- "overlapping_exons": [
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+ "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
+ "INTRON_VARIANT"
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"protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Pro31Leu",
- "protein_effect_location": {
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- "end": 31
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+ "hgvsp": null,
+ "protein_effect_location": null
},
{
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@@ -3195,13 +2862,13 @@
{
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"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.-333C>T",
+ "hgvs_cdna": "NM_001368143.2:c.-126C>G",
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],
"overlapping_exons": [
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@@ -3210,13 +2877,13 @@
{
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- "hgvs_cdna": "NM_001368144.2:c.-243C>T",
+ "hgvs_cdna": "NM_001368144.2:c.-126C>G",
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"FIVE_PRIME_UTR_VARIANT"
],
"overlapping_exons": [
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@@ -3252,329 +2919,382 @@
"genotypes": {
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{
- "label": "individual 58",
- "meta_label": "PMID_30968594_individual_58"
+ "label": "individual 17",
+ "meta_label": "PMID_30968594_individual_17"
}
],
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},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.5",
+ "gene_id": "TNXB",
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@@ -3582,8 +3302,8 @@
"genotypes": {
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{
- "label": "individual 58",
- "meta_label": "PMID_30968594_individual_58"
+ "label": "individual 18",
+ "meta_label": "PMID_30968594_individual_18"
}
],
"genotypes": [
@@ -3599,26 +3319,33 @@
"meta_label": "PMID_30968594_individual_19"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0000953",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
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},
{
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- "is_present": false
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},
{
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- "is_present": true
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},
{
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- "is_present": true
+ "is_present": true,
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}
],
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@@ -3657,7 +3384,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 91.3125,
+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -3810,71 +3541,79 @@
},
{
"labels": {
- "label": "individual 18",
- "meta_label": "PMID_30968594_individual_18"
+ "label": "individual 1",
+ "meta_label": "PMID_30968594_individual_1"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
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- "is_present": true
+ "is_present": true,
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},
{
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+ "term_id": "HP:0040171",
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{
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{
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- "is_present": true
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},
{
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- "is_present": true
+ "term_id": "HP:0025133",
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],
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{
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 535.0,
+ "test_result": 800.0,
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},
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 568.0,
+ "test_result": 127.0,
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},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 121.0,
+ "test_result": 180.2,
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},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 3.26,
+ "test_result": 116.6,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2842-3",
"test_name": "Prolactin [Mass/Vol]",
- "test_result": 29.89,
+ "test_result": 52.93,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2243-4",
"test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 8.31,
+ "test_result": 23.71,
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}
],
@@ -3882,7 +3621,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -3890,8 +3633,8 @@
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- "end": 32039081,
+ "start": 32040420,
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@@ -3902,7 +3645,7 @@
"strand": "POSITIVE"
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@@ -3911,43 +3654,38 @@
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+ "hgvs_cdna": "NM_000500.9:c.955C>T",
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- "INTRON_VARIANT"
+ "STOP_GAINED"
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- "is_preferred": true,
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+ "overlapping_exons": [
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- "overlapping_exons": null,
- "protein_id": "NP_001002029.3",
- "hgvsp": null,
- "protein_effect_location": null
+ "protein_id": "NP_000491.4",
+ "hgvsp": "NP_000491.4:p.Gln319Ter",
+ "protein_effect_location": {
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+ "end": 319
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{
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- "hgvs_cdna": "NM_001128590.4:c.203-13C>G",
+ "hgvs_cdna": "NM_001128590.4:c.865C>T",
"is_preferred": false,
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- "INTRON_VARIANT"
+ "STOP_GAINED"
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+ "hgvsp": "NP_001122062.3:p.Gln289Ter",
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@@ -3965,32 +3703,38 @@
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+ "hgvs_cdna": "NM_001368143.2:c.550C>T",
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@@ -4022,8 +3766,8 @@
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@@ -4033,215 +3777,400 @@
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},
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
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},
{
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"test_name": "Testosterone[Mass/Vol]",
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},
{
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},
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- "test_name": "Prolactin [Mass/Vol]",
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{
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],
@@ -4249,7 +4178,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -4389,12 +4322,12 @@
"genotypes": {
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{
- "label": "individual 59",
- "meta_label": "PMID_30968594_individual_59"
+ "label": "individual 20",
+ "meta_label": "PMID_30968594_individual_20"
}
],
"genotypes": [
- "HETEROZYGOUS"
+ "HOMOZYGOUS_ALTERNATE"
]
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@@ -4402,69 +4335,79 @@
},
{
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- "label": "individual 22",
- "meta_label": "PMID_30968594_individual_22"
+ "label": "individual 21",
+ "meta_label": "PMID_30968594_individual_21"
},
"sex": "MALE",
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+ "vital_status": null,
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- "is_present": true
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{
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{
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{
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{
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{
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{
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+ "test_name": "17-Hydroxyprogesterone[Mass/Vol]",
+ "test_result": 328.0,
+ "unit": "UCUM:ng/dL"
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{
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"test_name": "Testosterone[Mass/Vol]",
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},
{
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"test_name": "Corticotropin (P) [Mass/Vol]",
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},
{
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"test_name": "Cortisol [Mass/Vol]",
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},
{
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"test_name": "Prolactin [Mass/Vol]",
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{
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}
],
@@ -4472,7 +4415,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -4612,8 +4559,8 @@
"genotypes": {
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{
- "label": "individual 22",
- "meta_label": "PMID_30968594_individual_22"
+ "label": "individual 21",
+ "meta_label": "PMID_30968594_individual_21"
}
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@@ -4625,71 +4572,78 @@
},
{
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- "meta_label": "PMID_30968594_individual_34"
+ "label": "individual 22",
+ "meta_label": "PMID_30968594_individual_22"
},
- "sex": "FEMALE",
+ "sex": "MALE",
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+ "vital_status": null,
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{
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{
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{
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"test_name": "Testosterone[Mass/Vol]",
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"test_name": "Corticotropin (P) [Mass/Vol]",
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{
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"test_name": "Cortisol [Mass/Vol]",
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{
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"test_name": "Prolactin [Mass/Vol]",
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{
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@@ -4697,7 +4651,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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@@ -4837,158 +4795,12 @@
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- "meta_label": "PMID_30968594_individual_34"
+ "label": "individual 22",
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}
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- "ucsc_name": "chr6",
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- "strand": "POSITIVE"
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- "HETEROZYGOUS"
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}
}
@@ -4996,45 +4808,79 @@
},
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+ "meta_label": "PMID_30968594_individual_23"
},
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+ "test_name": "Testosterone[Mass/Vol]",
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},
{
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{
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+ "test_name": "Prolactin [Mass/Vol]",
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+ "unit": "UCUM:ng/dL"
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+ "test_name": "Estradiol (E2) [Mass/Vol]",
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],
@@ -5042,7 +4888,8 @@
{
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"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
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}
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@@ -5050,8 +4897,8 @@
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@@ -5061,8 +4908,8 @@
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@@ -5071,20 +4918,16 @@
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{
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{
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@@ -5133,38 +4972,32 @@
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@@ -5196,8 +5029,8 @@
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@@ -5207,222 +5040,356 @@
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+ "variant_coordinates": null,
+ "sv_info": {
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+ "variant_class": "DEL",
+ "gene_id": "HGNC:2600",
+ "gene_symbol": "CYP21A2"
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- "meta_label": "PMID_30968594_individual_7"
+ "label": "individual 24",
+ "meta_label": "PMID_30968594_individual_24"
},
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- "is_present": true
+ "is_present": true,
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}
],
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
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- {
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- "test_name": "Prolactin [Mass/Vol]",
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}
],
@@ -5430,7 +5397,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -5438,8 +5409,8 @@
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- "end": 32040182,
+ "start": 32039080,
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@@ -5449,9 +5420,9 @@
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},
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+ "ref": "C",
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},
@@ -5459,20 +5430,16 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_000500.9",
- "hgvs_cdna": "NM_000500.9:c.923dup",
+ "hgvs_cdna": "NM_000500.9:c.293-13C>G",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000491.4",
- "hgvsp": "NP_000491.4:p.Leu308PhefsTer6",
- "protein_effect_location": {
- "start": 305,
- "end": 306
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "C4B",
@@ -5490,20 +5457,16 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.833dup",
+ "hgvs_cdna": "NM_001128590.4:c.203-13C>G",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Leu278PhefsTer6",
- "protein_effect_location": {
- "start": 275,
- "end": 276
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TNXB",
@@ -5521,38 +5484,32 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.518dup",
+ "hgvs_cdna": "NM_001368143.2:c.-126C>G",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "FIVE_PRIME_UTR_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_001355072.1",
- "hgvsp": "NP_001355072.1:p.Leu173PhefsTer6",
- "protein_effect_location": {
- "start": 170,
- "end": 171
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.518dup",
+ "hgvs_cdna": "NM_001368144.2:c.-126C>G",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "FIVE_PRIME_UTR_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_001355073.1",
- "hgvsp": "NP_001355073.1:p.Leu173PhefsTer6",
- "protein_effect_location": {
- "start": 170,
- "end": 171
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TNXB",
@@ -5584,8 +5541,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 7",
- "meta_label": "PMID_30968594_individual_7"
+ "label": "individual 24",
+ "meta_label": "PMID_30968594_individual_24"
}
],
"genotypes": [
@@ -5595,318 +5552,134 @@
},
{
"variant_info": {
- "variant_coordinates": null,
- "sv_info": {
- "structural_type": "SO:1000029",
- "variant_class": "DEL",
- "gene_id": "HGNC:2600",
- "gene_symbol": "CYP21A2"
- }
+ "variant_coordinates": {
+ "region": {
+ "start": 32040534,
+ "end": 32040535,
+ "contig": {
+ "name": "6",
+ "genbank_acc": "CM000668.2",
+ "refseq_name": "NC_000006.12",
+ "ucsc_name": "chr6",
+ "length": 170805979
+ },
+ "strand": "POSITIVE"
+ },
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
+ },
+ "sv_info": null
},
"tx_annotations": [
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_001128590.4",
- "hgvs_cdna": null,
- "is_preferred": false,
- "variant_effects": [
- "TRANSCRIPT_ABLATION"
+ "gene_id": "CYP21A2",
+ "transcript_id": "NM_000500.9",
+ "hgvs_cdna": "NM_000500.9:c.1069C>T",
+ "is_preferred": true,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 0,
- 1,
- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
8
],
- "protein_id": null,
- "hgvsp": null,
- "protein_effect_location": null
+ "protein_id": "NP_000491.4",
+ "hgvsp": "NP_000491.4:p.Arg357Trp",
+ "protein_effect_location": {
+ "start": 356,
+ "end": 357
+ }
},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.6",
- "hgvs_cdna": null,
+ "gene_id": "CYP21A2",
+ "transcript_id": "NM_001128590.4",
+ "hgvs_cdna": "NM_001128590.4:c.979C>T",
"is_preferred": false,
"variant_effects": [
- "TRANSCRIPT_ABLATION"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 0,
- 1,
- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
- 8,
- 9
+ 7
],
- "protein_id": null,
- "hgvsp": null,
- "protein_effect_location": null
+ "protein_id": "NP_001122062.3",
+ "hgvsp": "NP_001122062.3:p.Arg327Trp",
+ "protein_effect_location": {
+ "start": 326,
+ "end": 327
+ }
},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_001368143.2",
+ "gene_id": "TNXB",
+ "transcript_id": "NM_001365276.2",
"hgvs_cdna": null,
- "is_preferred": false,
+ "is_preferred": true,
"variant_effects": [
- "TRANSCRIPT_ABLATION"
- ],
- "overlapping_exons": [
- 0,
- 1,
- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
- 8,
- 9
+ "DOWNSTREAM_GENE_VARIANT"
],
- "protein_id": null,
+ "overlapping_exons": null,
+ "protein_id": "NP_001352205.1",
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"protein_effect_location": null
},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_001128590.2",
- "hgvs_cdna": null,
+ "gene_id": "CYP21A2",
+ "transcript_id": "NM_001368143.2",
+ "hgvs_cdna": "NM_001368143.2:c.664C>T",
"is_preferred": false,
"variant_effects": [
- "TRANSCRIPT_ABLATION"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
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- 3,
- 4,
- 5,
- 6,
- 7,
8
],
- "protein_id": null,
- "hgvsp": null,
- "protein_effect_location": null
+ "protein_id": "NP_001355072.1",
+ "hgvsp": "NP_001355072.1:p.Arg222Trp",
+ "protein_effect_location": {
+ "start": 221,
+ "end": 222
+ }
},
{
- "gene_id": "HGNC:2600",
+ "gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": null,
- "is_preferred": false,
- "variant_effects": [
- "TRANSCRIPT_ABLATION"
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- "overlapping_exons": [
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- 6,
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- "protein_id": null,
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- "protein_effect_location": null
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- {
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_001128590.1",
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- {
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.9",
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- "protein_effect_location": null
- },
- {
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.8",
- "hgvs_cdna": null,
+ "hgvs_cdna": "NM_001368144.2:c.664C>T",
"is_preferred": false,
"variant_effects": [
- "TRANSCRIPT_ABLATION"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
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],
- "protein_id": null,
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- "protein_effect_location": null
+ "protein_id": "NP_001355073.1",
+ "hgvsp": "NP_001355073.1:p.Arg222Trp",
+ "protein_effect_location": {
+ "start": 221,
+ "end": 222
+ }
},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_001368143.1",
+ "gene_id": "TNXB",
+ "transcript_id": "NM_019105.8",
"hgvs_cdna": null,
"is_preferred": false,
"variant_effects": [
- "TRANSCRIPT_ABLATION"
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- "overlapping_exons": [
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- 1,
- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
- 8,
- 9
+ "DOWNSTREAM_GENE_VARIANT"
],
- "protein_id": null,
+ "overlapping_exons": null,
+ "protein_id": "NP_061978.6",
"hgvsp": null,
"protein_effect_location": null
},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_001368144.1",
+ "gene_id": "TNXB",
+ "transcript_id": "NM_032470.4",
"hgvs_cdna": null,
"is_preferred": false,
"variant_effects": [
- "TRANSCRIPT_ABLATION"
- ],
- "overlapping_exons": [
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- 1,
- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
- 8
+ "DOWNSTREAM_GENE_VARIANT"
],
- "protein_id": null,
- "hgvsp": null,
- "protein_effect_location": null
- },
- {
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_001128590.3",
- "hgvs_cdna": null,
- "is_preferred": false,
- "variant_effects": [
- "TRANSCRIPT_ABLATION"
- ],
- "overlapping_exons": [
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- 1,
- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
- 8
- ],
- "protein_id": null,
- "hgvsp": null,
- "protein_effect_location": null
- },
- {
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.7",
- "hgvs_cdna": null,
- "is_preferred": false,
- "variant_effects": [
- "TRANSCRIPT_ABLATION"
- ],
- "overlapping_exons": [
- 0,
- 1,
- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
- 8,
- 9
- ],
- "protein_id": null,
- "hgvsp": null,
- "protein_effect_location": null
- },
- {
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.5",
- "hgvs_cdna": null,
- "is_preferred": false,
- "variant_effects": [
- "TRANSCRIPT_ABLATION"
- ],
- "overlapping_exons": [
- 0,
- 1,
- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
- 8,
- 9
- ],
- "protein_id": null,
+ "overlapping_exons": null,
+ "protein_id": "NP_115859.2",
"hgvsp": null,
"protein_effect_location": null
}
@@ -5914,8 +5687,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 7",
- "meta_label": "PMID_30968594_individual_7"
+ "label": "individual 24",
+ "meta_label": "PMID_30968594_individual_24"
}
],
"genotypes": [
@@ -5927,75 +5700,79 @@
},
{
"labels": {
- "label": "individual 14",
- "meta_label": "PMID_30968594_individual_14"
+ "label": "individual 25",
+ "meta_label": "PMID_30968594_individual_25"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0010788",
- "is_present": true
- },
{
"term_id": "HP:0000953",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030087",
- "is_present": false
+ "term_id": "HP:0040171",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0003154",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011731",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000870",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0025133",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [
{
"test_term_id": "LOINC:1668-3",
"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 815.2,
+ "test_result": 785.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 664.0,
+ "test_result": 135.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 329.7,
+ "test_result": 404.5,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 350.9,
+ "test_result": 171.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2842-3",
"test_name": "Prolactin [Mass/Vol]",
- "test_result": 20.17,
+ "test_result": 47.63,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2243-4",
"test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 29.53,
+ "test_result": 24.0,
"unit": "UCUM:ng/dL"
}
],
@@ -6003,7 +5780,8 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6143,109 +5921,21 @@
"genotypes": {
"samples": [
{
- "label": "individual 14",
- "meta_label": "PMID_30968594_individual_14"
+ "label": "individual 25",
+ "meta_label": "PMID_30968594_individual_25"
}
],
"genotypes": [
- "HOMOZYGOUS_ALTERNATE"
+ "HETEROZYGOUS"
]
}
- }
- ]
- },
- {
- "labels": {
- "label": "individual 43",
- "meta_label": "PMID_30968594_individual_43"
- },
- "sex": "FEMALE",
- "phenotypes": [
- {
- "term_id": "HP:0001007",
- "is_present": true
- },
- {
- "term_id": "HP:0008665",
- "is_present": true
- },
- {
- "term_id": "HP:0001510",
- "is_present": true
- },
- {
- "term_id": "HP:0030088",
- "is_present": true
- },
- {
- "term_id": "HP:0003154",
- "is_present": true
- },
- {
- "term_id": "HP:0011731",
- "is_present": false
- },
- {
- "term_id": "HP:0000870",
- "is_present": true
- },
- {
- "term_id": "HP:0025133",
- "is_present": false
- }
- ],
- "measurements": [
- {
- "test_term_id": "LOINC:1668-3",
- "test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 87.5,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2986-8",
- "test_name": "Testosterone[Mass/Vol]",
- "test_result": 422.0,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2141-0",
- "test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 188.9,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2143-6",
- "test_name": "Cortisol [Mass/Vol]",
- "test_result": 432.6,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2842-3",
- "test_name": "Prolactin [Mass/Vol]",
- "test_result": 34.9,
- "unit": "UCUM:ng/dL"
},
- {
- "test_term_id": "LOINC:2243-4",
- "test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 31.7,
- "unit": "UCUM:ng/dL"
- }
- ],
- "diseases": [
- {
- "term_id": "OMIM:201910",
- "name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
- }
- ],
- "variants": [
{
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 32039425,
- "end": 32039426,
+ "start": 32040420,
+ "end": 32040421,
"contig": {
"name": "6",
"genbank_acc": "CM000668.2",
@@ -6255,8 +5945,8 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -6265,50 +5955,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_000500.9",
- "hgvs_cdna": "NM_000500.9:c.518T>A",
+ "hgvs_cdna": "NM_000500.9:c.955C>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_000491.4",
- "hgvsp": "NP_000491.4:p.Ile173Asn",
+ "hgvsp": "NP_000491.4:p.Gln319Ter",
"protein_effect_location": {
- "start": 172,
- "end": 173
+ "start": 318,
+ "end": 319
}
},
- {
- "gene_id": "C4B",
- "transcript_id": "NM_001002029.4",
- "hgvs_cdna": null,
- "is_preferred": true,
- "variant_effects": [
- "DOWNSTREAM_GENE_VARIANT"
- ],
- "overlapping_exons": null,
- "protein_id": "NP_001002029.3",
- "hgvsp": null,
- "protein_effect_location": null
- },
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.428T>A",
+ "hgvs_cdna": "NM_001128590.4:c.865C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Ile143Asn",
+ "hgvsp": "NP_001122062.3:p.Gln289Ter",
"protein_effect_location": {
- "start": 142,
- "end": 143
+ "start": 288,
+ "end": 289
}
},
{
@@ -6327,37 +6004,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.113T>A",
+ "hgvs_cdna": "NM_001368143.2:c.550C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_001355072.1",
- "hgvsp": "NP_001355072.1:p.Ile38Asn",
+ "hgvsp": "NP_001355072.1:p.Gln184Ter",
"protein_effect_location": {
- "start": 37,
- "end": 38
+ "start": 183,
+ "end": 184
}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.113T>A",
+ "hgvs_cdna": "NM_001368144.2:c.550C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_001355073.1",
- "hgvsp": "NP_001355073.1:p.Ile38Asn",
+ "hgvsp": "NP_001355073.1:p.Gln184Ter",
"protein_effect_location": {
- "start": 37,
- "end": 38
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}
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}
],
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]
}
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},
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@@ -6927,313 +8139,329 @@
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@@ -7241,8 +8469,8 @@
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@@ -7254,79 +8482,57 @@
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{
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+ "label": "individual 30",
+ "meta_label": "PMID_30968594_individual_30"
},
- "sex": "FEMALE",
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+ "vital_status": null,
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},
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
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},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
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},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
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- "test_name": "Estradiol (E2) [Mass/Vol]",
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}
],
@@ -7334,7 +8540,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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}
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@@ -7342,8 +8552,8 @@
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@@ -7354,7 +8564,7 @@
"strand": "POSITIVE"
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@@ -7363,441 +8573,263 @@
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{
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{
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@@ -7805,8 +8837,8 @@
"genotypes": {
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+ "label": "individual 30",
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}
],
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@@ -7818,69 +8850,63 @@
},
{
"labels": {
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- "meta_label": "PMID_30968594_individual_33"
+ "label": "individual 31",
+ "meta_label": "PMID_30968594_individual_31"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
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- {
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{
"term_id": "HP:0030087",
- "is_present": false
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},
{
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},
{
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{
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+ "is_present": true,
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}
],
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{
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},
{
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{
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{
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@@ -7888,7 +8914,8 @@
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@@ -7977,380 +9004,196 @@
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@@ -8371,71 +9214,84 @@
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},
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@@ -8443,7 +9299,11 @@
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@@ -8583,158 +9443,12 @@
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@@ -8742,75 +9456,78 @@
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{
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{
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{
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@@ -8818,7 +9535,11 @@
{
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"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
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+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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@@ -8826,8 +9547,8 @@
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@@ -8837,8 +9558,8 @@
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@@ -8847,20 +9568,16 @@
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@@ -8878,20 +9595,16 @@
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{
"gene_id": "TNXB",
@@ -8909,38 +9622,32 @@
{
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"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.113T>A",
+ "hgvs_cdna": "NM_001368143.2:c.-126C>G",
"is_preferred": false,
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+ "FIVE_PRIME_UTR_VARIANT"
],
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- "hgvsp": "NP_001355072.1:p.Ile38Asn",
- "protein_effect_location": {
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- "end": 38
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},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.113T>A",
+ "hgvs_cdna": "NM_001368144.2:c.-126C>G",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FIVE_PRIME_UTR_VARIANT"
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- "hgvsp": "NP_001355073.1:p.Ile38Asn",
- "protein_effect_location": {
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- "end": 38
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+ "protein_effect_location": null
},
{
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@@ -8972,8 +9679,8 @@
"genotypes": {
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{
- "label": "individual 48",
- "meta_label": "PMID_30968594_individual_48"
+ "label": "individual 33",
+ "meta_label": "PMID_30968594_individual_33"
}
],
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@@ -9280,21 +9987,255 @@
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- 2,
- 3,
- 4,
- 5,
- 6,
- 7,
- 8,
- 9
+ "TRANSCRIPT_ABLATION"
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+ "protein_effect_location": null
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+ "genotypes": {
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+ "label": "individual 33",
+ "meta_label": "PMID_30968594_individual_33"
+ }
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+ "genotypes": [
+ "HETEROZYGOUS"
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+ }
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+ "meta_label": "PMID_30968594_individual_34"
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+ "hgvs_cdna": "NM_001368143.2:c.-126C>G",
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+ "gene_id": "CYP21A2",
+ "transcript_id": "NM_001368144.2",
+ "hgvs_cdna": "NM_001368144.2:c.-126C>G",
+ "is_preferred": false,
+ "variant_effects": [
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+ "protein_id": "NP_001355073.1",
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+ "transcript_id": "NM_019105.8",
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+ "is_preferred": false,
+ "variant_effects": [
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+ "protein_id": "NP_061978.6",
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+ {
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+ "hgvs_cdna": null,
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+ "variant_effects": [
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}
@@ -9302,105 +10243,21 @@
"genotypes": {
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{
- "label": "individual 48",
- "meta_label": "PMID_30968594_individual_48"
+ "label": "individual 34",
+ "meta_label": "PMID_30968594_individual_34"
}
],
"genotypes": [
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]
}
- }
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- "meta_label": "PMID_30968594_individual_68"
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- "end": 32039592,
+ "start": 32040420,
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@@ -9410,8 +10267,8 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
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@@ -9420,50 +10277,37 @@
{
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],
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- "hgvsp": "NP_000491.4:p.Leu199Ter",
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{
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"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.506T>G",
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"variant_effects": [
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],
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}
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{
@@ -9482,37 +10326,37 @@
{
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"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.191T>G",
+ "hgvs_cdna": "NM_001368143.2:c.550C>T",
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],
"overlapping_exons": [
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],
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- "hgvsp": "NP_001355072.1:p.Leu64Ter",
+ "hgvsp": "NP_001355072.1:p.Gln184Ter",
"protein_effect_location": {
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}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.191T>G",
+ "hgvs_cdna": "NM_001368144.2:c.550C>T",
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"variant_effects": [
"STOP_GAINED"
],
"overlapping_exons": [
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],
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- "hgvsp": "NP_001355073.1:p.Leu64Ter",
+ "hgvsp": "NP_001355073.1:p.Gln184Ter",
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+ "start": 183,
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}
},
{
@@ -9545,15 +10389,57 @@
"genotypes": {
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{
- "label": "individual 68",
- "meta_label": "PMID_30968594_individual_68"
+ "label": "individual 34",
+ "meta_label": "PMID_30968594_individual_34"
}
],
"genotypes": [
"HETEROZYGOUS"
]
}
+ }
+ ]
+ },
+ {
+ "labels": {
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+ "meta_label": "PMID_30968594_individual_35"
+ },
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
+ "phenotypes": [
+ {
+ "term_id": "HP:0008665",
+ "is_present": true,
+ "onset": null
},
+ {
+ "term_id": "HP:0000953",
+ "is_present": true,
+ "onset": null
+ }
+ ],
+ "measurements": [
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+ "test_name": "17-Hydroxyprogesterone[Mass/Vol]",
+ "test_result": 246.4,
+ "unit": "UCUM:ng/dL"
+ }
+ ],
+ "diseases": [
+ {
+ "term_id": "OMIM:201910",
+ "name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
+ }
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+ "variants": [
{
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@@ -9690,12 +10576,12 @@
"genotypes": {
"samples": [
{
- "label": "individual 68",
- "meta_label": "PMID_30968594_individual_68"
+ "label": "individual 35",
+ "meta_label": "PMID_30968594_individual_35"
}
],
"genotypes": [
- "HETEROZYGOUS"
+ "HOMOZYGOUS_ALTERNATE"
]
}
}
@@ -9703,16 +10589,79 @@
},
{
"labels": {
- "label": "individual 29",
- "meta_label": "PMID_30968594_individual_29"
+ "label": "individual 36",
+ "meta_label": "PMID_30968594_individual_36"
},
- "sex": "MALE",
- "phenotypes": [],
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
+ "phenotypes": [
+ {
+ "term_id": "HP:0008665",
+ "is_present": true,
+ "onset": null
+ },
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+ "is_present": true,
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+ "onset": null
+ },
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+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0025133",
+ "is_present": false,
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{
- "test_term_id": "LOINC:1668-3",
- "test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 238.0,
+ "test_term_id": "LOINC:1668-3",
+ "test_name": "17-Hydroxyprogesterone[Mass/Vol]",
+ "test_result": 329.7,
+ "unit": "UCUM:ng/dL"
+ },
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+ "test_term_id": "LOINC:2986-8",
+ "test_name": "Testosterone[Mass/Vol]",
+ "test_result": 176.0,
+ "unit": "UCUM:ng/dL"
+ },
+ {
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+ "test_name": "Corticotropin (P) [Mass/Vol]",
+ "test_result": 81.4,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2143-6",
+ "test_name": "Cortisol [Mass/Vol]",
+ "test_result": 282.0,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2842-3",
+ "test_name": "Prolactin [Mass/Vol]",
+ "test_result": 99.66,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2243-4",
+ "test_name": "Estradiol (E2) [Mass/Vol]",
+ "test_result": 41.6,
"unit": "UCUM:ng/dL"
}
],
@@ -9720,7 +10669,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -9860,8 +10813,8 @@
"genotypes": {
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{
- "label": "individual 29",
- "meta_label": "PMID_30968594_individual_29"
+ "label": "individual 36",
+ "meta_label": "PMID_30968594_individual_36"
}
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@@ -10068,320 +11021,121 @@
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@@ -10402,71 +11156,46 @@
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@@ -10474,7 +11203,11 @@
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@@ -10482,8 +11215,8 @@
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@@ -10503,20 +11236,16 @@
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@@ -10534,20 +11263,16 @@
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@@ -10628,8 +11347,8 @@
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@@ -10641,8 +11360,8 @@
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@@ -10786,73 +11506,29 @@
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@@ -10992,8 +11668,8 @@
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+ "label": "individual 38",
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@@ -11005,8 +11681,8 @@
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@@ -11026,37 +11702,37 @@
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- "hgvsp": "NP_000491.4:p.Gln319Ter",
+ "hgvsp": "NP_000491.4:p.Arg357Trp",
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- "start": 318,
- "end": 319
+ "start": 356,
+ "end": 357
}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.865C>T",
+ "hgvs_cdna": "NM_001128590.4:c.979C>T",
"is_preferred": false,
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- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
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7
],
"protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Gln289Ter",
+ "hgvsp": "NP_001122062.3:p.Arg327Trp",
"protein_effect_location": {
- "start": 288,
- "end": 289
+ "start": 326,
+ "end": 327
}
},
{
@@ -11075,37 +11751,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.550C>T",
+ "hgvs_cdna": "NM_001368143.2:c.664C>T",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
8
],
"protein_id": "NP_001355072.1",
- "hgvsp": "NP_001355072.1:p.Gln184Ter",
+ "hgvsp": "NP_001355072.1:p.Arg222Trp",
"protein_effect_location": {
- "start": 183,
- "end": 184
+ "start": 221,
+ "end": 222
}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.550C>T",
+ "hgvs_cdna": "NM_001368144.2:c.664C>T",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
7
],
"protein_id": "NP_001355073.1",
- "hgvsp": "NP_001355073.1:p.Gln184Ter",
+ "hgvsp": "NP_001355073.1:p.Arg222Trp",
"protein_effect_location": {
- "start": 183,
- "end": 184
+ "start": 221,
+ "end": 222
}
},
{
@@ -11138,8 +11814,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 13",
- "meta_label": "PMID_30968594_individual_13"
+ "label": "individual 38",
+ "meta_label": "PMID_30968594_individual_38"
}
],
"genotypes": [
@@ -11151,25 +11827,79 @@
},
{
"labels": {
- "label": "individual 12",
- "meta_label": "PMID_30968594_individual_12"
+ "label": "individual 39",
+ "meta_label": "PMID_30968594_individual_39"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0008665",
- "is_present": true
+ "term_id": "HP:0000953",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000953",
- "is_present": true
+ "term_id": "HP:0040171",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003154",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011731",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000870",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0025133",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [
{
"test_term_id": "LOINC:1668-3",
"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 476.0,
+ "test_result": 69.0,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2986-8",
+ "test_name": "Testosterone[Mass/Vol]",
+ "test_result": 148.0,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2141-0",
+ "test_name": "Corticotropin (P) [Mass/Vol]",
+ "test_result": 190.0,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2143-6",
+ "test_name": "Cortisol [Mass/Vol]",
+ "test_result": 144.8,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2842-3",
+ "test_name": "Prolactin [Mass/Vol]",
+ "test_result": 73.31,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2243-4",
+ "test_name": "Estradiol (E2) [Mass/Vol]",
+ "test_result": 26.89,
"unit": "UCUM:ng/dL"
}
],
@@ -11177,7 +11907,8 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -11185,8 +11916,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 32040420,
- "end": 32040421,
+ "start": 32039425,
+ "end": 32039426,
"contig": {
"name": "6",
"genbank_acc": "CM000668.2",
@@ -11196,8 +11927,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "T",
+ "alt": "A",
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},
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@@ -11206,37 +11937,50 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_000500.9",
- "hgvs_cdna": "NM_000500.9:c.955C>T",
+ "hgvs_cdna": "NM_000500.9:c.518T>A",
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"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
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+ 4
],
"protein_id": "NP_000491.4",
- "hgvsp": "NP_000491.4:p.Gln319Ter",
+ "hgvsp": "NP_000491.4:p.Ile173Asn",
"protein_effect_location": {
- "start": 318,
- "end": 319
+ "start": 172,
+ "end": 173
}
},
+ {
+ "gene_id": "C4B",
+ "transcript_id": "NM_001002029.4",
+ "hgvs_cdna": null,
+ "is_preferred": true,
+ "variant_effects": [
+ "DOWNSTREAM_GENE_VARIANT"
+ ],
+ "overlapping_exons": null,
+ "protein_id": "NP_001002029.3",
+ "hgvsp": null,
+ "protein_effect_location": null
+ },
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.865C>T",
+ "hgvs_cdna": "NM_001128590.4:c.428T>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Gln289Ter",
+ "hgvsp": "NP_001122062.3:p.Ile143Asn",
"protein_effect_location": {
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- "end": 289
+ "start": 142,
+ "end": 143
}
},
{
@@ -11255,37 +11999,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.550C>T",
+ "hgvs_cdna": "NM_001368143.2:c.113T>A",
"is_preferred": false,
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- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
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+ 4
],
"protein_id": "NP_001355072.1",
- "hgvsp": "NP_001355072.1:p.Gln184Ter",
+ "hgvsp": "NP_001355072.1:p.Ile38Asn",
"protein_effect_location": {
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- "end": 184
+ "start": 37,
+ "end": 38
}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.550C>T",
+ "hgvs_cdna": "NM_001368144.2:c.113T>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
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+ 3
],
"protein_id": "NP_001355073.1",
- "hgvsp": "NP_001355073.1:p.Gln184Ter",
+ "hgvsp": "NP_001355073.1:p.Ile38Asn",
"protein_effect_location": {
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- "end": 184
+ "start": 37,
+ "end": 38
}
},
{
@@ -11318,8 +12062,8 @@
"genotypes": {
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{
- "label": "individual 12",
- "meta_label": "PMID_30968594_individual_12"
+ "label": "individual 39",
+ "meta_label": "PMID_30968594_individual_39"
}
],
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@@ -11648,8 +12392,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 12",
- "meta_label": "PMID_30968594_individual_12"
+ "label": "individual 39",
+ "meta_label": "PMID_30968594_individual_39"
}
],
"genotypes": [
@@ -11661,71 +12405,63 @@
},
{
"labels": {
- "label": "individual 45",
- "meta_label": "PMID_30968594_individual_45"
+ "label": "individual 3",
+ "meta_label": "PMID_30968594_individual_3"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0008665",
- "is_present": true
- },
- {
- "term_id": "HP:0030088",
- "is_present": true
+ "term_id": "HP:0030087",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003154",
- "is_present": true
- },
- {
- "term_id": "HP:0011731",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000870",
- "is_present": true
+ "term_id": "HP:0008163",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0025133",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
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{
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 158.4,
+ "test_result": 685.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 355.0,
+ "test_result": 340.0,
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},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 78.45,
+ "test_result": 135.6,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 251.0,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2842-3",
- "test_name": "Prolactin [Mass/Vol]",
- "test_result": 23.87,
+ "test_result": 78.3,
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},
{
"test_term_id": "LOINC:2243-4",
"test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 32.86,
+ "test_result": 26.9,
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}
],
@@ -11733,7 +12469,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 30.4375,
+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -11741,8 +12481,8 @@
"variant_info": {
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"region": {
- "start": 32039425,
- "end": 32039426,
+ "start": 32039131,
+ "end": 32039140,
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@@ -11752,9 +12492,9 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
- "change_length": 0
+ "ref": "GGAGACTAC",
+ "alt": "G",
+ "change_length": -8
},
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},
@@ -11762,175 +12502,20 @@
{
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- "protein_id": "NP_000491.4",
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- "protein_effect_location": {
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- "end": 173
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- "transcript_id": "NM_001002029.4",
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- "transcript_id": "NM_001128590.4",
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- "end": 143
- }
- },
- {
- "gene_id": "TNXB",
- "transcript_id": "NM_001365276.2",
- "hgvs_cdna": null,
+ "hgvs_cdna": "NM_000500.9:c.332_339del",
"is_preferred": true,
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- "hgvs_cdna": "NM_001368144.2:c.113T>A",
- "is_preferred": false,
- "variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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- "protein_id": "NP_001355073.1",
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- "meta_label": "PMID_30968594_individual_45"
- }
- ],
- "genotypes": [
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- ]
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- "end": 32039081,
- "contig": {
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- "ucsc_name": "chr6",
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- "transcript_id": "NM_000500.9",
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- "is_preferred": true,
- "variant_effects": [
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- "INTRON_VARIANT"
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_000491.4",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000491.4:p.Gly111ValfsTer21",
+ "protein_effect_location": {
+ "start": 110,
+ "end": 113
+ }
},
{
"gene_id": "C4B",
@@ -11948,16 +12533,20 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.203-13C>G",
+ "hgvs_cdna": "NM_001128590.4:c.242_249del",
"is_preferred": false,
"variant_effects": [
- "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
- "INTRON_VARIANT"
+ "FRAMESHIFT_VARIANT"
+ ],
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- "overlapping_exons": null,
"protein_id": "NP_001122062.3",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_001122062.3:p.Gly81ValfsTer21",
+ "protein_effect_location": {
+ "start": 80,
+ "end": 83
+ }
},
{
"gene_id": "TNXB",
@@ -11975,7 +12564,7 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.-126C>G",
+ "hgvs_cdna": "NM_001368143.2:c.-74_-67del",
"is_preferred": false,
"variant_effects": [
"FIVE_PRIME_UTR_VARIANT"
@@ -11990,7 +12579,7 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.-126C>G",
+ "hgvs_cdna": "NM_001368144.2:c.-74_-67del",
"is_preferred": false,
"variant_effects": [
"FIVE_PRIME_UTR_VARIANT"
@@ -12032,232 +12621,329 @@
"genotypes": {
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{
- "label": "individual 45",
- "meta_label": "PMID_30968594_individual_45"
+ "label": "individual 3",
+ "meta_label": "PMID_30968594_individual_3"
}
],
"genotypes": [
"HETEROZYGOUS"
]
}
- }
- ]
- },
- {
- "labels": {
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- "meta_label": "PMID_30968594_individual_53"
- },
- "sex": "FEMALE",
- "phenotypes": [
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- "is_present": true
- },
- {
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- "is_present": true
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- {
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- {
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- "is_present": true
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- {
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- "is_present": true
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- {
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- "is_present": true
- }
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- "test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 227.0,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2986-8",
- "test_name": "Testosterone[Mass/Vol]",
- "test_result": 80.0,
- "unit": "UCUM:ng/dL"
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- "test_name": "Corticotropin (P) [Mass/Vol]",
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- "unit": "UCUM:ng/dL"
},
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- "test_name": "Cortisol [Mass/Vol]",
- "test_result": 119.5,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2842-3",
- "test_name": "Prolactin [Mass/Vol]",
- "test_result": 85.57,
- "unit": "UCUM:ng/dL"
- }
- ],
- "diseases": [
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- "term_id": "OMIM:201910",
- "name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
- }
- ],
- "variants": [
{
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@@ -12265,12 +12951,12 @@
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@@ -12278,71 +12964,79 @@
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@@ -12350,7 +13044,8 @@
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@@ -12358,8 +13053,8 @@
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@@ -12406,16 +13105,20 @@
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@@ -12433,32 +13136,38 @@
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@@ -12490,8 +13199,8 @@
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+ "protein_id": "NP_001002029.3",
+ "hgvsp": null,
+ "protein_effect_location": null
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{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.979C>T",
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{
@@ -13660,37 +14297,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.664C>T",
+ "hgvs_cdna": "NM_001368143.2:c.113T>A",
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],
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- "hgvsp": "NP_001355072.1:p.Arg222Trp",
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}
},
{
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- "hgvs_cdna": "NM_001368144.2:c.664C>T",
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+ "hgvsp": "NP_001355073.1:p.Ile38Asn",
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- "end": 222
+ "start": 37,
+ "end": 38
}
},
{
@@ -13723,99 +14360,15 @@
"genotypes": {
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{
- "label": "individual 24",
- "meta_label": "PMID_30968594_individual_24"
+ "label": "individual 42",
+ "meta_label": "PMID_30968594_individual_42"
}
],
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]
- }
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- "meta_label": "PMID_30968594_individual_32"
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- "unit": "UCUM:ng/dL"
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- "name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
- }
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{
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@@ -13952,12 +14505,12 @@
"genotypes": {
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{
- "label": "individual 32",
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+ "label": "individual 42",
+ "meta_label": "PMID_30968594_individual_42"
}
],
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+ "HETEROZYGOUS"
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}
}
@@ -13965,67 +14518,89 @@
},
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- "label": "individual 65",
- "meta_label": "PMID_30968594_individual_65"
+ "label": "individual 43",
+ "meta_label": "PMID_30968594_individual_43"
},
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+ "vital_status": null,
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- "term_id": "HP:0030087",
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+ "term_id": "HP:0001007",
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},
{
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{
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{
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{
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@@ -14033,324 +14608,302 @@
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- "is_observed": true
+ "is_observed": true,
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{
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+ "gene_id": "CYP21A2",
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{
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},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.5",
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@@ -14358,8 +14911,8 @@
"genotypes": {
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{
- "label": "individual 65",
- "meta_label": "PMID_30968594_individual_65"
+ "label": "individual 43",
+ "meta_label": "PMID_30968594_individual_43"
}
],
"genotypes": [
@@ -14371,71 +14924,79 @@
},
{
"labels": {
- "label": "individual 1",
- "meta_label": "PMID_30968594_individual_1"
+ "label": "individual 44",
+ "meta_label": "PMID_30968594_individual_44"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0000953",
- "is_present": true
+ "term_id": "HP:0002014",
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},
{
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{
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{
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},
{
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},
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{
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@@ -14443,7 +15004,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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@@ -14451,8 +15016,8 @@
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@@ -14462,8 +15027,8 @@
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@@ -14472,37 +15037,50 @@
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{
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@@ -14521,37 +15099,37 @@
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@@ -14584,8 +15162,8 @@
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@@ -14595,318 +15173,133 @@
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{
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@@ -14914,8 +15307,8 @@
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+ "label": "individual 44",
+ "meta_label": "PMID_30968594_individual_44"
}
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@@ -14927,61 +15320,79 @@
},
{
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- "meta_label": "PMID_30968594_individual_27"
+ "label": "individual 45",
+ "meta_label": "PMID_30968594_individual_45"
},
- "sex": "MALE",
+ "sex": "FEMALE",
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+ "vital_status": null,
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{
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+ "term_id": "HP:0008665",
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{
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{
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{
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{
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+ "is_present": true,
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],
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},
{
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{
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},
{
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},
{
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+ "test_result": 23.87,
+ "unit": "UCUM:ng/dL"
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+ {
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}
],
@@ -14989,7 +15400,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
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@@ -14997,8 +15412,8 @@
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@@ -15008,8 +15423,8 @@
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@@ -15018,16 +15433,20 @@
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@@ -15045,16 +15464,20 @@
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@@ -15072,32 +15495,38 @@
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@@ -15129,8 +15558,8 @@
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@@ -15142,8 +15571,8 @@
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@@ -15154,7 +15583,7 @@
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@@ -15163,38 +15592,43 @@
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@@ -15212,38 +15646,32 @@
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@@ -15275,8 +15703,8 @@
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@@ -15288,57 +15716,68 @@
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{
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{
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@@ -15346,7 +15785,11 @@
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@@ -15354,8 +15797,8 @@
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@@ -15365,8 +15808,8 @@
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@@ -15375,16 +15818,20 @@
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@@ -15402,16 +15849,20 @@
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@@ -15429,202 +15880,392 @@
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@@ -15632,8 +16273,8 @@
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@@ -15645,21 +16286,78 @@
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+ "label": "individual 47",
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+ "unit": "UCUM:ng/dL"
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@@ -15667,7 +16365,11 @@
{
"term_id": "OMIM:201910",
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+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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@@ -15675,8 +16377,8 @@
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@@ -15686,8 +16388,8 @@
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@@ -15696,37 +16398,50 @@
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{
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@@ -15808,8 +16523,8 @@
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@@ -15819,318 +16534,134 @@
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{
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},
{
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@@ -16138,8 +16669,8 @@
"genotypes": {
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{
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- "meta_label": "PMID_30968594_individual_66"
+ "label": "individual 47",
+ "meta_label": "PMID_30968594_individual_47"
}
],
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@@ -16151,75 +16682,84 @@
},
{
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- "label": "individual 2",
- "meta_label": "PMID_30968594_individual_2"
+ "label": "individual 48",
+ "meta_label": "PMID_30968594_individual_48"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
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{
- "term_id": "HP:0000028",
- "is_present": true
+ "term_id": "HP:0008665",
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},
{
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{
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+ "term_id": "HP:0030087",
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{
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{
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+ "term_id": "HP:0008163",
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{
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{
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],
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 526.0,
+ "test_result": 140.0,
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},
{
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"test_name": "Testosterone[Mass/Vol]",
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},
{
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"test_name": "Corticotropin (P) [Mass/Vol]",
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+ "test_result": 234.3,
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},
{
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"test_name": "Cortisol [Mass/Vol]",
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},
{
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"test_name": "Prolactin [Mass/Vol]",
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},
{
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],
@@ -16227,7 +16767,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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}
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@@ -16235,8 +16779,8 @@
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@@ -16246,9 +16790,9 @@
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+ "ref": "T",
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@@ -16256,19 +16800,19 @@
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@@ -16287,19 +16831,19 @@
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@@ -16318,32 +16862,38 @@
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{
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+ "hgvsp": "NP_001355073.1:p.Ile38Asn",
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{
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@@ -16375,8 +16925,8 @@
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@@ -17287,61 +18251,35 @@
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@@ -17846,39 +18603,35 @@
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},
{
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- "test_name": "Cortisol [Mass/Vol]",
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@@ -17886,7 +18639,11 @@
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+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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@@ -18040,8 +18797,8 @@
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@@ -18053,31 +18810,73 @@
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},
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+ "test_name": "Testosterone[Mass/Vol]",
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+ "unit": "UCUM:ng/dL"
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+ "test_result": 119.5,
+ "unit": "UCUM:ng/dL"
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+ "test_name": "Prolactin [Mass/Vol]",
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@@ -18085,7 +18884,8 @@
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@@ -18239,21 +19039,107 @@
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],
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+ "HOMOZYGOUS_ALTERNATE"
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+ "unit": "UCUM:ng/dL"
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+ "test_name": "Testosterone[Mass/Vol]",
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+ "unit": "UCUM:ng/dL"
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+ "test_name": "Corticotropin (P) [Mass/Vol]",
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+ "test_name": "Cortisol [Mass/Vol]",
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+ "unit": "UCUM:ng/dL"
},
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+ "test_term_id": "LOINC:2842-3",
+ "test_name": "Prolactin [Mass/Vol]",
+ "test_result": 22.87,
+ "unit": "UCUM:ng/dL"
+ }
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+ "diseases": [
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+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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@@ -18263,8 +19149,8 @@
},
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@@ -18273,16 +19159,20 @@
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+ "hgvs_cdna": "NM_000500.9:c.518T>A",
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- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
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+ "protein_effect_location": {
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{
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@@ -18300,16 +19190,20 @@
{
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- "hgvs_cdna": "NM_001128590.4:c.203-13C>G",
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- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
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+ "hgvsp": "NP_001122062.3:p.Ile143Asn",
+ "protein_effect_location": {
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+ "end": 143
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{
"gene_id": "TNXB",
@@ -18327,32 +19221,38 @@
{
"gene_id": "CYP21A2",
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+ "MISSENSE_VARIANT"
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- "protein_effect_location": null
+ "hgvsp": "NP_001355072.1:p.Ile38Asn",
+ "protein_effect_location": {
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+ "end": 38
+ }
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.-126C>G",
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+ "MISSENSE_VARIANT"
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+ "hgvsp": "NP_001355073.1:p.Ile38Asn",
+ "protein_effect_location": {
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+ "end": 38
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},
{
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@@ -18384,12 +19284,12 @@
"genotypes": {
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{
- "label": "individual 51",
- "meta_label": "PMID_30968594_individual_51"
+ "label": "individual 54",
+ "meta_label": "PMID_30968594_individual_54"
}
],
"genotypes": [
- "HETEROZYGOUS"
+ "HOMOZYGOUS_ALTERNATE"
]
}
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@@ -18397,69 +19297,73 @@
},
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- "meta_label": "PMID_30968594_individual_47"
+ "label": "individual 55",
+ "meta_label": "PMID_30968594_individual_55"
},
- "sex": "FEMALE",
+ "sex": "MALE",
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+ "vital_status": null,
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- "is_present": true
- },
{
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{
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{
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{
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{
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+ "term_id": "HP:0025133",
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],
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},
{
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},
{
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"test_name": "Cortisol [Mass/Vol]",
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},
{
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},
{
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}
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@@ -18467,7 +19371,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
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+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
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}
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@@ -18475,8 +19383,8 @@
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+ "start": 32040071,
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@@ -18486,8 +19394,8 @@
},
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},
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@@ -18496,19 +19404,19 @@
{
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- "hgvs_cdna": "NM_000500.9:c.518T>A",
+ "hgvs_cdna": "NM_000500.9:c.806G>C",
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],
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@@ -18527,19 +19435,19 @@
{
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- "hgvsp": "NP_001122062.3:p.Ile143Asn",
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@@ -18558,37 +19466,37 @@
{
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- "hgvs_cdna": "NM_001368143.2:c.113T>A",
+ "hgvs_cdna": "NM_001368143.2:c.401G>C",
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],
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- "hgvsp": "NP_001355072.1:p.Ile38Asn",
+ "hgvsp": "NP_001355072.1:p.Ser134Thr",
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},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.113T>A",
+ "hgvs_cdna": "NM_001368144.2:c.401G>C",
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"MISSENSE_VARIANT"
],
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- "hgvsp": "NP_001355073.1:p.Ile38Asn",
+ "hgvsp": "NP_001355073.1:p.Ser134Thr",
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{
@@ -18621,8 +19529,8 @@
"genotypes": {
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{
- "label": "individual 47",
- "meta_label": "PMID_30968594_individual_47"
+ "label": "individual 55",
+ "meta_label": "PMID_30968594_individual_55"
}
],
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@@ -18634,8 +19542,8 @@
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+ "start": 32040181,
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@@ -18645,9 +19553,9 @@
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},
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- "change_length": 0
+ "ref": "G",
+ "alt": "GT",
+ "change_length": 1
},
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@@ -18655,37 +19563,50 @@
{
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- "hgvs_cdna": "NM_000500.9:c.955C>T",
+ "hgvs_cdna": "NM_000500.9:c.923dup",
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+ "FRAMESHIFT_VARIANT"
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- "hgvsp": "NP_000491.4:p.Gln319Ter",
+ "hgvsp": "NP_000491.4:p.Leu308PhefsTer6",
"protein_effect_location": {
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- "end": 319
+ "start": 305,
+ "end": 306
}
},
+ {
+ "gene_id": "C4B",
+ "transcript_id": "NM_001002029.4",
+ "hgvs_cdna": null,
+ "is_preferred": true,
+ "variant_effects": [
+ "DOWNSTREAM_GENE_VARIANT"
+ ],
+ "overlapping_exons": null,
+ "protein_id": "NP_001002029.3",
+ "hgvsp": null,
+ "protein_effect_location": null
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{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.865C>T",
+ "hgvs_cdna": "NM_001128590.4:c.833dup",
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+ "FRAMESHIFT_VARIANT"
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- "hgvsp": "NP_001122062.3:p.Gln289Ter",
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@@ -18704,37 +19625,37 @@
{
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- "hgvs_cdna": "NM_001368143.2:c.550C>T",
+ "hgvs_cdna": "NM_001368143.2:c.518dup",
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+ "FRAMESHIFT_VARIANT"
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- "hgvsp": "NP_001355072.1:p.Gln184Ter",
+ "hgvsp": "NP_001355072.1:p.Leu173PhefsTer6",
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}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.550C>T",
+ "hgvs_cdna": "NM_001368144.2:c.518dup",
"is_preferred": false,
"variant_effects": [
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+ "FRAMESHIFT_VARIANT"
],
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- "hgvsp": "NP_001355073.1:p.Gln184Ter",
+ "hgvsp": "NP_001355073.1:p.Leu173PhefsTer6",
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- "end": 184
+ "start": 170,
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{
@@ -18767,8 +19688,8 @@
"genotypes": {
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{
- "label": "individual 47",
- "meta_label": "PMID_30968594_individual_47"
+ "label": "individual 55",
+ "meta_label": "PMID_30968594_individual_55"
}
],
"genotypes": [
@@ -18780,69 +19701,74 @@
},
{
"labels": {
- "label": "individual 10",
- "meta_label": "PMID_30968594_individual_10"
+ "label": "individual 56",
+ "meta_label": "PMID_30968594_individual_56"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0008665",
- "is_present": true
- },
- {
- "term_id": "HP:0000953",
- "is_present": true
- },
- {
- "term_id": "HP:0030088",
- "is_present": true
+ "term_id": "HP:0040171",
+ "is_present": true,
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},
{
"term_id": "HP:0003154",
- "is_present": true
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+ "onset": null
},
{
- "term_id": "HP:0008163",
- "is_present": true
+ "term_id": "HP:0011731",
+ "is_present": false,
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{
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- "is_present": true
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},
{
"term_id": "HP:0025133",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
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+ "test_term_id": "LOINC:1668-3",
+ "test_name": "17-Hydroxyprogesterone[Mass/Vol]",
+ "test_result": 30.0,
+ "unit": "UCUM:ng/dL"
+ },
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 614.0,
+ "test_result": 150.0,
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},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
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},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
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},
{
"test_term_id": "LOINC:2842-3",
"test_name": "Prolactin [Mass/Vol]",
- "test_result": 131.28,
+ "test_result": 27.8,
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},
{
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+ "test_result": 23.3,
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}
],
@@ -18850,7 +19776,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -18858,8 +19788,8 @@
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- "end": 32040421,
+ "start": 32038513,
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@@ -18879,38 +19809,196 @@
{
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- "hgvs_cdna": "NM_000500.9:c.955C>T",
+ "hgvs_cdna": "NM_000500.9:c.92C>T",
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+ "MISSENSE_VARIANT"
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- "hgvsp": "NP_000491.4:p.Gln319Ter",
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- "end": 319
+ "start": 30,
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}
},
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+ "is_preferred": true,
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{
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- "hgvsp": "NP_001122062.3:p.Gln289Ter",
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+ "transcript_id": "NM_001368143.2",
+ "hgvs_cdna": "NM_001368143.2:c.-333C>T",
+ "is_preferred": false,
+ "variant_effects": [
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@@ -18991,329 +20073,247 @@
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+ "label": "individual 56",
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}
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@@ -19321,12 +20321,12 @@
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+ "label": "individual 57",
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}
],
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- "HETEROZYGOUS"
+ "HOMOZYGOUS_ALTERNATE"
]
}
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@@ -19334,57 +20334,74 @@
},
{
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- "meta_label": "PMID_30968594_individual_3"
+ "label": "individual 58",
+ "meta_label": "PMID_30968594_individual_58"
},
"sex": "MALE",
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+ "vital_status": null,
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+ "term_id": "HP:0040171",
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},
{
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+ "term_id": "HP:0011043",
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},
{
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+ "term_id": "HP:0011731",
+ "is_present": false,
+ "onset": null
+ },
+ {
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{
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- "test_result": 685.0,
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},
{
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"test_name": "Testosterone[Mass/Vol]",
- "test_result": 340.0,
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},
{
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"test_name": "Corticotropin (P) [Mass/Vol]",
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},
{
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"test_name": "Cortisol [Mass/Vol]",
- "test_result": 78.3,
+ "test_result": 405.2,
+ "unit": "UCUM:ng/dL"
+ },
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+ "test_name": "Prolactin [Mass/Vol]",
+ "test_result": 61.71,
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},
{
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@@ -19392,7 +20409,11 @@
{
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"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
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}
],
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@@ -19400,8 +20421,8 @@
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@@ -19411,9 +20432,9 @@
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+ "ref": "C",
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@@ -19421,19 +20442,19 @@
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- "hgvsp": "NP_000491.4:p.Gly111ValfsTer21",
+ "hgvsp": "NP_000491.4:p.Pro31Leu",
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{
@@ -19483,13 +20504,13 @@
{
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- "hgvs_cdna": "NM_001368143.2:c.-74_-67del",
+ "hgvs_cdna": "NM_001368143.2:c.-333C>T",
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],
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@@ -19498,13 +20519,13 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.-74_-67del",
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],
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@@ -19540,8 +20561,8 @@
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{
- "label": "individual 3",
- "meta_label": "PMID_30968594_individual_3"
+ "label": "individual 58",
+ "meta_label": "PMID_30968594_individual_58"
}
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@@ -19553,8 +20574,8 @@
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- "variant_class": "DEL",
+ "structural_type": "SO:1000037",
+ "variant_class": "DUP",
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"gene_symbol": "CYP21A2"
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@@ -19870,8 +20891,8 @@
"genotypes": {
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{
- "label": "individual 3",
- "meta_label": "PMID_30968594_individual_3"
+ "label": "individual 58",
+ "meta_label": "PMID_30968594_individual_58"
}
],
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@@ -19883,61 +20904,74 @@
},
{
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- "label": "individual 67",
- "meta_label": "PMID_30968594_individual_67"
+ "label": "individual 59",
+ "meta_label": "PMID_30968594_individual_59"
},
- "sex": "MALE",
+ "sex": "FEMALE",
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+ "vital_status": null,
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{
- "term_id": "HP:0000953",
- "is_present": true
- },
- {
- "term_id": "HP:0040171",
- "is_present": true
+ "term_id": "HP:0030087",
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{
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{
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+ "term_id": "HP:0011731",
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{
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- "is_present": true
+ "is_present": true,
+ "onset": null
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+ {
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],
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},
{
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"test_name": "Testosterone[Mass/Vol]",
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},
{
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"test_name": "Corticotropin (P) [Mass/Vol]",
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{
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{
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+ "test_result": 25.57,
+ "unit": "UCUM:ng/dL"
+ },
+ {
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+ "test_name": "Estradiol (E2) [Mass/Vol]",
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@@ -19945,7 +20979,11 @@
{
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"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
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}
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@@ -19953,154 +20991,8 @@
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@@ -20110,9 +21002,9 @@
},
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},
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@@ -20120,20 +21012,16 @@
{
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- "hgvsp": "NP_000491.4:p.Leu308PhefsTer6",
- "protein_effect_location": {
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- "end": 306
- }
+ "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
+ "INTRON_VARIANT"
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+ "protein_id": "NP_000491.4",
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{
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@@ -20151,20 +21039,16 @@
{
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- "hgvs_cdna": "NM_001128590.4:c.833dup",
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- "protein_effect_location": {
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{
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@@ -20182,38 +21066,32 @@
{
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- "hgvs_cdna": "NM_001368143.2:c.518dup",
+ "hgvs_cdna": "NM_001368143.2:c.-126C>G",
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+ "FIVE_PRIME_UTR_VARIANT"
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{
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- "hgvs_cdna": "NM_001368144.2:c.518dup",
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+ "FIVE_PRIME_UTR_VARIANT"
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- "protein_effect_location": {
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},
{
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@@ -20245,8 +21123,8 @@
"genotypes": {
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{
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- "meta_label": "PMID_30968594_individual_67"
+ "label": "individual 59",
+ "meta_label": "PMID_30968594_individual_59"
}
],
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@@ -20258,51 +21136,68 @@
},
{
"labels": {
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- "meta_label": "PMID_30968594_individual_30"
+ "label": "individual 5",
+ "meta_label": "PMID_30968594_individual_5"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
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{
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- "is_present": true
+ "term_id": "HP:0002014",
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{
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{
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},
{
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+ "term_id": "HP:0008163",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000870",
+ "is_present": true,
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}
],
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 312.9,
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},
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 87.0,
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},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
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},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 440.2,
+ "test_result": 84.22,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2842-3",
+ "test_name": "Prolactin [Mass/Vol]",
+ "test_result": 19.53,
"unit": "UCUM:ng/dL"
}
],
@@ -20310,7 +21205,8 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
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@@ -20318,8 +21214,8 @@
"variant_info": {
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- "end": 32039081,
+ "start": 32040420,
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@@ -20330,119 +21226,450 @@
"strand": "POSITIVE"
},
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},
- "sv_info": null
- },
- "tx_annotations": [
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+ },
+ "tx_annotations": [
+ {
+ "gene_id": "CYP21A2",
+ "transcript_id": "NM_000500.9",
+ "hgvs_cdna": "NM_000500.9:c.955C>T",
+ "is_preferred": true,
+ "variant_effects": [
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+ "protein_id": "NP_000491.4",
+ "hgvsp": "NP_000491.4:p.Gln319Ter",
+ "protein_effect_location": {
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+ "end": 319
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+ {
+ "gene_id": "CYP21A2",
+ "transcript_id": "NM_001128590.4",
+ "hgvs_cdna": "NM_001128590.4:c.865C>T",
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+ "variant_effects": [
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+ "protein_id": "NP_001122062.3",
+ "hgvsp": "NP_001122062.3:p.Gln289Ter",
+ "protein_effect_location": {
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+ "end": 289
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+ "transcript_id": "NM_001365276.2",
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+ "hgvsp": "NP_001355072.1:p.Gln184Ter",
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+ "meta_label": "PMID_30968594_individual_5"
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@@ -20603,95 +21893,15 @@
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@@ -20862,37 +22179,50 @@
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@@ -20974,224 +22304,329 @@
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- "label": "individual 26",
- "meta_label": "PMID_30968594_individual_26"
+ "label": "individual 61",
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]
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@@ -21199,12 +22634,12 @@
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- "meta_label": "PMID_30968594_individual_17"
+ "label": "individual 61",
+ "meta_label": "PMID_30968594_individual_61"
}
],
"genotypes": [
- "HOMOZYGOUS_ALTERNATE"
+ "HETEROZYGOUS"
]
}
}
@@ -21212,71 +22647,84 @@
},
{
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- "label": "individual 40",
- "meta_label": "PMID_30968594_individual_40"
+ "label": "individual 62",
+ "meta_label": "PMID_30968594_individual_62"
},
- "sex": "MALE",
+ "sex": "FEMALE",
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+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0000953",
- "is_present": true
+ "term_id": "HP:0000789",
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},
{
- "term_id": "HP:0040171",
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+ "term_id": "HP:0008665",
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{
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{
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],
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 71.2,
+ "test_result": 27.3,
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},
{
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"test_name": "Testosterone[Mass/Vol]",
- "test_result": 153.0,
+ "test_result": 220.00000000000003,
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},
{
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"test_name": "Corticotropin (P) [Mass/Vol]",
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+ "test_result": 176.4,
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},
{
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"test_name": "Cortisol [Mass/Vol]",
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},
{
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"test_name": "Prolactin [Mass/Vol]",
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},
{
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}
],
@@ -21284,7 +22732,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -21292,8 +22744,8 @@
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- "end": 32039426,
+ "start": 32038513,
+ "end": 32038514,
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@@ -21303,8 +22755,8 @@
},
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},
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- "alt": "A",
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@@ -21313,19 +22765,19 @@
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],
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@@ -21344,19 +22796,19 @@
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+ "hgvsp": "NP_001122062.3:p.Pro31Leu",
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{
@@ -21375,38 +22827,32 @@
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- "hgvs_cdna": "NM_001368143.2:c.113T>A",
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- "end": 38
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},
{
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- "hgvs_cdna": "NM_001368144.2:c.113T>A",
+ "hgvs_cdna": "NM_001368144.2:c.-243C>T",
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- "hgvsp": "NP_001355073.1:p.Ile38Asn",
- "protein_effect_location": {
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- "end": 38
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{
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@@ -21438,8 +22884,8 @@
"genotypes": {
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{
- "label": "individual 40",
- "meta_label": "PMID_30968594_individual_40"
+ "label": "individual 62",
+ "meta_label": "PMID_30968594_individual_62"
}
],
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@@ -21768,8 +23214,8 @@
"genotypes": {
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{
- "label": "individual 40",
- "meta_label": "PMID_30968594_individual_40"
+ "label": "individual 62",
+ "meta_label": "PMID_30968594_individual_62"
}
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@@ -21781,67 +23227,51 @@
},
{
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- "meta_label": "PMID_30968594_individual_56"
+ "label": "individual 63",
+ "meta_label": "PMID_30968594_individual_63"
},
- "sex": "MALE",
+ "sex": "FEMALE",
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+ "vital_status": null,
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{
- "term_id": "HP:0040171",
- "is_present": true
- },
- {
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- "is_present": true
+ "term_id": "HP:0008665",
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},
{
- "term_id": "HP:0011731",
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+ "term_id": "HP:0000953",
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},
{
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+ "term_id": "HP:0003154",
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{
- "term_id": "HP:0025133",
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+ "term_id": "HP:0008163",
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- "test_result": 30.0,
- "unit": "UCUM:ng/dL"
- },
- {
- "test_term_id": "LOINC:2986-8",
- "test_name": "Testosterone[Mass/Vol]",
- "test_result": 150.0,
+ "test_result": 75.5,
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@@ -21849,7 +23279,11 @@
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+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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@@ -21857,8 +23291,8 @@
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},
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@@ -21878,19 +23312,19 @@
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@@ -21997,8 +23437,8 @@
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@@ -22021,8 +23461,8 @@
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@@ -22031,16 +23471,20 @@
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@@ -22058,16 +23502,20 @@
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@@ -22085,32 +23533,38 @@
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@@ -22142,8 +23596,8 @@
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@@ -22154,76 +23608,90 @@
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@@ -22231,7 +23699,11 @@
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@@ -22239,8 +23711,8 @@
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@@ -22260,50 +23732,37 @@
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@@ -22715,8 +24174,8 @@
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@@ -22728,71 +24187,74 @@
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},
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@@ -22800,139 +24262,325 @@
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@@ -23135,8 +24771,8 @@
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@@ -23281,8 +25101,8 @@
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@@ -23294,51 +25114,68 @@
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+ "term_id": "HP:0000953",
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},
{
- "term_id": "HP:0025133",
- "is_present": false
+ "term_id": "HP:0000870",
+ "is_present": true,
+ "onset": null
}
],
"measurements": [
{
"test_term_id": "LOINC:1668-3",
"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 87.5,
+ "test_result": 370.3,
+ "unit": "UCUM:ng/dL"
+ },
+ {
+ "test_term_id": "LOINC:2986-8",
+ "test_name": "Testosterone[Mass/Vol]",
+ "test_result": 282.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 91.91,
+ "test_result": 369.0,
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},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 444.8,
+ "test_result": 102.6,
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},
{
- "test_term_id": "LOINC:2243-4",
- "test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 67.55,
+ "test_term_id": "LOINC:2842-3",
+ "test_name": "Prolactin [Mass/Vol]",
+ "test_result": 92.19,
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}
],
@@ -23346,7 +25183,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 60.875,
+ "timeline": "POSTNATAL"
+ }
}
],
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@@ -23354,8 +25195,8 @@
"variant_info": {
"variant_coordinates": {
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- "start": 32041096,
- "end": 32041097,
+ "start": 32040420,
+ "end": 32040424,
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@@ -23365,9 +25206,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
- "change_length": 0
+ "ref": "CAGG",
+ "alt": "C",
+ "change_length": -3
},
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},
@@ -23375,37 +25216,37 @@
{
"gene_id": "CYP21A2",
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- "hgvs_cdna": "NM_000500.9:c.1451G>A",
+ "hgvs_cdna": "NM_000500.9:c.961_963del",
"is_preferred": true,
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- "MISSENSE_VARIANT"
+ "INFRAME_DELETION"
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- "hgvsp": "NP_000491.4:p.Arg484Gln",
+ "hgvsp": "NP_000491.4:p.Glu321del",
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- "end": 484
+ "start": 318,
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}
},
{
"gene_id": "CYP21A2",
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- "hgvs_cdna": "NM_001128590.4:c.1361G>A",
+ "hgvs_cdna": "NM_001128590.4:c.871_873del",
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+ "INFRAME_DELETION"
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- "hgvsp": "NP_001122062.3:p.Arg454Gln",
+ "hgvsp": "NP_001122062.3:p.Glu291del",
"protein_effect_location": {
- "start": 453,
- "end": 454
+ "start": 288,
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}
},
{
@@ -23424,37 +25265,37 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.1046G>A",
+ "hgvs_cdna": "NM_001368143.2:c.556_558del",
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- "MISSENSE_VARIANT"
+ "INFRAME_DELETION"
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],
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- "hgvsp": "NP_001355072.1:p.Arg349Gln",
+ "hgvsp": "NP_001355072.1:p.Glu186del",
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}
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.1046G>A",
+ "hgvs_cdna": "NM_001368144.2:c.556_558del",
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- "MISSENSE_VARIANT"
+ "INFRAME_DELETION"
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"protein_id": "NP_001355073.1",
- "hgvsp": "NP_001355073.1:p.Arg349Gln",
+ "hgvsp": "NP_001355073.1:p.Glu186del",
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- "end": 349
+ "start": 183,
+ "end": 185
}
},
{
@@ -23487,8 +25328,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 60",
- "meta_label": "PMID_30968594_individual_60"
+ "label": "individual 67",
+ "meta_label": "PMID_30968594_individual_67"
}
],
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@@ -23500,8 +25341,8 @@
"variant_info": {
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- "end": 32039081,
+ "start": 32040181,
+ "end": 32040182,
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@@ -23511,9 +25352,9 @@
},
"strand": "POSITIVE"
},
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- "alt": "G",
- "change_length": 0
+ "ref": "G",
+ "alt": "GT",
+ "change_length": 1
},
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},
@@ -23521,16 +25362,20 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_000500.9",
- "hgvs_cdna": "NM_000500.9:c.293-13C>G",
+ "hgvs_cdna": "NM_000500.9:c.923dup",
"is_preferred": true,
"variant_effects": [
- "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
- "INTRON_VARIANT"
+ "FRAMESHIFT_VARIANT"
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],
- "overlapping_exons": null,
"protein_id": "NP_000491.4",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000491.4:p.Leu308PhefsTer6",
+ "protein_effect_location": {
+ "start": 305,
+ "end": 306
+ }
},
{
"gene_id": "C4B",
@@ -23548,16 +25393,20 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.203-13C>G",
+ "hgvs_cdna": "NM_001128590.4:c.833dup",
"is_preferred": false,
"variant_effects": [
- "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
- "INTRON_VARIANT"
+ "FRAMESHIFT_VARIANT"
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"protein_id": "NP_001122062.3",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_001122062.3:p.Leu278PhefsTer6",
+ "protein_effect_location": {
+ "start": 275,
+ "end": 276
+ }
},
{
"gene_id": "TNXB",
@@ -23575,32 +25424,38 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.-126C>G",
+ "hgvs_cdna": "NM_001368143.2:c.518dup",
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+ "FRAMESHIFT_VARIANT"
],
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- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_001355072.1:p.Leu173PhefsTer6",
+ "protein_effect_location": {
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+ "end": 171
+ }
},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.-126C>G",
+ "hgvs_cdna": "NM_001368144.2:c.518dup",
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+ "FRAMESHIFT_VARIANT"
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- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_001355073.1:p.Leu173PhefsTer6",
+ "protein_effect_location": {
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+ "end": 171
+ }
},
{
"gene_id": "TNXB",
@@ -23632,8 +25487,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 60",
- "meta_label": "PMID_30968594_individual_60"
+ "label": "individual 67",
+ "meta_label": "PMID_30968594_individual_67"
}
],
"genotypes": [
@@ -23645,71 +25500,84 @@
},
{
"labels": {
- "label": "individual 4",
- "meta_label": "PMID_30968594_individual_4"
+ "label": "individual 68",
+ "meta_label": "PMID_30968594_individual_68"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0008665",
+ "is_present": true,
+ "onset": null
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{
"term_id": "HP:0000953",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0040171",
- "is_present": true
+ "term_id": "HP:0030087",
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},
{
- "term_id": "HP:0011043",
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+ "term_id": "HP:0003154",
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},
{
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- "is_present": true
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{
"term_id": "HP:0000870",
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{
"term_id": "HP:0008214",
- "is_present": true
+ "is_present": true,
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],
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{
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 488.0,
+ "test_result": 647.0,
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},
{
"test_term_id": "LOINC:2986-8",
"test_name": "Testosterone[Mass/Vol]",
- "test_result": 78.0,
+ "test_result": 25.0,
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},
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
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+ "test_result": 357.3,
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},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 63.03,
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},
{
"test_term_id": "LOINC:2842-3",
"test_name": "Prolactin [Mass/Vol]",
- "test_result": 116.21,
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},
{
"test_term_id": "LOINC:2243-4",
"test_name": "Estradiol (E2) [Mass/Vol]",
- "test_result": 2.52,
+ "test_result": 5.0,
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}
],
@@ -23717,7 +25585,8 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -23725,8 +25594,8 @@
"variant_info": {
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- "end": 32040535,
+ "start": 32039591,
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@@ -23736,8 +25605,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
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+ "ref": "T",
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},
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@@ -23746,441 +25615,269 @@
{
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- "hgvs_cdna": "NM_000500.9:c.1069C>T",
+ "hgvs_cdna": "NM_000500.9:c.596T>G",
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+ "STOP_GAINED"
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- "protein_id": "NP_001122062.3",
- "hgvsp": "NP_001122062.3:p.Arg327Trp",
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}
},
{
- "gene_id": "TNXB",
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+ "gene_id": "C4B",
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- "transcript_id": "NM_001368144.2",
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@@ -24201,61 +25898,84 @@
},
{
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+ "label": "individual 69",
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},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.5",
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@@ -24734,8 +26284,8 @@
"genotypes": {
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{
- "label": "individual 5",
- "meta_label": "PMID_30968594_individual_5"
+ "label": "individual 69",
+ "meta_label": "PMID_30968594_individual_69"
}
],
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@@ -24747,83 +26297,78 @@
},
{
"labels": {
- "label": "individual 61",
- "meta_label": "PMID_30968594_individual_61"
+ "label": "individual 6",
+ "meta_label": "PMID_30968594_individual_6"
},
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- "is_present": true
- },
- {
- "term_id": "HP:0001007",
- "is_present": true
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+ "sex": "MALE",
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+ "vital_status": null,
+ "phenotypes": [
{
- "term_id": "HP:0001061",
- "is_present": true
+ "term_id": "HP:0000822",
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{
- "term_id": "HP:0000953",
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{
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"test_name": "Testosterone[Mass/Vol]",
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},
{
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},
{
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},
{
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},
{
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}
],
@@ -24831,7 +26376,11 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
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@@ -24839,8 +26388,8 @@
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@@ -24850,8 +26399,8 @@
},
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@@ -24860,50 +26409,37 @@
{
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+ "hgvs_cdna": "NM_000500.9:c.955C>T",
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+ "STOP_GAINED"
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}
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{
"gene_id": "CYP21A2",
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- "hgvs_cdna": "NM_001128590.4:c.716G>C",
+ "hgvs_cdna": "NM_001128590.4:c.865C>T",
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- "hgvsp": "NP_001122062.3:p.Ser239Thr",
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}
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{
@@ -24922,37 +26458,37 @@
{
"gene_id": "CYP21A2",
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{
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{
@@ -24985,8 +26521,8 @@
"genotypes": {
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{
- "label": "individual 61",
- "meta_label": "PMID_30968594_individual_61"
+ "label": "individual 6",
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@@ -24996,318 +26532,134 @@
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{
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},
{
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{
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+ "end": 222
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},
{
- "gene_id": "HGNC:2600",
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+ "gene_id": "CYP21A2",
+ "transcript_id": "NM_001368144.2",
+ "hgvs_cdna": "NM_001368144.2:c.664C>T",
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+ "hgvsp": "NP_001355073.1:p.Arg222Trp",
+ "protein_effect_location": {
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+ "end": 222
+ }
},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.7",
+ "gene_id": "TNXB",
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},
{
- "gene_id": "HGNC:2600",
- "transcript_id": "NM_000500.5",
+ "gene_id": "TNXB",
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@@ -25315,8 +26667,8 @@
"genotypes": {
"samples": [
{
- "label": "individual 61",
- "meta_label": "PMID_30968594_individual_61"
+ "label": "individual 6",
+ "meta_label": "PMID_30968594_individual_6"
}
],
"genotypes": [
@@ -25328,41 +26680,44 @@
},
{
"labels": {
- "label": "individual 36",
- "meta_label": "PMID_30968594_individual_36"
+ "label": "individual 7",
+ "meta_label": "PMID_30968594_individual_7"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0008665",
- "is_present": true
+ "term_id": "HP:0000953",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030088",
- "is_present": true
+ "term_id": "HP:0040171",
+ "is_present": true,
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},
{
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+ "term_id": "HP:0011043",
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+ "onset": null
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{
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},
{
"term_id": "HP:0000870",
- "is_present": true
- },
- {
- "term_id": "HP:0025133",
- "is_present": false
+ "is_present": true,
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}
],
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"test_name": "17-Hydroxyprogesterone[Mass/Vol]",
- "test_result": 329.7,
+ "test_result": 638.0,
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},
{
@@ -25374,25 +26729,19 @@
{
"test_term_id": "LOINC:2141-0",
"test_name": "Corticotropin (P) [Mass/Vol]",
- "test_result": 81.4,
+ "test_result": 15.85,
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},
{
"test_term_id": "LOINC:2143-6",
"test_name": "Cortisol [Mass/Vol]",
- "test_result": 282.0,
+ "test_result": 480.0,
"unit": "UCUM:ng/dL"
},
{
"test_term_id": "LOINC:2842-3",
"test_name": "Prolactin [Mass/Vol]",
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- "unit": "UCUM:ng/dL"
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- {
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- "test_name": "Estradiol (E2) [Mass/Vol]",
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+ "test_result": 43.19,
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}
],
@@ -25400,7 +26749,8 @@
{
"term_id": "OMIM:201910",
"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -25408,8 +26758,8 @@
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- "end": 32039081,
+ "start": 32040181,
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@@ -25419,9 +26769,9 @@
},
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},
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- "change_length": 0
+ "ref": "G",
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},
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},
@@ -25429,16 +26779,20 @@
{
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- "hgvs_cdna": "NM_000500.9:c.293-13C>G",
+ "hgvs_cdna": "NM_000500.9:c.923dup",
"is_preferred": true,
"variant_effects": [
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- "INTRON_VARIANT"
+ "FRAMESHIFT_VARIANT"
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- "overlapping_exons": null,
"protein_id": "NP_000491.4",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000491.4:p.Leu308PhefsTer6",
+ "protein_effect_location": {
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+ "end": 306
+ }
},
{
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@@ -25456,16 +26810,20 @@
{
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"transcript_id": "NM_001128590.4",
- "hgvs_cdna": "NM_001128590.4:c.203-13C>G",
+ "hgvs_cdna": "NM_001128590.4:c.833dup",
"is_preferred": false,
"variant_effects": [
- "SPLICE_POLYPYRIMIDINE_TRACT_VARIANT",
- "INTRON_VARIANT"
+ "FRAMESHIFT_VARIANT"
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],
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"protein_id": "NP_001122062.3",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_001122062.3:p.Leu278PhefsTer6",
+ "protein_effect_location": {
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+ "end": 276
+ }
},
{
"gene_id": "TNXB",
@@ -25483,32 +26841,38 @@
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368143.2",
- "hgvs_cdna": "NM_001368143.2:c.-126C>G",
+ "hgvs_cdna": "NM_001368143.2:c.518dup",
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+ "FRAMESHIFT_VARIANT"
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- "protein_effect_location": null
+ "hgvsp": "NP_001355072.1:p.Leu173PhefsTer6",
+ "protein_effect_location": {
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+ "end": 171
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},
{
"gene_id": "CYP21A2",
"transcript_id": "NM_001368144.2",
- "hgvs_cdna": "NM_001368144.2:c.-126C>G",
+ "hgvs_cdna": "NM_001368144.2:c.518dup",
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+ "FRAMESHIFT_VARIANT"
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- "protein_effect_location": null
+ "hgvsp": "NP_001355073.1:p.Leu173PhefsTer6",
+ "protein_effect_location": {
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+ "end": 171
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},
{
"gene_id": "TNXB",
@@ -25540,8 +26904,8 @@
"genotypes": {
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{
- "label": "individual 36",
- "meta_label": "PMID_30968594_individual_36"
+ "label": "individual 7",
+ "meta_label": "PMID_30968594_individual_7"
}
],
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@@ -25833,251 +27197,36 @@
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{
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@@ -26085,12 +27234,12 @@
"genotypes": {
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+ "label": "individual 7",
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}
],
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}
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@@ -26098,75 +27247,84 @@
},
{
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+ "label": "individual 8",
+ "meta_label": "PMID_30968594_individual_8"
},
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+ "vital_status": null,
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{
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{
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{
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{
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},
{
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},
{
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}
],
@@ -26174,7 +27332,8 @@
{
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"name": "Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency",
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}
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@@ -26182,8 +27341,8 @@
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@@ -26203,305 +27362,154 @@
{
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@@ -26525,7 +27532,7 @@
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@@ -26549,7 +27556,7 @@
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@@ -26572,7 +27580,7 @@
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@@ -26595,7 +27603,7 @@
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@@ -26619,7 +27626,7 @@
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@@ -26884,12 +27817,12 @@
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+ "label": "individual 8",
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}
],
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+ "HETEROZYGOUS"
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@@ -26897,67 +27830,84 @@
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+ "label": "individual 9",
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},
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+ "vital_status": null,
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{
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{
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@@ -26965,7 +27915,11 @@
{
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+ "is_observed": true,
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+ "timeline": "POSTNATAL"
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}
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@@ -26973,8 +27927,8 @@
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@@ -26984,8 +27938,8 @@
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@@ -26994,50 +27948,37 @@
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@@ -27056,37 +27997,37 @@
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@@ -27119,8 +28060,8 @@
"genotypes": {
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- "label": "individual 41",
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+ "label": "individual 9",
+ "meta_label": "PMID_30968594_individual_9"
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@@ -27449,8 +28390,8 @@
"genotypes": {
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+ "label": "individual 9",
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@@ -27459,227 +28400,6 @@
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- }
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- "genotypes": {
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- {
- "label": "individual 16",
- "meta_label": "PMID_30968594_individual_16"
- }
- ],
- "genotypes": [
- "HOMOZYGOUS_ALTERNATE"
- ]
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}
],
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diff --git a/docs/cohort-data/RERE.0.1.20.json b/docs/cohort-data/RERE.0.1.20.json
index 9c75a4dd..201b235f 100644
--- a/docs/cohort-data/RERE.0.1.20.json
+++ b/docs/cohort-data/RERE.0.1.20.json
@@ -2,318 +2,350 @@
"members": [
{
"labels": {
- "label": "Subject 9",
- "meta_label": "PMID_27087320_Subject_9"
+ "label": "Subject 10",
+ "meta_label": "PMID_27087320_Subject_10"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 5113.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
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- "is_present": true
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- "is_present": true
- },
{
"term_id": "HP:0000729",
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+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001263",
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+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001249",
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- {
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- {
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+ "is_present": true,
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{
"term_id": "HP:0000463",
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},
{
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{
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{
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+ "onset": null
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{
"term_id": "HP:0000294",
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+ "onset": null
},
{
"term_id": "HP:0000341",
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{
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{
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{
"term_id": "HP:0011800",
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"term_id": "HP:0000325",
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{
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000581",
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+ "is_present": false,
+ "onset": null
+ },
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+ "term_id": "HP:0002007",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011229",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000490",
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},
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{
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{
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+ "onset": null
},
{
"term_id": "HP:0004467",
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+ "onset": null
},
{
"term_id": "HP:0000378",
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{
"term_id": "HP:0000396",
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{
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},
{
"term_id": "HP:0000494",
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+ "onset": null
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},
{
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- "term_id": "HP:0000028",
- "is_present": false
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- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
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+ "onset": null
},
{
"term_id": "HP:0001511",
- "is_present": false
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{
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+ "onset": null
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{
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- "is_present": false
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},
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},
{
"term_id": "HP:0001260",
- "is_present": false
- },
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- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002384",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001252",
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+ "onset": null
},
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- "is_present": false
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+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0010772",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000369",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000358",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000407",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000107",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0004209",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0006097",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001734",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000954",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011304",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0012168",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002938",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002033",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003186",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002650",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -321,7 +353,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -329,8 +362,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 8361235,
- "end": 8361236,
+ "start": 8361228,
+ "end": 8361229,
"contig": {
"name": "1",
"genbank_acc": "CM000663.2",
@@ -340,9 +373,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "CCCTGGAGGAGCTGAGGAGGGAG",
- "change_length": 22
+ "ref": "G",
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -350,63 +383,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.2249_2270dup",
+ "hgvs_cdna": "NM_001042681.2:c.2278C>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
18
],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.Thr758SerfsTer36",
+ "hgvsp": "NP_001036146.1:p.Gln760Ter",
"protein_effect_location": {
- "start": 756,
- "end": 757
+ "start": 759,
+ "end": 760
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_001042682.2",
- "hgvs_cdna": "NM_001042682.2:c.587_608dup",
+ "hgvs_cdna": "NM_001042682.2:c.616C>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
8
],
"protein_id": "NP_001036147.1",
- "hgvsp": "NP_001036147.1:p.Thr204SerfsTer36",
+ "hgvsp": "NP_001036147.1:p.Gln206Ter",
"protein_effect_location": {
- "start": 202,
- "end": 203
+ "start": 205,
+ "end": 206
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.2249_2270dup",
+ "hgvs_cdna": "NM_012102.4:c.2278C>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
19
],
"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.Thr758SerfsTer36",
+ "hgvsp": "NP_036234.3:p.Gln760Ter",
"protein_effect_location": {
- "start": 756,
- "end": 757
+ "start": 759,
+ "end": 760
}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 9",
- "meta_label": "PMID_27087320_Subject_9"
+ "label": "Subject 10",
+ "meta_label": "PMID_27087320_Subject_10"
}
],
"genotypes": [
@@ -418,338 +451,430 @@
},
{
"labels": {
- "label": "Subject 5",
- "meta_label": "PMID_27087320_Subject_5"
+ "label": "Subject 1",
+ "meta_label": "PMID_27087320_Subject_1"
},
"sex": "MALE",
+ "age": {
+ "days": 1095.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0002384",
- "is_present": true
+ "term_id": "HP:0001511",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000414",
- "is_present": true
+ "term_id": "HP:0000589",
+ "is_present": true,
+ "onset": null
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{
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+ "term_id": "HP:0000047",
+ "is_present": true,
+ "onset": null
},
{
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+ "term_id": "HP:0002020",
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{
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+ "term_id": "HP:0011968",
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+ "term_id": "HP:0001320",
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{
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- },
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@@ -757,7 +882,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -765,8 +891,8 @@
"variant_info": {
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"region": {
- "start": 8358241,
- "end": 8358242,
+ "start": 8359915,
+ "end": 8359916,
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"genbank_acc": "CM000663.2",
@@ -776,7 +902,7 @@
},
"strand": "POSITIVE"
},
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+ "ref": "C",
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},
@@ -786,63 +912,63 @@
{
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"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.4293C>A",
+ "hgvs_cdna": "NM_001042681.2:c.3466G>A",
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"variant_effects": [
"MISSENSE_VARIANT"
],
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],
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},
{
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+ "hgvs_cdna": "NM_001042682.2:c.1804G>A",
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"variant_effects": [
"MISSENSE_VARIANT"
],
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}
},
{
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"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.4293C>A",
+ "hgvs_cdna": "NM_012102.4:c.3466G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
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],
"protein_id": "NP_036234.3",
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}
],
"genotypes": {
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{
- "label": "Subject 5",
- "meta_label": "PMID_27087320_Subject_5"
+ "label": "Subject 1",
+ "meta_label": "PMID_27087320_Subject_1"
}
],
"genotypes": [
@@ -854,198 +980,400 @@
},
{
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- "label": "Subject 7",
- "meta_label": "PMID_29330883_Subject_7"
+ "label": "Subject 2",
+ "meta_label": "PMID_27087320_Subject_2"
},
"sex": "MALE",
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+ "timeline": "POSTNATAL"
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+ "onset": null
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+ "is_present": false,
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+ "is_present": false,
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+ "is_present": false,
+ "onset": null
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},
{
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"measurements": [],
@@ -1053,7 +1381,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -1137,8 +1466,8 @@
"genotypes": {
"samples": [
{
- "label": "Subject 7",
- "meta_label": "PMID_29330883_Subject_7"
+ "label": "Subject 2",
+ "meta_label": "PMID_27087320_Subject_2"
}
],
"genotypes": [
@@ -1150,219 +1479,428 @@
},
{
"labels": {
- "label": "Subject 6",
- "meta_label": "PMID_29330883_Subject_6"
+ "label": "Subject 3",
+ "meta_label": "PMID_27087320_Subject_3"
},
"sex": "MALE",
+ "age": {
+ "days": 852.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0010945",
- "is_present": true
+ "term_id": "HP:0000089",
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{
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{
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{
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{
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{
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{
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+ "name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
+ "is_observed": true,
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@@ -1372,8 +1910,8 @@
},
"strand": "POSITIVE"
},
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@@ -1382,7 +1920,7 @@
{
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@@ -1391,16 +1929,16 @@
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},
{
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+ "hgvs_cdna": "NM_001042682.2:c.2123C>G",
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@@ -1409,16 +1947,16 @@
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{
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@@ -1427,18 +1965,18 @@
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}
}
],
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{
- "label": "Subject 6",
- "meta_label": "PMID_29330883_Subject_6"
+ "label": "Subject 3",
+ "meta_label": "PMID_27087320_Subject_3"
}
],
"genotypes": [
@@ -1454,306 +1992,386 @@
"meta_label": "PMID_27087320_Subject_4"
},
"sex": "FEMALE",
+ "age": {
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+ "timeline": "POSTNATAL"
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@@ -1761,7 +2379,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -1858,326 +2477,428 @@
},
{
"labels": {
- "label": "Subject 8",
- "meta_label": "PMID_27087320_Subject_8"
+ "label": "Subject 5",
+ "meta_label": "PMID_27087320_Subject_5"
},
"sex": "MALE",
+ "age": {
+ "days": 4626.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0000347",
- "is_present": true
+ "term_id": "HP:0002384",
+ "is_present": true,
+ "onset": {
+ "days": 2922.0,
+ "timeline": "POSTNATAL"
+ }
},
{
- "term_id": "HP:0000494",
- "is_present": true
+ "term_id": "HP:0000414",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000187",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000218",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000581",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002007",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000490",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000076",
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},
{
"term_id": "HP:0002020",
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+ "is_present": true,
+ "onset": null
},
{
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+ "term_id": "HP:0011968",
+ "is_present": true,
+ "onset": null
},
{
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- "is_present": true
+ "term_id": "HP:0000648",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0007018",
- "is_present": true
+ "term_id": "HP:0000486",
+ "is_present": true,
+ "onset": null
},
{
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- "is_present": true
+ "term_id": "HP:0100704",
+ "is_present": true,
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},
{
- "term_id": "HP:0001249",
- "is_present": true
+ "term_id": "HP:0034295",
+ "is_present": true,
+ "onset": null
},
{
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- "is_present": true
+ "term_id": "HP:0002119",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002033",
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+ "term_id": "HP:0001320",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003186",
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+ "term_id": "HP:0000729",
+ "is_present": true,
+ "onset": null
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+ "is_present": true,
+ "onset": null
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+ "is_present": true,
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+ "is_present": true,
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},
{
"term_id": "HP:0000463",
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{
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{
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{
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{
"term_id": "HP:0000341",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011220",
- "is_present": false
- },
- {
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+ "is_present": false,
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},
{
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{
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{
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{
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- },
- {
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- "is_present": false
- },
- {
- "term_id": "HP:0002007",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011229",
- "is_present": false
- },
- {
- "term_id": "HP:0000490",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005280",
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+ "is_present": false,
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},
{
"term_id": "HP:0011240",
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{
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{
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{
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000286",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000347",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000664",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000582",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000494",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000601",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000316",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0020206",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000453",
- "is_present": false
- },
- {
- "term_id": "HP:0000076",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000028",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000047",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002247",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001511",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0004322",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000508",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000568",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000659",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000589",
- "is_present": false
- },
- {
- "term_id": "HP:0034295",
- "is_present": false
- },
- {
- "term_id": "HP:0002119",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002188",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0030303",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0012110",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001320",
- "is_present": false
+ "term_id": "HP:0007018",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001260",
- "is_present": false
- },
- {
- "term_id": "HP:0033725",
- "is_present": false
- },
- {
- "term_id": "HP:0002384",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001252",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001285",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0010772",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001629",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000369",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000358",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000407",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000107",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0004209",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0006097",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001734",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000954",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011304",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0012168",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002938",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002033",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003186",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002650",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -2185,7 +2906,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -2193,8 +2915,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 8495061,
- "end": 8495063,
+ "start": 8358241,
+ "end": 8358242,
"contig": {
"name": "1",
"genbank_acc": "CM000663.2",
@@ -2204,9 +2926,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CT",
- "alt": "C",
- "change_length": -1
+ "ref": "G",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -2214,47 +2936,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.1104del",
+ "hgvs_cdna": "NM_001042681.2:c.4293C>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 10
+ 20
],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.Leu369CysfsTer16",
+ "hgvsp": "NP_001036146.1:p.His1431Gln",
"protein_effect_location": {
- "start": 367,
- "end": 368
+ "start": 1430,
+ "end": 1431
+ }
+ },
+ {
+ "gene_id": "RERE",
+ "transcript_id": "NM_001042682.2",
+ "hgvs_cdna": "NM_001042682.2:c.2631C>A",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 10
+ ],
+ "protein_id": "NP_001036147.1",
+ "hgvsp": "NP_001036147.1:p.His877Gln",
+ "protein_effect_location": {
+ "start": 876,
+ "end": 877
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.1104del",
+ "hgvs_cdna": "NM_012102.4:c.4293C>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 11
+ 21
],
"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.Leu369CysfsTer16",
+ "hgvsp": "NP_036234.3:p.His1431Gln",
"protein_effect_location": {
- "start": 367,
- "end": 368
+ "start": 1430,
+ "end": 1431
}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 8",
- "meta_label": "PMID_27087320_Subject_8"
+ "label": "Subject 5",
+ "meta_label": "PMID_27087320_Subject_5"
}
],
"genotypes": [
@@ -2266,326 +3004,360 @@
},
{
"labels": {
- "label": "Subject 3",
- "meta_label": "PMID_27087320_Subject_3"
+ "label": "Subject 6",
+ "meta_label": "PMID_27087320_Subject_6"
},
- "sex": "MALE",
- "phenotypes": [
- {
- "term_id": "HP:0000089",
- "is_present": true
- },
- {
- "term_id": "HP:0002247",
- "is_present": true
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- "is_present": true
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- "is_present": true
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- "is_present": true
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- "is_present": true
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- "is_present": true
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- {
- "term_id": "HP:0000286",
- "is_present": true
- },
- {
- "term_id": "HP:0000347",
- "is_present": true
- },
+ "sex": "FEMALE",
+ "age": {
+ "days": 2191.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
+ "phenotypes": [
{
- "term_id": "HP:0000582",
- "is_present": true
+ "term_id": "HP:0000463",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000601",
- "is_present": true
+ "term_id": "HP:0000319",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000076",
- "is_present": true
+ "term_id": "HP:0000256",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0004322",
- "is_present": true
+ "term_id": "HP:0000325",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000568",
- "is_present": true
+ "term_id": "HP:0011229",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000659",
- "is_present": true
+ "term_id": "HP:0000316",
+ "is_present": true,
+ "onset": null
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{
- "term_id": "HP:0034295",
- "is_present": true
+ "term_id": "HP:0000729",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002119",
- "is_present": true
+ "term_id": "HP:0001252",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000729",
- "is_present": true
+ "term_id": "HP:0001263",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0033725",
- "is_present": true
+ "term_id": "HP:0001249",
+ "is_present": true,
+ "onset": null
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{
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+ "term_id": "HP:0000369",
+ "is_present": true,
+ "onset": null
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{
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+ "term_id": "HP:0000358",
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{
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{
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{
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+ "onset": null
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{
"term_id": "HP:0410030",
- "is_present": false
- },
- {
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- "is_present": false
+ "is_present": false,
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{
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{
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{
"term_id": "HP:0011800",
- "is_present": false
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{
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{
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{
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{
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+ "onset": null
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{
"term_id": "HP:0005280",
- "is_present": false
+ "is_present": false,
+ "onset": null
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{
"term_id": "HP:0008589",
- "is_present": false
+ "is_present": false,
+ "onset": null
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{
"term_id": "HP:0000378",
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+ "is_present": false,
+ "onset": null
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{
"term_id": "HP:0000396",
- "is_present": false
+ "is_present": false,
+ "onset": null
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+ "is_present": false,
+ "onset": null
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+ "is_present": false,
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{
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- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
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+ "onset": null
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{
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- "is_present": false
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@@ -2593,7 +3365,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
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+ "is_observed": true,
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}
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@@ -2601,8 +3374,8 @@
"variant_info": {
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@@ -2612,9 +3385,9 @@
},
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@@ -2622,63 +3395,63 @@
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{
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@@ -2690,448 +3463,496 @@
},
{
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},
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- "transcript_id": "NM_001042681.2",
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- "is_preferred": true,
- "variant_effects": [
- "TRANSCRIPT_ABLATION"
+ "FIVE_PRIME_UTR_VARIANT"
],
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- 16,
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],
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},
{
- "gene_id": "HGNC:9965",
- "transcript_id": "NM_001042682.2",
- "hgvs_cdna": null,
+ "gene_id": "RERE",
+ "transcript_id": "NM_012102.4",
+ "hgvs_cdna": "NM_012102.4:c.1411G>A",
"is_preferred": false,
"variant_effects": [
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+ "MISSENSE_VARIANT"
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- 2,
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- 7,
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+ "protein_id": "NP_036234.3",
+ "hgvsp": "NP_036234.3:p.Val471Ile",
+ "protein_effect_location": {
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+ "end": 471
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 1",
- "meta_label": "PMID_29330883_Subject_1"
+ "label": "Subject 7",
+ "meta_label": "PMID_27087320_Subject_7"
}
],
"genotypes": [
@@ -3143,318 +3964,410 @@
},
{
"labels": {
- "label": "Subject 2",
- "meta_label": "PMID_27087320_Subject_2"
+ "label": "Subject 8",
+ "meta_label": "PMID_27087320_Subject_8"
},
"sex": "MALE",
+ "age": {
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+ "timeline": "POSTNATAL"
+ },
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{
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{
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{
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{
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+ "is_present": false,
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{
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+ "is_present": false,
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{
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{
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+ "is_present": false,
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{
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{
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{
"term_id": "HP:0002938",
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- "is_present": false
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- {
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- "is_present": false
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+ "onset": null
},
{
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- "is_present": false
+ "is_present": false,
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}
],
"measurements": [],
@@ -3462,7 +4375,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -3470,8 +4384,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 8358215,
- "end": 8358216,
+ "start": 8495061,
+ "end": 8495063,
"contig": {
"name": "1",
"genbank_acc": "CM000663.2",
@@ -3481,9 +4395,9 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "TGGTGGA",
- "change_length": 6
+ "ref": "CT",
+ "alt": "C",
+ "change_length": -1
},
"sv_info": null
},
@@ -3491,63 +4405,47 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.4313_4318dup",
+ "hgvs_cdna": "NM_001042681.2:c.1104del",
"is_preferred": true,
"variant_effects": [
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- "overlapping_exons": [
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- "hgvs_cdna": "NM_001042682.2:c.2651_2656dup",
- "is_preferred": false,
- "variant_effects": [
- "INFRAME_INSERTION"
+ "FRAMESHIFT_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
10
],
- "protein_id": "NP_001036147.1",
- "hgvsp": "NP_001036147.1:p.Leu884_His885dup",
+ "protein_id": "NP_001036146.1",
+ "hgvsp": "NP_001036146.1:p.Leu369CysfsTer16",
"protein_effect_location": {
- "start": 885,
- "end": 886
+ "start": 367,
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}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.4313_4318dup",
+ "hgvs_cdna": "NM_012102.4:c.1104del",
"is_preferred": false,
"variant_effects": [
- "INFRAME_INSERTION"
+ "FRAMESHIFT_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 21
+ 11
],
"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.Leu1438_His1439dup",
+ "hgvsp": "NP_036234.3:p.Leu369CysfsTer16",
"protein_effect_location": {
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- "end": 1440
+ "start": 367,
+ "end": 368
}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 2",
- "meta_label": "PMID_27087320_Subject_2"
+ "label": "Subject 8",
+ "meta_label": "PMID_27087320_Subject_8"
}
],
"genotypes": [
@@ -3559,206 +4457,400 @@
},
{
"labels": {
- "label": "Subject 3",
- "meta_label": "PMID_29330883_Subject_3"
+ "label": "Subject 9",
+ "meta_label": "PMID_27087320_Subject_9"
},
"sex": "MALE",
+ "age": {
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+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
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+ "is_present": true,
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+ "is_present": true,
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+ "is_present": true,
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{
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{
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@@ -3766,7 +4858,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -3774,8 +4867,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 8358234,
- "end": 8358235,
+ "start": 8361235,
+ "end": 8361236,
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@@ -3785,9 +4878,9 @@
},
"strand": "POSITIVE"
},
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- "alt": "G",
- "change_length": 0
+ "ref": "C",
+ "alt": "CCCTGGAGGAGCTGAGGAGGGAG",
+ "change_length": 22
},
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},
@@ -3795,63 +4888,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.4300T>C",
+ "hgvs_cdna": "NM_001042681.2:c.2249_2270dup",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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+ 18
],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.Ser1434Pro",
+ "hgvsp": "NP_001036146.1:p.Thr758SerfsTer36",
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},
{
"gene_id": "RERE",
"transcript_id": "NM_001042682.2",
- "hgvs_cdna": "NM_001042682.2:c.2638T>C",
+ "hgvs_cdna": "NM_001042682.2:c.587_608dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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],
"protein_id": "NP_001036147.1",
- "hgvsp": "NP_001036147.1:p.Ser880Pro",
+ "hgvsp": "NP_001036147.1:p.Thr204SerfsTer36",
"protein_effect_location": {
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}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.4300T>C",
+ "hgvs_cdna": "NM_012102.4:c.2249_2270dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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],
"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.Ser1434Pro",
+ "hgvsp": "NP_036234.3:p.Thr758SerfsTer36",
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}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 3",
- "meta_label": "PMID_29330883_Subject_3"
+ "label": "Subject 9",
+ "meta_label": "PMID_27087320_Subject_9"
}
],
"genotypes": [
@@ -3864,341 +4957,224 @@
{
"labels": {
"label": "Subject 1",
- "meta_label": "PMID_27087320_Subject_1"
+ "meta_label": "PMID_29330883_Subject_1"
},
"sex": "MALE",
+ "age": {
+ "days": 1461.0,
+ "timeline": "POSTNATAL"
+ },
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@@ -4206,92 +5182,270 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
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- "strand": "POSITIVE"
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+ "sv_info": {
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+ "variant_class": "DEL",
+ "gene_id": "HGNC:9965",
+ "gene_symbol": "RERE"
+ }
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+ "gene_id": "HGNC:9965",
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{
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{
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{
"label": "Subject 1",
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+ "meta_label": "PMID_29330883_Subject_1"
}
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"genotypes": [
@@ -4303,278 +5457,240 @@
},
{
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- "meta_label": "PMID_27087320_Subject_10"
+ "label": "Subject 2",
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},
- "sex": "FEMALE",
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{
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],
"measurements": [],
@@ -4582,7 +5698,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
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}
],
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@@ -4590,8 +5707,8 @@
"variant_info": {
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"region": {
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- "end": 8361229,
+ "start": 8656048,
+ "end": 8656049,
"contig": {
"name": "1",
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@@ -4601,9 +5718,9 @@
},
"strand": "POSITIVE"
},
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+ "ref": "C",
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},
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},
@@ -4611,63 +5728,45 @@
{
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+ "hgvs_cdna": "NM_001042681.2:c.248dup",
"is_preferred": true,
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+ "FRAMESHIFT_VARIANT"
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- "protein_id": "NP_001036147.1",
- "hgvsp": "NP_001036147.1:p.Gln206Ter",
+ "hgvsp": "NP_001036146.1:p.Ser84ValfsTer4",
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+ "start": 82,
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},
{
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- "hgvs_cdna": "NM_012102.4:c.2278C>T",
+ "hgvs_cdna": "NM_012102.4:c.248dup",
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"variant_effects": [
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+ "FRAMESHIFT_VARIANT"
],
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"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.Gln760Ter",
+ "hgvsp": "NP_036234.3:p.Ser84ValfsTer4",
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}
}
],
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{
- "label": "Subject 10",
- "meta_label": "PMID_27087320_Subject_10"
+ "label": "Subject 2",
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}
],
"genotypes": [
@@ -4679,190 +5778,260 @@
},
{
"labels": {
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- "meta_label": "PMID_29330883_Subject_2"
+ "label": "Subject 3",
+ "meta_label": "PMID_29330883_Subject_3"
},
"sex": "MALE",
+ "age": {
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+ "timeline": "POSTNATAL"
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+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001249",
- "is_present": false
+ "term_id": "HP:0000453",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000407",
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+ "term_id": "HP:0000076",
+ "is_present": false,
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},
{
- "term_id": "HP:0002650",
- "is_present": false
+ "term_id": "HP:0000589",
+ "is_present": false,
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}
],
"measurements": [],
@@ -4870,7 +6039,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -4878,8 +6048,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 8656048,
- "end": 8656049,
+ "start": 8358234,
+ "end": 8358235,
"contig": {
"name": "1",
"genbank_acc": "CM000663.2",
@@ -4889,9 +6059,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "CT",
- "change_length": 1
+ "ref": "A",
+ "alt": "G",
+ "change_length": 0
},
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},
@@ -4899,45 +6069,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.248dup",
+ "hgvs_cdna": "NM_001042681.2:c.4300T>C",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
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+ 20
],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.Ser84ValfsTer4",
+ "hgvsp": "NP_001036146.1:p.Ser1434Pro",
"protein_effect_location": {
- "start": 82,
- "end": 83
+ "start": 1433,
+ "end": 1434
+ }
+ },
+ {
+ "gene_id": "RERE",
+ "transcript_id": "NM_001042682.2",
+ "hgvs_cdna": "NM_001042682.2:c.2638T>C",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
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+ ],
+ "protein_id": "NP_001036147.1",
+ "hgvsp": "NP_001036147.1:p.Ser880Pro",
+ "protein_effect_location": {
+ "start": 879,
+ "end": 880
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.248dup",
+ "hgvs_cdna": "NM_012102.4:c.4300T>C",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
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+ 21
],
"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.Ser84ValfsTer4",
+ "hgvsp": "NP_036234.3:p.Ser1434Pro",
"protein_effect_location": {
- "start": 82,
- "end": 83
+ "start": 1433,
+ "end": 1434
}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 2",
- "meta_label": "PMID_29330883_Subject_2"
+ "label": "Subject 3",
+ "meta_label": "PMID_29330883_Subject_3"
}
],
"genotypes": [
@@ -4949,186 +6137,230 @@
},
{
"labels": {
- "label": "Subject 9",
- "meta_label": "PMID_29330883_Subject_9"
+ "label": "Subject 4",
+ "meta_label": "PMID_29330883_Subject_4"
},
"sex": "FEMALE",
+ "age": {
+ "days": 4748.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
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- {
- "term_id": "HP:0000664",
- "is_present": true
- },
- {
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+ "term_id": "HP:0007033",
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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+ "onset": null
},
{
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- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
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{
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{
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},
{
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- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
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+ "is_present": false,
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},
{
"term_id": "HP:0020206",
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+ "is_present": false,
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{
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{
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{
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},
{
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+ "is_present": false,
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{
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+ "is_present": false,
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},
{
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+ "is_present": false,
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}
],
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@@ -5136,7 +6368,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -5144,8 +6377,8 @@
"variant_info": {
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"region": {
- "start": 8356194,
- "end": 8356195,
+ "start": 8358231,
+ "end": 8358232,
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"genbank_acc": "CM000663.2",
@@ -5155,8 +6388,8 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "C",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
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@@ -5165,63 +6398,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.4391A>G",
+ "hgvs_cdna": "NM_001042681.2:c.4303C>T",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
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+ 20
],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.His1464Arg",
+ "hgvsp": "NP_001036146.1:p.His1435Tyr",
"protein_effect_location": {
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- "end": 1464
+ "start": 1434,
+ "end": 1435
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_001042682.2",
- "hgvs_cdna": "NM_001042682.2:c.2729A>G",
+ "hgvs_cdna": "NM_001042682.2:c.2641C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 11
+ 10
],
"protein_id": "NP_001036147.1",
- "hgvsp": "NP_001036147.1:p.His910Arg",
+ "hgvsp": "NP_001036147.1:p.His881Tyr",
"protein_effect_location": {
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- "end": 910
+ "start": 880,
+ "end": 881
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.4391A>G",
+ "hgvs_cdna": "NM_012102.4:c.4303C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
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+ 21
],
"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.His1464Arg",
+ "hgvsp": "NP_036234.3:p.His1435Tyr",
"protein_effect_location": {
- "start": 1463,
- "end": 1464
+ "start": 1434,
+ "end": 1435
}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 9",
- "meta_label": "PMID_29330883_Subject_9"
+ "label": "Subject 4",
+ "meta_label": "PMID_29330883_Subject_4"
}
],
"genotypes": [
@@ -5237,198 +6470,251 @@
"meta_label": "PMID_29330883_Subject_5"
},
"sex": "FEMALE",
+ "age": {
+ "days": 8035.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
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{
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- "is_present": true
+ "is_present": true,
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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],
"measurements": [],
@@ -5436,7 +6722,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -5533,322 +6820,255 @@
},
{
"labels": {
- "label": "Subject 7",
- "meta_label": "PMID_27087320_Subject_7"
+ "label": "Subject 6",
+ "meta_label": "PMID_29330883_Subject_6"
},
"sex": "MALE",
+ "age": {
+ "days": 2922.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0410030",
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- {
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- },
- {
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+ "term_id": "HP:0010945",
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{
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{
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"measurements": [],
@@ -5856,7 +7076,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -5864,8 +7085,8 @@
"variant_info": {
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"region": {
- "start": 8365847,
- "end": 8365848,
+ "start": 8358230,
+ "end": 8358231,
"contig": {
"name": "1",
"genbank_acc": "CM000663.2",
@@ -5875,8 +7096,8 @@
},
"strand": "POSITIVE"
},
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+ "ref": "T",
+ "alt": "A",
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},
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@@ -5885,60 +7106,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.1411G>A",
+ "hgvs_cdna": "NM_001042681.2:c.4304A>T",
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"variant_effects": [
"MISSENSE_VARIANT"
],
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],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.Val471Ile",
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}
},
{
"gene_id": "RERE",
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+ "hgvs_cdna": "NM_001042682.2:c.2642A>T",
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+ "MISSENSE_VARIANT"
],
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- "protein_effect_location": null
+ "hgvsp": "NP_001036147.1:p.His881Leu",
+ "protein_effect_location": {
+ "start": 880,
+ "end": 881
+ }
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.1411G>A",
+ "hgvs_cdna": "NM_012102.4:c.4304A>T",
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"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
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"protein_id": "NP_036234.3",
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+ "hgvsp": "NP_036234.3:p.His1435Leu",
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}
}
],
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{
- "label": "Subject 7",
- "meta_label": "PMID_27087320_Subject_7"
+ "label": "Subject 6",
+ "meta_label": "PMID_29330883_Subject_6"
}
],
"genotypes": [
@@ -5950,286 +7174,250 @@
},
{
"labels": {
- "label": "Subject 6",
- "meta_label": "PMID_27087320_Subject_6"
+ "label": "Subject 7",
+ "meta_label": "PMID_29330883_Subject_7"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": {
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+ "timeline": "POSTNATAL"
+ },
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{
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{
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{
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{
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{
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"measurements": [],
@@ -6237,7 +7425,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -6245,8 +7434,8 @@
"variant_info": {
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"region": {
- "start": 8360383,
- "end": 8360385,
+ "start": 8358215,
+ "end": 8358216,
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@@ -6256,9 +7445,9 @@
},
"strand": "POSITIVE"
},
- "ref": "AG",
- "alt": "A",
- "change_length": -1
+ "ref": "T",
+ "alt": "TGGTGGA",
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},
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@@ -6266,63 +7455,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.3122del",
+ "hgvs_cdna": "NM_001042681.2:c.4313_4318dup",
"is_preferred": true,
"variant_effects": [
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+ "INFRAME_INSERTION"
],
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+ 20
],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.Pro1041LeufsTer40",
+ "hgvsp": "NP_001036146.1:p.Leu1438_His1439dup",
"protein_effect_location": {
- "start": 1040,
- "end": 1041
+ "start": 1439,
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{
"gene_id": "RERE",
"transcript_id": "NM_001042682.2",
- "hgvs_cdna": "NM_001042682.2:c.1460del",
+ "hgvs_cdna": "NM_001042682.2:c.2651_2656dup",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "INFRAME_INSERTION"
],
"overlapping_exons": [
- 8
+ 10
],
"protein_id": "NP_001036147.1",
- "hgvsp": "NP_001036147.1:p.Pro487LeufsTer40",
+ "hgvsp": "NP_001036147.1:p.Leu884_His885dup",
"protein_effect_location": {
- "start": 486,
- "end": 487
+ "start": 885,
+ "end": 886
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.3122del",
+ "hgvs_cdna": "NM_012102.4:c.4313_4318dup",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "INFRAME_INSERTION"
],
"overlapping_exons": [
- 19
+ 21
],
"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.Pro1041LeufsTer40",
+ "hgvsp": "NP_036234.3:p.Leu1438_His1439dup",
"protein_effect_location": {
- "start": 1040,
- "end": 1041
+ "start": 1439,
+ "end": 1440
}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 6",
- "meta_label": "PMID_27087320_Subject_6"
+ "label": "Subject 7",
+ "meta_label": "PMID_29330883_Subject_7"
}
],
"genotypes": [
@@ -6334,182 +7523,245 @@
},
{
"labels": {
- "label": "Subject 4",
- "meta_label": "PMID_29330883_Subject_4"
+ "label": "Subject 8",
+ "meta_label": "PMID_29330883_Subject_8"
},
"sex": "FEMALE",
+ "age": {
+ "days": 2922.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0007033",
- "is_present": true
+ "term_id": "HP:0011240",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001252",
- "is_present": true
+ "term_id": "HP:0000316",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000453",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001561",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001511",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0004322",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000589",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001263",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001249",
- "is_present": true
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000407",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002650",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0004384",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0000463",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000154",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0410030",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000319",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000294",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000341",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011220",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000414",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000256",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001357",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011800",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000325",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000187",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000218",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000581",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002007",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011229",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000490",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005280",
- "is_present": false
- },
- {
- "term_id": "HP:0011240",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0008589",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0004467",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000378",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000396",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009908",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000286",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000347",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000664",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000582",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000494",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000601",
- "is_present": false
- },
- {
- "term_id": "HP:0000316",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0020206",
- "is_present": false
- },
- {
- "term_id": "HP:0000453",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000076",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000508",
- "is_present": false
- },
- {
- "term_id": "HP:0000589",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000407",
- "is_present": false
- },
- {
- "term_id": "HP:0002650",
- "is_present": false
+ "term_id": "HP:0001252",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6517,7 +7769,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6525,8 +7778,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 8358231,
- "end": 8358232,
+ "start": 8358215,
+ "end": 8358216,
"contig": {
"name": "1",
"genbank_acc": "CM000663.2",
@@ -6536,9 +7789,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
- "change_length": 0
+ "ref": "T",
+ "alt": "TGGTGGA",
+ "change_length": 6
},
"sv_info": null
},
@@ -6546,63 +7799,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.4303C>T",
+ "hgvs_cdna": "NM_001042681.2:c.4313_4318dup",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "INFRAME_INSERTION"
],
"overlapping_exons": [
20
],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.His1435Tyr",
+ "hgvsp": "NP_001036146.1:p.Leu1438_His1439dup",
"protein_effect_location": {
- "start": 1434,
- "end": 1435
+ "start": 1439,
+ "end": 1440
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_001042682.2",
- "hgvs_cdna": "NM_001042682.2:c.2641C>T",
+ "hgvs_cdna": "NM_001042682.2:c.2651_2656dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "INFRAME_INSERTION"
],
"overlapping_exons": [
10
],
"protein_id": "NP_001036147.1",
- "hgvsp": "NP_001036147.1:p.His881Tyr",
+ "hgvsp": "NP_001036147.1:p.Leu884_His885dup",
"protein_effect_location": {
- "start": 880,
- "end": 881
+ "start": 885,
+ "end": 886
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.4303C>T",
+ "hgvs_cdna": "NM_012102.4:c.4313_4318dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "INFRAME_INSERTION"
],
"overlapping_exons": [
21
],
"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.His1435Tyr",
+ "hgvsp": "NP_036234.3:p.Leu1438_His1439dup",
"protein_effect_location": {
- "start": 1434,
- "end": 1435
+ "start": 1439,
+ "end": 1440
}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 4",
- "meta_label": "PMID_29330883_Subject_4"
+ "label": "Subject 8",
+ "meta_label": "PMID_29330883_Subject_8"
}
],
"genotypes": [
@@ -6614,194 +7867,235 @@
},
{
"labels": {
- "label": "Subject 8",
- "meta_label": "PMID_29330883_Subject_8"
+ "label": "Subject 9",
+ "meta_label": "PMID_29330883_Subject_9"
},
"sex": "FEMALE",
+ "age": {
+ "days": 1461.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0011240",
- "is_present": true
+ "term_id": "HP:0000463",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000316",
- "is_present": true
+ "term_id": "HP:0000154",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000453",
- "is_present": true
+ "term_id": "HP:0000664",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001561",
- "is_present": true
+ "term_id": "HP:0000316",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001511",
- "is_present": true
+ "term_id": "HP:0000729",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0004322",
- "is_present": true
+ "term_id": "HP:0000722",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000589",
- "is_present": true
+ "term_id": "HP:0001252",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001263",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001249",
- "is_present": true
- },
- {
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- "is_present": true
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- {
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- },
- {
- "term_id": "HP:0000463",
- "is_present": false
- },
- {
- "term_id": "HP:0000154",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0410030",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000319",
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+ "onset": null
},
{
"term_id": "HP:0000294",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000341",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011220",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000414",
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+ "onset": null
},
{
"term_id": "HP:0000256",
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+ "onset": null
},
{
"term_id": "HP:0001357",
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+ "is_present": false,
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},
{
"term_id": "HP:0011800",
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+ "onset": null
},
{
"term_id": "HP:0000325",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000187",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000218",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000581",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002007",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011229",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000490",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005280",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011240",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0008589",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0004467",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000378",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000396",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009908",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000286",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000347",
- "is_present": false
- },
- {
- "term_id": "HP:0000664",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000582",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000494",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000601",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0020206",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000453",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000076",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000508",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001252",
- "is_present": false
+ "term_id": "HP:0000589",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000407",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002650",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6809,7 +8103,8 @@
{
"term_id": "OMIM:616975",
"name": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6817,8 +8112,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 8358215,
- "end": 8358216,
+ "start": 8356194,
+ "end": 8356195,
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"name": "1",
"genbank_acc": "CM000663.2",
@@ -6829,8 +8124,8 @@
"strand": "POSITIVE"
},
"ref": "T",
- "alt": "TGGTGGA",
- "change_length": 6
+ "alt": "C",
+ "change_length": 0
},
"sv_info": null
},
@@ -6838,63 +8133,63 @@
{
"gene_id": "RERE",
"transcript_id": "NM_001042681.2",
- "hgvs_cdna": "NM_001042681.2:c.4313_4318dup",
+ "hgvs_cdna": "NM_001042681.2:c.4391A>G",
"is_preferred": true,
"variant_effects": [
- "INFRAME_INSERTION"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 20
+ 21
],
"protein_id": "NP_001036146.1",
- "hgvsp": "NP_001036146.1:p.Leu1438_His1439dup",
+ "hgvsp": "NP_001036146.1:p.His1464Arg",
"protein_effect_location": {
- "start": 1439,
- "end": 1440
+ "start": 1463,
+ "end": 1464
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_001042682.2",
- "hgvs_cdna": "NM_001042682.2:c.2651_2656dup",
+ "hgvs_cdna": "NM_001042682.2:c.2729A>G",
"is_preferred": false,
"variant_effects": [
- "INFRAME_INSERTION"
+ "MISSENSE_VARIANT"
],
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+ 11
],
"protein_id": "NP_001036147.1",
- "hgvsp": "NP_001036147.1:p.Leu884_His885dup",
+ "hgvsp": "NP_001036147.1:p.His910Arg",
"protein_effect_location": {
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- "end": 886
+ "start": 909,
+ "end": 910
}
},
{
"gene_id": "RERE",
"transcript_id": "NM_012102.4",
- "hgvs_cdna": "NM_012102.4:c.4313_4318dup",
+ "hgvs_cdna": "NM_012102.4:c.4391A>G",
"is_preferred": false,
"variant_effects": [
- "INFRAME_INSERTION"
+ "MISSENSE_VARIANT"
],
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+ 22
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"protein_id": "NP_036234.3",
- "hgvsp": "NP_036234.3:p.Leu1438_His1439dup",
+ "hgvsp": "NP_036234.3:p.His1464Arg",
"protein_effect_location": {
- "start": 1439,
- "end": 1440
+ "start": 1463,
+ "end": 1464
}
}
],
"genotypes": {
"samples": [
{
- "label": "Subject 8",
- "meta_label": "PMID_29330883_Subject_8"
+ "label": "Subject 9",
+ "meta_label": "PMID_29330883_Subject_9"
}
],
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diff --git a/docs/cohort-data/TBX5.0.1.20.json b/docs/cohort-data/TBX5.0.1.20.json
index e4530577..bcb83d8e 100644
--- a/docs/cohort-data/TBX5.0.1.20.json
+++ b/docs/cohort-data/TBX5.0.1.20.json
@@ -2,58 +2,80 @@
"members": [
{
"labels": {
- "label": "Family A IV-14",
- "meta_label": "PMID_10077612_Family_A_IV_14"
+ "label": "Family A III-10",
+ "meta_label": "PMID_10077612_Family_A_III_10"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 21184.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001191",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0031546",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -61,7 +83,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -145,8 +168,8 @@
"genotypes": {
"samples": [
{
- "label": "Family A IV-14",
- "meta_label": "PMID_10077612_Family_A_IV_14"
+ "label": "Family A III-10",
+ "meta_label": "PMID_10077612_Family_A_III_10"
}
],
"genotypes": [
@@ -158,78 +181,75 @@
},
{
"labels": {
- "label": "K4:II-1",
- "meta_label": "PMID_12789647_K4_II_1"
+ "label": "Family A III-12",
+ "meta_label": "PMID_10077612_Family_A_III_12"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 22645.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0002984",
- "is_present": true
- },
- {
- "term_id": "HP:0000774",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
- },
- {
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -237,7 +257,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -245,8 +266,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399513,
- "end": 114399514,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -256,8 +277,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "C",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -266,66 +287,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.361T>G",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Trp121Gly",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 120,
- "end": 121
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.211T>G",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Trp71Gly",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 70,
- "end": 71
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.361T>G",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Trp121Gly",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 120,
- "end": 121
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "K4:II-1",
- "meta_label": "PMID_12789647_K4_II_1"
+ "label": "Family A III-12",
+ "meta_label": "PMID_10077612_Family_A_III_12"
}
],
"genotypes": [
@@ -337,62 +355,75 @@
},
{
"labels": {
- "label": "K5:II-1",
- "meta_label": "PMID_12789647_K5_II_1"
+ "label": "Family A III-3",
+ "meta_label": "PMID_10077612_Family_A_III_3"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 26298.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -400,7 +431,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -408,8 +440,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385562,
- "end": 114385563,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -419,8 +451,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -429,63 +461,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.668C>T",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr223Met",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 222,
- "end": 223
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.518C>T",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr173Met",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 172,
- "end": 173
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.668C>T",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr223Met",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 222,
- "end": 223
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "K5:II-1",
- "meta_label": "PMID_12789647_K5_II_1"
+ "label": "Family A III-3",
+ "meta_label": "PMID_10077612_Family_A_III_3"
}
],
"genotypes": [
@@ -497,62 +529,75 @@
},
{
"labels": {
- "label": "Individual B",
- "meta_label": "PMID_33866394_Individual_B"
+ "label": "Family A IV-11",
+ "meta_label": "PMID_10077612_Family_A_IV_11"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 16801.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003834",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001377",
- "is_present": true
+ "term_id": "HP:0005301",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001233",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -560,7 +605,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -568,8 +614,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366240,
- "end": 114366242,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -579,9 +625,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CT",
- "alt": "C",
- "change_length": -1
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -589,63 +635,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.905del",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gln302ArgfsTer92",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 301,
- "end": 302
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.755del",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gln252ArgfsTer92",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 251,
- "end": 252
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.905del",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gln302ArgfsTer92",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 301,
- "end": 302
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "Individual B",
- "meta_label": "PMID_33866394_Individual_B"
+ "label": "Family A IV-11",
+ "meta_label": "PMID_10077612_Family_A_IV_11"
}
],
"genotypes": [
@@ -657,90 +703,75 @@
},
{
"labels": {
- "label": "III-2",
- "meta_label": "PMID_34490705_III_2"
+ "label": "Family A IV-12",
+ "meta_label": "PMID_10077612_Family_A_IV_12"
},
"sex": "MALE",
+ "age": {
+ "days": 13879.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0001684",
- "is_present": true
- },
{
"term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0002092",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0005301",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": true
- },
- {
- "term_id": "HP:0005180",
- "is_present": true
- },
- {
- "term_id": "HP:0001674",
- "is_present": false
- },
- {
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
- },
- {
- "term_id": "HP:0003022",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011664",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -748,7 +779,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -756,8 +788,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385474,
- "end": 114385475,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -777,48 +809,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.755+1G>A",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "protein_effect_location": {
+ "start": 79,
+ "end": 80
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.605+1G>A",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 2
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "protein_effect_location": {
+ "start": 29,
+ "end": 30
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.755+1G>A",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "protein_effect_location": {
+ "start": 79,
+ "end": 80
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "III-2",
- "meta_label": "PMID_34490705_III_2"
+ "label": "Family A IV-12",
+ "meta_label": "PMID_10077612_Family_A_IV_12"
}
],
"genotypes": [
@@ -830,70 +877,75 @@
},
{
"labels": {
- "label": "K5:III-1",
- "meta_label": "PMID_12789647_K5_III_1"
+ "label": "Family A IV-14",
+ "meta_label": "PMID_10077612_Family_A_IV_14"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 15340.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": true
- },
- {
- "term_id": "HP:0001199",
- "is_present": true
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
- },
- {
- "term_id": "HP:0003022",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -901,7 +953,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -909,8 +962,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385562,
- "end": 114385563,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -920,8 +973,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -930,63 +983,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.668C>T",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr223Met",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 222,
- "end": 223
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.518C>T",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr173Met",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 172,
- "end": 173
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.668C>T",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr223Met",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 222,
- "end": 223
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "K5:III-1",
- "meta_label": "PMID_12789647_K5_III_1"
+ "label": "Family A IV-14",
+ "meta_label": "PMID_10077612_Family_A_IV_14"
}
],
"genotypes": [
@@ -998,42 +1051,75 @@
},
{
"labels": {
- "label": "Family B IV-2",
- "meta_label": "PMID_10077612_Family_B_IV_2"
+ "label": "Family A IV-18",
+ "meta_label": "PMID_10077612_Family_A_IV_18"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 14610.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009813",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001629",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -1041,7 +1127,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -1049,8 +1136,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -1070,63 +1157,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B IV-2",
- "meta_label": "PMID_10077612_Family_B_IV_2"
+ "label": "Family A IV-18",
+ "meta_label": "PMID_10077612_Family_A_IV_18"
}
],
"genotypes": [
@@ -1138,66 +1225,80 @@
},
{
"labels": {
- "label": "Family 1 Patient 1",
- "meta_label": "PMID_25216260_Family_1_Patient_1"
+ "label": "Family A IV-20",
+ "meta_label": "PMID_10077612_Family_A_IV_20"
},
"sex": "FEMALE",
+ "age": {
+ "days": 14244.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0011682",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -1205,7 +1306,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -1213,8 +1315,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366266,
- "end": 114366267,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -1225,7 +1327,7 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "A",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -1234,63 +1336,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.880G>T",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Glu294Ter",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 293,
- "end": 294
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.730G>T",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Glu244Ter",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 243,
- "end": 244
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.880G>T",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Glu294Ter",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 293,
- "end": 294
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family 1 Patient 1",
- "meta_label": "PMID_25216260_Family_1_Patient_1"
+ "label": "Family A IV-20",
+ "meta_label": "PMID_10077612_Family_A_IV_20"
}
],
"genotypes": [
@@ -1302,58 +1404,75 @@
},
{
"labels": {
- "label": "Family B III-15",
- "meta_label": "PMID_10077612_Family_B_III_15"
+ "label": "Family A IV-21",
+ "meta_label": "PMID_10077612_Family_A_IV_21"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 13514.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001629",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -1361,7 +1480,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -1369,8 +1489,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -1390,63 +1510,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B III-15",
- "meta_label": "PMID_10077612_Family_B_III_15"
+ "label": "Family A IV-21",
+ "meta_label": "PMID_10077612_Family_A_IV_21"
}
],
"genotypes": [
@@ -1458,66 +1578,80 @@
},
{
"labels": {
- "label": "patient",
- "meta_label": "PMID_30538526_patient"
+ "label": "Family A IV-4",
+ "meta_label": "PMID_10077612_Family_A_IV_4"
},
"sex": "FEMALE",
+ "age": {
+ "days": 21184.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": true
- },
- {
- "term_id": "HP:0002092",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -1525,7 +1659,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -1533,8 +1668,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399632,
- "end": 114399633,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -1545,7 +1680,7 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "G",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -1554,48 +1689,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.243-1G>C",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_ACCEPTOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "protein_effect_location": {
+ "start": 79,
+ "end": 80
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.93-1G>C",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_ACCEPTOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 2
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "protein_effect_location": {
+ "start": 29,
+ "end": 30
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.243-1G>C",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
- "SPLICE_ACCEPTOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "protein_effect_location": {
+ "start": 79,
+ "end": 80
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "patient",
- "meta_label": "PMID_30538526_patient"
+ "label": "Family A IV-4",
+ "meta_label": "PMID_10077612_Family_A_IV_4"
}
],
"genotypes": [
@@ -1607,54 +1757,75 @@
},
{
"labels": {
- "label": "K14:II-1",
- "meta_label": "PMID_12789647_K14_II_1"
+ "label": "Family A IV-7",
+ "meta_label": "PMID_10077612_Family_A_IV_7"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": {
+ "days": 15705.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -1662,7 +1833,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -1670,8 +1842,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366365,
- "end": 114366366,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -1681,8 +1853,8 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -1691,63 +1863,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.781A>T",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ser261Cys",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 260,
- "end": 261
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.631A>T",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ser211Cys",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 210,
- "end": 211
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.781A>T",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ser261Cys",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 260,
- "end": 261
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "K14:II-1",
- "meta_label": "PMID_12789647_K14_II_1"
+ "label": "Family A IV-7",
+ "meta_label": "PMID_10077612_Family_A_IV_7"
}
],
"genotypes": [
@@ -1759,66 +1931,80 @@
},
{
"labels": {
- "label": "Family 2 Patient 3",
- "meta_label": "PMID_25216260_Family_2_Patient_3"
+ "label": "Family A VI-1",
+ "meta_label": "PMID_10077612_Family_A_VI_1"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": {
+ "days": 5478.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0001688",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -1826,7 +2012,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -1834,8 +2021,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385473,
- "end": 114385474,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -1845,8 +2032,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "G",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -1855,48 +2042,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.755+2T>C",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "protein_effect_location": {
+ "start": 79,
+ "end": 80
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.605+2T>C",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 2
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "protein_effect_location": {
+ "start": 29,
+ "end": 30
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.755+2T>C",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "protein_effect_location": {
+ "start": 79,
+ "end": 80
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "Family 2 Patient 3",
- "meta_label": "PMID_25216260_Family_2_Patient_3"
+ "label": "Family A VI-1",
+ "meta_label": "PMID_10077612_Family_A_VI_1"
}
],
"genotypes": [
@@ -1908,58 +2110,75 @@
},
{
"labels": {
- "label": "Family A IV-18",
- "meta_label": "PMID_10077612_Family_A_IV_18"
+ "label": "Family A VI-2",
+ "meta_label": "PMID_10077612_Family_A_VI_2"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": {
+ "days": 4748.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -1967,7 +2186,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -2051,8 +2271,8 @@
"genotypes": {
"samples": [
{
- "label": "Family A IV-18",
- "meta_label": "PMID_10077612_Family_A_IV_18"
+ "label": "Family A VI-2",
+ "meta_label": "PMID_10077612_Family_A_VI_2"
}
],
"genotypes": [
@@ -2064,62 +2284,80 @@
},
{
"labels": {
- "label": "666-2 ",
- "meta_label": "PMID_16917909_666_2"
+ "label": "Family A VI-5",
+ "meta_label": "PMID_10077612_Family_A_VI_5"
},
"sex": "MALE",
+ "age": {
+ "days": 3652.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001674",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001191",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -2127,7 +2365,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -2135,8 +2374,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114394761,
- "end": 114394763,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -2146,9 +2385,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CA",
- "alt": "C",
- "change_length": -1
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -2156,63 +2395,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.641del",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 6
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Val214GlyfsTer12",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 213,
- "end": 214
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.491del",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Val164GlyfsTer12",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 163,
- "end": 164
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.641del",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 6
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Val214GlyfsTer12",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 213,
- "end": 214
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "666-2 ",
- "meta_label": "PMID_16917909_666_2"
+ "label": "Family A VI-5",
+ "meta_label": "PMID_10077612_Family_A_VI_5"
}
],
"genotypes": [
@@ -2224,74 +2463,75 @@
},
{
"labels": {
- "label": "4-month-old female infant",
- "meta_label": "PMID_26219450_4_month_old_female_infant"
+ "label": "Family A V-10",
+ "meta_label": "PMID_10077612_Family_A_V_10"
},
"sex": "FEMALE",
+ "age": {
+ "days": 12053.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": true
- },
- {
- "term_id": "HP:0005180",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000347",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000185",
- "is_present": true
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0011565",
- "is_present": false
- },
- {
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -2299,7 +2539,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -2307,8 +2548,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401852,
- "end": 114401853,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -2318,7 +2559,7 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
+ "ref": "C",
"alt": "T",
"change_length": 0
},
@@ -2328,7 +2569,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.215C>A",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -2337,16 +2578,16 @@
3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr72Lys",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 71,
- "end": 72
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.65C>A",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -2355,16 +2596,16 @@
2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr22Lys",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 21,
- "end": 22
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.215C>A",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -2373,18 +2614,18 @@
3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr72Lys",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 71,
- "end": 72
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "4-month-old female infant",
- "meta_label": "PMID_26219450_4_month_old_female_infant"
+ "label": "Family A V-10",
+ "meta_label": "PMID_10077612_Family_A_V_10"
}
],
"genotypes": [
@@ -2396,58 +2637,60 @@
},
{
"labels": {
- "label": "Family A IV-7",
- "meta_label": "PMID_10077612_Family_A_IV_7"
+ "label": "Family A V-12",
+ "meta_label": "PMID_10077612_Family_A_V_12"
},
"sex": "FEMALE",
+ "age": {
+ "days": 4383.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0031546",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0001643",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -2455,7 +2698,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -2539,8 +2783,8 @@
"genotypes": {
"samples": [
{
- "label": "Family A IV-7",
- "meta_label": "PMID_10077612_Family_A_IV_7"
+ "label": "Family A V-12",
+ "meta_label": "PMID_10077612_Family_A_V_12"
}
],
"genotypes": [
@@ -2552,50 +2796,80 @@
},
{
"labels": {
- "label": "Family B ",
- "meta_label": "PMID_10077612_Family_B"
+ "label": "Family A V-13",
+ "meta_label": "PMID_10077612_Family_A_V_13"
},
"sex": "FEMALE",
+ "age": {
+ "days": 3287.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
+ },
{
"term_id": "HP:0001191",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001631",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001629",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -2603,7 +2877,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -2611,8 +2886,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -2632,63 +2907,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B ",
- "meta_label": "PMID_10077612_Family_B"
+ "label": "Family A V-13",
+ "meta_label": "PMID_10077612_Family_A_V_13"
}
],
"genotypes": [
@@ -2700,62 +2975,75 @@
},
{
"labels": {
- "label": "8-year-old male patient",
- "meta_label": "PMID_24408148_8_year_old_male_patient"
+ "label": "Family A V-5",
+ "meta_label": "PMID_10077612_Family_A_V_5"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 13149.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0000767",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003042",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001643",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -2763,7 +3051,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -2771,8 +3060,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401872,
- "end": 114401874,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -2782,9 +3071,9 @@
},
"strand": "POSITIVE"
},
- "ref": "TA",
+ "ref": "C",
"alt": "T",
- "change_length": -1
+ "change_length": 0
},
"sv_info": null
},
@@ -2792,63 +3081,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.194del",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Leu65GlnfsTer10",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 64,
- "end": 65
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.44del",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Leu15GlnfsTer10",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 14,
- "end": 15
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.194del",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Leu65GlnfsTer10",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 64,
- "end": 65
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "8-year-old male patient",
- "meta_label": "PMID_24408148_8_year_old_male_patient"
+ "label": "Family A V-5",
+ "meta_label": "PMID_10077612_Family_A_V_5"
}
],
"genotypes": [
@@ -2860,74 +3149,75 @@
},
{
"labels": {
- "label": "K17:II-5",
- "meta_label": "PMID_12789647_K17_II_5"
+ "label": "Family A V-7",
+ "meta_label": "PMID_10077612_Family_A_V_7"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": {
+ "days": 12783.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": true
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": true
- },
- {
- "term_id": "HP:0001674",
- "is_present": false
- },
- {
- "term_id": "HP:0001655",
- "is_present": false
- },
- {
- "term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -2935,7 +3225,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -2943,8 +3234,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385562,
- "end": 114385563,
+ "start": 114401829,
+ "end": 114401830,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -2954,8 +3245,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -2964,63 +3255,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.668C>T",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr223Met",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 222,
- "end": 223
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.518C>T",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr173Met",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 172,
- "end": 173
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.668C>T",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr223Met",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 222,
- "end": 223
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "K17:II-5",
- "meta_label": "PMID_12789647_K17_II_5"
+ "label": "Family A V-7",
+ "meta_label": "PMID_10077612_Family_A_V_7"
}
],
"genotypes": [
@@ -3032,66 +3323,65 @@
},
{
"labels": {
- "label": "668-2",
- "meta_label": "PMID_16917909_668_2"
+ "label": "Family B ",
+ "meta_label": "PMID_10077612_Family_B"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 1826.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0011636",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001631",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -3099,7 +3389,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -3107,8 +3398,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385473,
- "end": 114385474,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -3118,8 +3409,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "G",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -3128,48 +3419,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.755+2T>C",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "protein_effect_location": {
+ "start": 236,
+ "end": 237
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.605+2T>C",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 6
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "protein_effect_location": {
+ "start": 186,
+ "end": 187
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.755+2T>C",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "protein_effect_location": {
+ "start": 236,
+ "end": 237
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "668-2",
- "meta_label": "PMID_16917909_668_2"
+ "label": "Family B ",
+ "meta_label": "PMID_10077612_Family_B"
}
],
"genotypes": [
@@ -3181,74 +3487,55 @@
},
{
"labels": {
- "label": "K1:II-2",
- "meta_label": "PMID_12789647_K1_II_2"
+ "label": "Family B III-11",
+ "meta_label": "PMID_10077612_Family_B_III_11"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": {
+ "days": 12053.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0003974",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
- },
- {
- "term_id": "HP:0001674",
- "is_present": false
- },
- {
- "term_id": "HP:0001655",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -3256,7 +3543,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -3264,8 +3552,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398625,
- "end": 114398627,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -3275,9 +3563,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CG",
- "alt": "C",
- "change_length": -1
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -3285,63 +3573,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.456del",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Val153SerfsTer21",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 151,
- "end": 152
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.306del",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Val103SerfsTer21",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 101,
- "end": 102
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.456del",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Val153SerfsTer21",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 151,
- "end": 152
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "K1:II-2",
- "meta_label": "PMID_12789647_K1_II_2"
+ "label": "Family B III-11",
+ "meta_label": "PMID_10077612_Family_B_III_11"
}
],
"genotypes": [
@@ -3353,26 +3641,75 @@
},
{
"labels": {
- "label": "Family B III-18",
- "meta_label": "PMID_10077612_Family_B_III_18"
+ "label": "Family B III-13",
+ "meta_label": "PMID_10077612_Family_B_III_13"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": {
+ "days": 11322.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
{
"term_id": "HP:0009813",
- "is_present": true
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -3380,7 +3717,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -3464,8 +3802,8 @@
"genotypes": {
"samples": [
{
- "label": "Family B III-18",
- "meta_label": "PMID_10077612_Family_B_III_18"
+ "label": "Family B III-13",
+ "meta_label": "PMID_10077612_Family_B_III_13"
}
],
"genotypes": [
@@ -3477,58 +3815,75 @@
},
{
"labels": {
- "label": "HOS-B2",
- "meta_label": "PMID_10842287_HOS_B2"
+ "label": "Family B III-15",
+ "meta_label": "PMID_10077612_Family_B_III_15"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 10592.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -3536,7 +3891,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -3544,8 +3900,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403753,
- "end": 114403754,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -3555,7 +3911,7 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
+ "ref": "C",
"alt": "T",
"change_length": 0
},
@@ -3565,60 +3921,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.145C>A",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gln49Lys",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 48,
- "end": 49
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1834C>A",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 6
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "protein_effect_location": {
+ "start": 186,
+ "end": 187
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.145C>A",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gln49Lys",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 48,
- "end": 49
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "HOS-B2",
- "meta_label": "PMID_10842287_HOS_B2"
+ "label": "Family B III-15",
+ "meta_label": "PMID_10077612_Family_B_III_15"
}
],
"genotypes": [
@@ -3630,86 +3989,35 @@
},
{
"labels": {
- "label": "619-2",
- "meta_label": "PMID_16917909_619_2"
+ "label": "Family B III-18",
+ "meta_label": "PMID_10077612_Family_B_III_18"
},
"sex": "FEMALE",
+ "age": {
+ "days": 13149.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0001634",
- "is_present": true
- },
- {
- "term_id": "HP:0001704",
- "is_present": true
- },
- {
- "term_id": "HP:0001653",
- "is_present": true
- },
- {
- "term_id": "HP:0006394",
- "is_present": true
- },
- {
- "term_id": "HP:0005773",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
- },
- {
- "term_id": "HP:0001674",
- "is_present": false
- },
- {
- "term_id": "HP:0001655",
- "is_present": false
- },
- {
- "term_id": "HP:0002092",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
- },
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -3717,7 +4025,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -3725,8 +4034,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398577,
- "end": 114398579,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -3736,9 +4045,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CA",
- "alt": "C",
- "change_length": -1
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -3746,63 +4055,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.504del",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Phe168LeufsTer6",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 167,
- "end": 168
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.354del",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Phe118LeufsTer6",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 117,
- "end": 118
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.504del",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Phe168LeufsTer6",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 167,
- "end": 168
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "619-2",
- "meta_label": "PMID_16917909_619_2"
+ "label": "Family B III-18",
+ "meta_label": "PMID_10077612_Family_B_III_18"
}
],
"genotypes": [
@@ -3814,26 +4123,40 @@
},
{
"labels": {
- "label": "Family B II-11",
- "meta_label": "PMID_10077612_Family_B_II_11"
+ "label": "Family B III-2",
+ "meta_label": "PMID_10077612_Family_B_III_2"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": {
+ "days": 13514.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0009813",
- "is_present": true
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -3841,7 +4164,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -3925,8 +4249,8 @@
"genotypes": {
"samples": [
{
- "label": "Family B II-11",
- "meta_label": "PMID_10077612_Family_B_II_11"
+ "label": "Family B III-2",
+ "meta_label": "PMID_10077612_Family_B_III_2"
}
],
"genotypes": [
@@ -3938,62 +4262,75 @@
},
{
"labels": {
- "label": "649-1",
- "meta_label": "PMID_16917909_649_1"
+ "label": "Family B III-5",
+ "meta_label": "PMID_10077612_Family_B_III_5"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": {
+ "days": 12053.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -4001,7 +4338,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -4009,8 +4347,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114356063,
- "end": 114356065,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -4020,9 +4358,9 @@
},
"strand": "POSITIVE"
},
- "ref": "TA",
+ "ref": "C",
"alt": "T",
- "change_length": -1
+ "change_length": 0
},
"sv_info": null
},
@@ -4030,64 +4368,64 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.1024del",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 9
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr342ThrfsTer52",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 341,
- "end": 342
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.874del",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr292ThrfsTer52",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 291,
- "end": 292
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.1024del",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 9
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr342ThrfsTer52",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 341,
- "end": 342
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "649-1",
- "meta_label": "PMID_16917909_649_1"
- }
+ "label": "Family B III-5",
+ "meta_label": "PMID_10077612_Family_B_III_5"
+ }
],
"genotypes": [
"HETEROZYGOUS"
@@ -4098,78 +4436,75 @@
},
{
"labels": {
- "label": "K11:II-2",
- "meta_label": "PMID_12789647_K11_II_2"
+ "label": "Family B III-7",
+ "meta_label": "PMID_10077612_Family_B_III_7"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 9131.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001655",
- "is_present": true
- },
- {
- "term_id": "HP:0010487",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
- },
- {
- "term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -4177,7 +4512,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -4261,8 +4597,8 @@
"genotypes": {
"samples": [
{
- "label": "K11:II-2",
- "meta_label": "PMID_12789647_K11_II_2"
+ "label": "Family B III-7",
+ "meta_label": "PMID_10077612_Family_B_III_7"
}
],
"genotypes": [
@@ -4274,58 +4610,80 @@
},
{
"labels": {
- "label": "Family B III-7",
- "meta_label": "PMID_10077612_Family_B_III_7"
+ "label": "Family B III-9",
+ "meta_label": "PMID_10077612_Family_B_III_9"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 12418.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
+ },
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001191",
- "is_present": true
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031546",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001629",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0031546",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -4333,7 +4691,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -4417,8 +4776,8 @@
"genotypes": {
"samples": [
{
- "label": "Family B III-7",
- "meta_label": "PMID_10077612_Family_B_III_7"
+ "label": "Family B III-9",
+ "meta_label": "PMID_10077612_Family_B_III_9"
}
],
"genotypes": [
@@ -4430,58 +4789,35 @@
},
{
"labels": {
- "label": "Family A V-5",
- "meta_label": "PMID_10077612_Family_A_V_5"
+ "label": "Family B II-11",
+ "meta_label": "PMID_10077612_Family_B_II_11"
},
"sex": "FEMALE",
+ "age": {
+ "days": 24471.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0002984",
- "is_present": true
- },
- {
- "term_id": "HP:0001191",
- "is_present": true
- },
- {
- "term_id": "HP:0031546",
- "is_present": true
- },
- {
- "term_id": "HP:0001643",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
- },
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -4489,7 +4825,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -4497,8 +4834,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -4518,63 +4855,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A V-5",
- "meta_label": "PMID_10077612_Family_A_V_5"
+ "label": "Family B II-11",
+ "meta_label": "PMID_10077612_Family_B_II_11"
}
],
"genotypes": [
@@ -4586,74 +4923,80 @@
},
{
"labels": {
- "label": "HH24",
- "meta_label": "PMID_17534187_HH24"
+ "label": "Family B II-2",
+ "meta_label": "PMID_10077612_Family_B_II_2"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": {
+ "days": 23741.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0001674",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": true
- },
- {
- "term_id": "HP:0001653",
- "is_present": true
- },
- {
- "term_id": "HP:0001642",
- "is_present": true
- },
- {
- "term_id": "HP:0000878",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000882",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -4661,7 +5004,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -4669,8 +5013,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385552,
- "end": 114385553,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -4681,7 +5025,7 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "A",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -4690,7 +5034,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.678G>T",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -4699,16 +5043,16 @@
7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Lys226Asn",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 225,
- "end": 226
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.528G>T",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -4717,16 +5061,16 @@
6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Lys176Asn",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 175,
- "end": 176
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.678G>T",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -4735,18 +5079,18 @@
7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Lys226Asn",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 225,
- "end": 226
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "HH24",
- "meta_label": "PMID_17534187_HH24"
+ "label": "Family B II-2",
+ "meta_label": "PMID_10077612_Family_B_II_2"
}
],
"genotypes": [
@@ -4758,62 +5102,55 @@
},
{
"labels": {
- "label": "15\u2010month\u2010old male patient",
- "meta_label": "PMID_15710732_15_month_old_male_patient"
+ "label": "Family B II-5",
+ "meta_label": "PMID_10077612_Family_B_II_5"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 20454.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0001655",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0003974",
- "is_present": true
- },
- {
- "term_id": "HP:0005792",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -4821,7 +5158,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -4829,8 +5167,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399621,
- "end": 114399622,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -4840,7 +5178,7 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
+ "ref": "C",
"alt": "T",
"change_length": 0
},
@@ -4850,63 +5188,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.253C>A",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Pro85Thr",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 84,
- "end": 85
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.103C>A",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Pro35Thr",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 34,
- "end": 35
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.253C>A",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Pro85Thr",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 84,
- "end": 85
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "15\u2010month\u2010old male patient",
- "meta_label": "PMID_15710732_15_month_old_male_patient"
+ "label": "Family B II-5",
+ "meta_label": "PMID_10077612_Family_B_II_5"
}
],
"genotypes": [
@@ -4918,58 +5256,75 @@
},
{
"labels": {
- "label": "Family A VI-2",
- "meta_label": "PMID_10077612_Family_A_VI_2"
+ "label": "Family B II-8",
+ "meta_label": "PMID_10077612_Family_B_II_8"
},
"sex": "MALE",
+ "age": {
+ "days": 18627.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0001629",
- "is_present": true
- },
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001191",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -4977,7 +5332,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -4985,8 +5341,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -5006,63 +5362,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A VI-2",
- "meta_label": "PMID_10077612_Family_A_VI_2"
+ "label": "Family B II-8",
+ "meta_label": "PMID_10077612_Family_B_II_8"
}
],
"genotypes": [
@@ -5074,54 +5430,80 @@
},
{
"labels": {
- "label": "HH8",
- "meta_label": "PMID_17534187_HH8"
+ "label": "Family B IV-10",
+ "meta_label": "PMID_10077612_Family_B_IV_10"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": {
+ "days": 1826.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0009623",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0004220",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -5129,7 +5511,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -5137,8 +5520,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366311,
- "end": 114366312,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -5148,8 +5531,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -5158,63 +5541,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.835C>T",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg279Ter",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 278,
- "end": 279
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.685C>T",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg229Ter",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 228,
- "end": 229
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.835C>T",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg279Ter",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 278,
- "end": 279
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "HH8",
- "meta_label": "PMID_17534187_HH8"
+ "label": "Family B IV-10",
+ "meta_label": "PMID_10077612_Family_B_IV_10"
}
],
"genotypes": [
@@ -5226,66 +5609,85 @@
},
{
"labels": {
- "label": "K15:IV-2",
- "meta_label": "PMID_12789647_K15_IV_2"
+ "label": "Family B IV-1",
+ "meta_label": "PMID_10077612_Family_B_IV_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 3287.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -5293,7 +5695,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -5301,8 +5704,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398681,
- "end": 114398682,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -5313,8 +5716,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "CG",
- "change_length": 1
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -5322,63 +5725,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.400dup",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 133,
- "end": 134
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.250dup",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 83,
- "end": 84
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.400dup",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 133,
- "end": 134
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "K15:IV-2",
- "meta_label": "PMID_12789647_K15_IV_2"
+ "label": "Family B IV-1",
+ "meta_label": "PMID_10077612_Family_B_IV_1"
}
],
"genotypes": [
@@ -5390,50 +5793,55 @@
},
{
"labels": {
- "label": "HOS-G",
- "meta_label": "PMID_10842287_HOS_G"
+ "label": "Family B IV-2",
+ "meta_label": "PMID_10077612_Family_B_IV_2"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 1461.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0009813",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
- },
- {
- "term_id": "HP:0001674",
- "is_present": false
- },
- {
- "term_id": "HP:0001655",
- "is_present": false
- },
- {
- "term_id": "HP:0011664",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -5441,7 +5849,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -5449,8 +5858,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401906,
- "end": 114401907,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -5460,8 +5869,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "G",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -5470,63 +5879,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.161T>C",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ile54Thr",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 53,
- "end": 54
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.11T>C",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ile4Thr",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 3,
- "end": 4
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.161T>C",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ile54Thr",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 53,
- "end": 54
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "HOS-G",
- "meta_label": "PMID_10842287_HOS_G"
+ "label": "Family B IV-2",
+ "meta_label": "PMID_10077612_Family_B_IV_2"
}
],
"genotypes": [
@@ -5542,42 +5951,56 @@
"meta_label": "PMID_10077612_Family_B_IV_3"
},
"sex": "FEMALE",
+ "age": {
+ "days": 4383.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001629",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031546",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -5585,7 +6008,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -5682,66 +6106,80 @@
},
{
"labels": {
- "label": "B III/1",
- "meta_label": "PMID_12818525_B_III_1"
+ "label": "Family B IV-5",
+ "meta_label": "PMID_10077612_Family_B_IV_5"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 1461.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0030241",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -5749,7 +6187,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -5757,8 +6196,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398674,
- "end": 114398675,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -5768,7 +6207,7 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
+ "ref": "C",
"alt": "T",
"change_length": 0
},
@@ -5778,63 +6217,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.408C>A",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr136Ter",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.258C>A",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr86Ter",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 85,
- "end": 86
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.408C>A",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr136Ter",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "B III/1",
- "meta_label": "PMID_12818525_B_III_1"
+ "label": "Family B IV-5",
+ "meta_label": "PMID_10077612_Family_B_IV_5"
}
],
"genotypes": [
@@ -5846,70 +6285,85 @@
},
{
"labels": {
- "label": "K16:III-3",
- "meta_label": "PMID_12789647_K16_III_3"
+ "label": "Family B IV-9",
+ "meta_label": "PMID_10077612_Family_B_IV_9"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 1095.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0003974",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": true
- },
- {
- "term_id": "HP:0003022",
- "is_present": true
- },
- {
- "term_id": "HP:0005792",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -5917,7 +6371,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -5925,8 +6380,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398655,
- "end": 114398656,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -5937,8 +6392,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "CG",
- "change_length": 1
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -5946,63 +6401,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.426dup",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala143ArgfsTer40",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 141,
- "end": 143
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.276dup",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ala93ArgfsTer40",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 91,
- "end": 93
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.426dup",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala143ArgfsTer40",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 141,
- "end": 143
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "K16:III-3",
- "meta_label": "PMID_12789647_K16_III_3"
+ "label": "Family B IV-9",
+ "meta_label": "PMID_10077612_Family_B_IV_9"
}
],
"genotypes": [
@@ -6014,62 +6469,65 @@
},
{
"labels": {
- "label": "patient",
- "meta_label": "PMID_27652283_patient"
+ "label": "nan",
+ "meta_label": "PMID_10077612_nan"
},
"sex": "MALE",
+ "age": {
+ "days": 26298.0,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0001655",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005180",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0031546",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0001643",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6077,7 +6535,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6085,9 +6544,9 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401852,
- "end": 114401853,
- "contig": {
+ "start": 114401829,
+ "end": 114401830,
+ "contig": {
"name": "12",
"genbank_acc": "CM000674.2",
"refseq_name": "NC_000012.12",
@@ -6096,7 +6555,7 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
+ "ref": "C",
"alt": "T",
"change_length": 0
},
@@ -6106,7 +6565,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.215C>A",
+ "hgvs_cdna": "NM_000192.3:c.238G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -6115,16 +6574,16 @@
3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr72Lys",
+ "hgvsp": "NP_000183.2:p.Gly80Arg",
"protein_effect_location": {
- "start": 71,
- "end": 72
+ "start": 79,
+ "end": 80
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.65C>A",
+ "hgvs_cdna": "NM_080717.4:c.88G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -6133,16 +6592,16 @@
2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr22Lys",
+ "hgvsp": "NP_542448.1:p.Gly30Arg",
"protein_effect_location": {
- "start": 21,
- "end": 22
+ "start": 29,
+ "end": 30
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.215C>A",
+ "hgvs_cdna": "NM_181486.4:c.238G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -6151,18 +6610,18 @@
3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr72Lys",
+ "hgvsp": "NP_852259.1:p.Gly80Arg",
"protein_effect_location": {
- "start": 71,
- "end": 72
+ "start": 79,
+ "end": 80
}
}
],
"genotypes": {
"samples": [
{
- "label": "patient",
- "meta_label": "PMID_27652283_patient"
+ "label": "nan",
+ "meta_label": "PMID_10077612_nan"
}
],
"genotypes": [
@@ -6174,62 +6633,72 @@
},
{
"labels": {
- "label": "K15:III-1",
- "meta_label": "PMID_12789647_K15_III_1"
+ "label": "HOS-A1",
+ "meta_label": "PMID_10842287_HOS_A1"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0009813",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
- },
- {
- "term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6237,7 +6706,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6245,8 +6715,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398681,
- "end": 114398682,
+ "start": 114398665,
+ "end": 114398667,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -6256,9 +6726,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "CG",
- "change_length": 1
+ "ref": "TG",
+ "alt": "T",
+ "change_length": -1
},
"sv_info": null
},
@@ -6266,7 +6736,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.400dup",
+ "hgvs_cdna": "NM_000192.3:c.416del",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -6275,16 +6745,16 @@
5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
+ "hgvsp": "NP_000183.2:p.Pro139GlnfsTer11",
"protein_effect_location": {
- "start": 133,
- "end": 134
+ "start": 138,
+ "end": 139
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.250dup",
+ "hgvs_cdna": "NM_080717.4:c.266del",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -6293,16 +6763,16 @@
4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
+ "hgvsp": "NP_542448.1:p.Pro89GlnfsTer11",
"protein_effect_location": {
- "start": 83,
- "end": 84
+ "start": 88,
+ "end": 89
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.400dup",
+ "hgvs_cdna": "NM_181486.4:c.416del",
"is_preferred": true,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -6311,18 +6781,18 @@
5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
+ "hgvsp": "NP_852259.1:p.Pro139GlnfsTer11",
"protein_effect_location": {
- "start": 133,
- "end": 134
+ "start": 138,
+ "end": 139
}
}
],
"genotypes": {
"samples": [
{
- "label": "K15:III-1",
- "meta_label": "PMID_12789647_K15_III_1"
+ "label": "HOS-A1",
+ "meta_label": "PMID_10842287_HOS_A1"
}
],
"genotypes": [
@@ -6334,62 +6804,82 @@
},
{
"labels": {
- "label": "Family A III-10",
- "meta_label": "PMID_10077612_Family_A_III_10"
+ "label": "HOS-A2",
+ "meta_label": "PMID_10842287_HOS_A2"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0002986",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0003031",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6397,7 +6887,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6405,8 +6896,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114398665,
+ "end": 114398667,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -6416,9 +6907,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
+ "ref": "TG",
"alt": "T",
- "change_length": 0
+ "change_length": -1
},
"sv_info": null
},
@@ -6426,63 +6917,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.416del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Pro139GlnfsTer11",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 138,
+ "end": 139
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.266del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 2
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Pro89GlnfsTer11",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 88,
+ "end": 89
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.416del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Pro139GlnfsTer11",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 138,
+ "end": 139
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A III-10",
- "meta_label": "PMID_10077612_Family_A_III_10"
+ "label": "HOS-A2",
+ "meta_label": "PMID_10842287_HOS_A2"
}
],
"genotypes": [
@@ -6494,66 +6985,82 @@
},
{
"labels": {
- "label": "A III/3",
- "meta_label": "PMID_12818525_A_III_3"
+ "label": "HOS-B1",
+ "meta_label": "PMID_10842287_HOS_B1"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030241",
- "is_present": true
+ "term_id": "HP:0006097",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009460",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6561,7 +7068,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6569,8 +7077,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398674,
- "end": 114398675,
+ "start": 114403753,
+ "end": 114403754,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -6590,63 +7098,60 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.408C>A",
+ "hgvs_cdna": "NM_000192.3:c.145C>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 5
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr136Ter",
+ "hgvsp": "NP_000183.2:p.Gln49Lys",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 48,
+ "end": 49
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.258C>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1834C>A",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
- ],
- "overlapping_exons": [
- 4
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr86Ter",
- "protein_effect_location": {
- "start": 85,
- "end": 86
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.408C>A",
+ "hgvs_cdna": "NM_181486.4:c.145C>A",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 5
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr136Ter",
+ "hgvsp": "NP_852259.1:p.Gln49Lys",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 48,
+ "end": 49
}
}
],
"genotypes": {
"samples": [
{
- "label": "A III/3",
- "meta_label": "PMID_12818525_A_III_3"
+ "label": "HOS-B1",
+ "meta_label": "PMID_10842287_HOS_B1"
}
],
"genotypes": [
@@ -6658,58 +7163,72 @@
},
{
"labels": {
- "label": "1",
- "meta_label": "PMID_20519243_1"
+ "label": "HOS-B2",
+ "meta_label": "PMID_10842287_HOS_B2"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0004756",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6717,7 +7236,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6725,8 +7245,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401845,
- "end": 114401846,
+ "start": 114403753,
+ "end": 114403754,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -6736,8 +7256,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "G",
+ "ref": "G",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -6746,63 +7266,60 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.222G>C",
+ "hgvs_cdna": "NM_000192.3:c.145C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Met74Ile",
+ "hgvsp": "NP_000183.2:p.Gln49Lys",
"protein_effect_location": {
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- "end": 74
+ "start": 48,
+ "end": 49
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.72G>C",
+ "hgvs_cdna": "NM_080717.4:c.-3-1834C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 2
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Met24Ile",
- "protein_effect_location": {
- "start": 23,
- "end": 24
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.222G>C",
+ "hgvs_cdna": "NM_181486.4:c.145C>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Met74Ile",
+ "hgvsp": "NP_852259.1:p.Gln49Lys",
"protein_effect_location": {
- "start": 73,
- "end": 74
+ "start": 48,
+ "end": 49
}
}
],
"genotypes": {
"samples": [
{
- "label": "1",
- "meta_label": "PMID_20519243_1"
+ "label": "HOS-B2",
+ "meta_label": "PMID_10842287_HOS_B2"
}
],
"genotypes": [
@@ -6814,66 +7331,62 @@
},
{
"labels": {
- "label": "706-1",
- "meta_label": "PMID_16917909_706_1"
+ "label": "HOS-G",
+ "meta_label": "PMID_10842287_HOS_G"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0001199",
- "is_present": true
- },
- {
- "term_id": "HP:0001643",
- "is_present": true
- },
- {
- "term_id": "HP:0010035",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6881,7 +7394,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6889,8 +7403,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114355722,
- "end": 114355723,
+ "start": 114401906,
+ "end": 114401907,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -6900,8 +7414,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
+ "ref": "A",
+ "alt": "G",
"change_length": 0
},
"sv_info": null
@@ -6910,63 +7424,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.1366C>T",
+ "hgvs_cdna": "NM_000192.3:c.161T>C",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 9
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gln456Ter",
+ "hgvsp": "NP_000183.2:p.Ile54Thr",
"protein_effect_location": {
- "start": 455,
- "end": 456
+ "start": 53,
+ "end": 54
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.1216C>T",
+ "hgvs_cdna": "NM_080717.4:c.11T>C",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gln406Ter",
+ "hgvsp": "NP_542448.1:p.Ile4Thr",
"protein_effect_location": {
- "start": 405,
- "end": 406
+ "start": 3,
+ "end": 4
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.1366C>T",
+ "hgvs_cdna": "NM_181486.4:c.161T>C",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 9
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gln456Ter",
+ "hgvsp": "NP_852259.1:p.Ile54Thr",
"protein_effect_location": {
- "start": 455,
- "end": 456
+ "start": 53,
+ "end": 54
}
}
],
"genotypes": {
"samples": [
{
- "label": "706-1",
- "meta_label": "PMID_16917909_706_1"
+ "label": "HOS-G",
+ "meta_label": "PMID_10842287_HOS_G"
}
],
"genotypes": [
@@ -6978,58 +7492,82 @@
},
{
"labels": {
- "label": "Family A IV-12",
- "meta_label": "PMID_10077612_Family_A_IV_12"
+ "label": "K10:II-4",
+ "meta_label": "PMID_12789647_K10_II_4"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -7037,7 +7575,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -7045,8 +7584,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114385521,
+ "end": 114385522,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -7056,8 +7595,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -7066,63 +7605,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.709C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Arg237Trp",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.559C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Arg187Trp",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.709C>T",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Arg237Trp",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A IV-12",
- "meta_label": "PMID_10077612_Family_A_IV_12"
+ "label": "K10:II-4",
+ "meta_label": "PMID_12789647_K10_II_4"
}
],
"genotypes": [
@@ -7134,62 +7673,97 @@
},
{
"labels": {
- "label": "Family B IV-10",
- "meta_label": "PMID_10077612_Family_B_IV_10"
+ "label": "K11:III-1",
+ "meta_label": "PMID_12789647_K11_III_1"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0010487",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -7197,7 +7771,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -7281,8 +7856,8 @@
"genotypes": {
"samples": [
{
- "label": "Family B IV-10",
- "meta_label": "PMID_10077612_Family_B_IV_10"
+ "label": "K11:III-1",
+ "meta_label": "PMID_12789647_K11_III_1"
}
],
"genotypes": [
@@ -7294,70 +7869,92 @@
},
{
"labels": {
- "label": "370-1",
- "meta_label": "PMID_16917909_370_1"
+ "label": "K11:III-2",
+ "meta_label": "PMID_12789647_K11_III_2"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0006394",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011927",
- "is_present": true
+ "term_id": "HP:0003022",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -7365,7 +7962,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -7373,8 +7971,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366206,
- "end": 114366208,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -7384,9 +7982,9 @@
},
"strand": "POSITIVE"
},
- "ref": "GC",
- "alt": "G",
- "change_length": -1
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -7394,63 +7992,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.939del",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gln315ArgfsTer79",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 312,
- "end": 313
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.789del",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gln265ArgfsTer79",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 262,
- "end": 263
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.939del",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gln315ArgfsTer79",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 312,
- "end": 313
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "370-1",
- "meta_label": "PMID_16917909_370_1"
+ "label": "K11:III-2",
+ "meta_label": "PMID_12789647_K11_III_2"
}
],
"genotypes": [
@@ -7462,62 +8060,97 @@
},
{
"labels": {
- "label": "Family A V-13",
- "meta_label": "PMID_10077612_Family_A_V_13"
+ "label": "K11:II-2",
+ "meta_label": "PMID_12789647_K11_II_2"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0010487",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -7525,7 +8158,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -7533,8 +8167,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114385520,
+ "end": 114385521,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -7554,63 +8188,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.710G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Arg237Gln",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.560G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Arg187Gln",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.710G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Arg237Gln",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A V-13",
- "meta_label": "PMID_10077612_Family_A_V_13"
+ "label": "K11:II-2",
+ "meta_label": "PMID_12789647_K11_II_2"
}
],
"genotypes": [
@@ -7622,62 +8256,87 @@
},
{
"labels": {
- "label": "Family 2:IV:1",
- "meta_label": "PMID_29755943_Family_2_IV_1"
+ "label": "K12:III-2",
+ "meta_label": "PMID_12789647_K12_III_2"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011664",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -7685,7 +8344,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -7693,8 +8353,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403791,
- "end": 114403792,
+ "start": 114385562,
+ "end": 114385563,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -7704,9 +8364,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "CG",
- "change_length": 1
+ "ref": "G",
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -7714,58 +8374,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.106_107insC",
+ "hgvs_cdna": "NM_000192.3:c.668C>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
+ "hgvsp": "NP_000183.2:p.Thr223Met",
"protein_effect_location": {
- "start": 35,
- "end": 36
+ "start": 222,
+ "end": 223
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
+ "hgvs_cdna": "NM_080717.4:c.518C>T",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 6
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Thr173Met",
+ "protein_effect_location": {
+ "start": 172,
+ "end": 173
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.106_107insC",
+ "hgvs_cdna": "NM_181486.4:c.668C>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
+ "hgvsp": "NP_852259.1:p.Thr223Met",
"protein_effect_location": {
- "start": 35,
- "end": 36
+ "start": 222,
+ "end": 223
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family 2:IV:1",
- "meta_label": "PMID_29755943_Family_2_IV_1"
+ "label": "K12:III-2",
+ "meta_label": "PMID_12789647_K12_III_2"
}
],
"genotypes": [
@@ -7777,74 +8442,87 @@
},
{
"labels": {
- "label": "K12:I-2",
- "meta_label": "PMID_12789647_K12_I_2"
+ "label": "K12:II-2",
+ "meta_label": "PMID_12789647_K12_II_2"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0010704",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
- },
- {
- "term_id": "HP:0002984",
- "is_present": false
- },
- {
- "term_id": "HP:0003022",
- "is_present": false
- },
- {
- "term_id": "HP:0005792",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -7852,7 +8530,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -7936,8 +8615,8 @@
"genotypes": {
"samples": [
{
- "label": "K12:I-2",
- "meta_label": "PMID_12789647_K12_I_2"
+ "label": "K12:II-2",
+ "meta_label": "PMID_12789647_K12_II_2"
}
],
"genotypes": [
@@ -7949,58 +8628,87 @@
},
{
"labels": {
- "label": "Family B III-13",
- "meta_label": "PMID_10077612_Family_B_III_13"
+ "label": "K12:II-3",
+ "meta_label": "PMID_12789647_K12_II_3"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
+ },
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0010704",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -8008,7 +8716,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -8016,8 +8725,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114385562,
+ "end": 114385563,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -8027,8 +8736,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -8037,7 +8746,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.668C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -8046,16 +8755,16 @@
7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Thr223Met",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 222,
+ "end": 223
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.518C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -8064,16 +8773,16 @@
6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Thr173Met",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 172,
+ "end": 173
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.668C>T",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -8082,18 +8791,18 @@
7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Thr223Met",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 222,
+ "end": 223
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B III-13",
- "meta_label": "PMID_10077612_Family_B_III_13"
+ "label": "K12:II-3",
+ "meta_label": "PMID_12789647_K12_II_3"
}
],
"genotypes": [
@@ -8105,62 +8814,92 @@
},
{
"labels": {
- "label": "Family A VI-5",
- "meta_label": "PMID_10077612_Family_A_VI_5"
+ "label": "K12:I-2",
+ "meta_label": "PMID_12789647_K12_I_2"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -8168,7 +8907,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -8176,8 +8916,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114385562,
+ "end": 114385563,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -8187,8 +8927,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -8197,63 +8937,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.668C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Thr223Met",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 222,
+ "end": 223
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.518C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Thr173Met",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 172,
+ "end": 173
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.668C>T",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Thr223Met",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 222,
+ "end": 223
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A VI-5",
- "meta_label": "PMID_10077612_Family_A_VI_5"
+ "label": "K12:I-2",
+ "meta_label": "PMID_12789647_K12_I_2"
}
],
"genotypes": [
@@ -8265,62 +9005,92 @@
},
{
"labels": {
- "label": "Family 2 Patient 4",
- "meta_label": "PMID_25216260_Family_2_Patient_4"
+ "label": "K13:II-2",
+ "meta_label": "PMID_12789647_K13_II_2"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0011682",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -8328,7 +9098,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -8336,8 +9107,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385473,
- "end": 114385474,
+ "start": 114385521,
+ "end": 114385522,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -8347,8 +9118,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "G",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -8357,48 +9128,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.755+2T>C",
+ "hgvs_cdna": "NM_000192.3:c.709C>T",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Arg237Trp",
+ "protein_effect_location": {
+ "start": 236,
+ "end": 237
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.605+2T>C",
+ "hgvs_cdna": "NM_080717.4:c.559C>T",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 6
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Arg187Trp",
+ "protein_effect_location": {
+ "start": 186,
+ "end": 187
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.755+2T>C",
+ "hgvs_cdna": "NM_181486.4:c.709C>T",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Arg237Trp",
+ "protein_effect_location": {
+ "start": 236,
+ "end": 237
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "Family 2 Patient 4",
- "meta_label": "PMID_25216260_Family_2_Patient_4"
+ "label": "K13:II-2",
+ "meta_label": "PMID_12789647_K13_II_2"
}
],
"genotypes": [
@@ -8410,58 +9196,92 @@
},
{
"labels": {
- "label": "4-year old male patient",
- "meta_label": "PMID_18828908_4_year_old_male_patient"
+ "label": "K13:I-1",
+ "meta_label": "PMID_12789647_K13_I_1"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": true
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000347",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000343",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000894",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -8469,7 +9289,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -8477,8 +9298,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114355754,
- "end": 114355756,
+ "start": 114385521,
+ "end": 114385522,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -8488,9 +9309,9 @@
},
"strand": "POSITIVE"
},
- "ref": "TG",
- "alt": "T",
- "change_length": -1
+ "ref": "G",
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -8498,63 +9319,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.1333del",
+ "hgvs_cdna": "NM_000192.3:c.709C>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
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- 9
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.His445MetfsTer137",
+ "hgvsp": "NP_000183.2:p.Arg237Trp",
"protein_effect_location": {
- "start": 444,
- "end": 445
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.1183del",
+ "hgvs_cdna": "NM_080717.4:c.559C>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
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- 8
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.His395MetfsTer137",
+ "hgvsp": "NP_542448.1:p.Arg187Trp",
"protein_effect_location": {
- "start": 394,
- "end": 395
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.1333del",
+ "hgvs_cdna": "NM_181486.4:c.709C>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
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- 9
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.His445MetfsTer137",
+ "hgvsp": "NP_852259.1:p.Arg237Trp",
"protein_effect_location": {
- "start": 444,
- "end": 445
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "4-year old male patient",
- "meta_label": "PMID_18828908_4_year_old_male_patient"
+ "label": "K13:I-1",
+ "meta_label": "PMID_12789647_K13_I_1"
}
],
"genotypes": [
@@ -8566,62 +9387,77 @@
},
{
"labels": {
- "label": "K3:II-1",
- "meta_label": "PMID_12789647_K3_II_1"
+ "label": "K14:III-3",
+ "meta_label": "PMID_12789647_K14_III_3"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": true
+ "term_id": "HP:0001719",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": true
+ "term_id": "HP:0009535",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0006156",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
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- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -8629,7 +9465,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -8637,8 +9474,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403797,
- "end": 114403798,
+ "start": 114366365,
+ "end": 114366366,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -8648,9 +9485,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "GC",
- "change_length": 1
+ "ref": "T",
+ "alt": "A",
+ "change_length": 0
},
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},
@@ -8658,58 +9495,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.100dup",
+ "hgvs_cdna": "NM_000192.3:c.781A>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala34GlyfsTer27",
+ "hgvsp": "NP_000183.2:p.Ser261Cys",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 260,
+ "end": 261
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1879dup",
+ "hgvs_cdna": "NM_080717.4:c.631A>T",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Ser211Cys",
+ "protein_effect_location": {
+ "start": 210,
+ "end": 211
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.100dup",
+ "hgvs_cdna": "NM_181486.4:c.781A>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala34GlyfsTer27",
+ "hgvsp": "NP_852259.1:p.Ser261Cys",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 260,
+ "end": 261
}
}
],
"genotypes": {
"samples": [
{
- "label": "K3:II-1",
- "meta_label": "PMID_12789647_K3_II_1"
+ "label": "K14:III-3",
+ "meta_label": "PMID_12789647_K14_III_3"
}
],
"genotypes": [
@@ -8721,74 +9563,67 @@
},
{
"labels": {
- "label": "K2:II-1",
- "meta_label": "PMID_12789647_K2_II_1"
+ "label": "K14:III-4",
+ "meta_label": "PMID_12789647_K14_III_4"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001684",
- "is_present": true
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0000882",
- "is_present": true
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
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+ "onset": null
},
{
"term_id": "HP:0001655",
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- },
- {
- "term_id": "HP:0009778",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
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+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
- },
- {
- "term_id": "HP:0003022",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -8796,7 +9631,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -8804,8 +9640,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403797,
- "end": 114403799,
+ "start": 114366365,
+ "end": 114366366,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -8815,9 +9651,9 @@
},
"strand": "POSITIVE"
},
- "ref": "GC",
- "alt": "G",
- "change_length": -1
+ "ref": "T",
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -8825,58 +9661,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.100del",
+ "hgvs_cdna": "NM_000192.3:c.781A>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala34ProfsTer32",
+ "hgvsp": "NP_000183.2:p.Ser261Cys",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 260,
+ "end": 261
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1879del",
+ "hgvs_cdna": "NM_080717.4:c.631A>T",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Ser211Cys",
+ "protein_effect_location": {
+ "start": 210,
+ "end": 211
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.100del",
+ "hgvs_cdna": "NM_181486.4:c.781A>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala34ProfsTer32",
+ "hgvsp": "NP_852259.1:p.Ser261Cys",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 260,
+ "end": 261
}
}
],
"genotypes": {
"samples": [
{
- "label": "K2:II-1",
- "meta_label": "PMID_12789647_K2_II_1"
+ "label": "K14:III-4",
+ "meta_label": "PMID_12789647_K14_III_4"
}
],
"genotypes": [
@@ -8888,70 +9729,67 @@
},
{
"labels": {
- "label": "Patient I-2",
- "meta_label": "PMID_18351627_Patient_I_2"
+ "label": "K14:II-1",
+ "meta_label": "PMID_12789647_K14_II_1"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0100379",
- "is_present": true
- },
- {
- "term_id": "HP:0010035",
- "is_present": true
- },
- {
- "term_id": "HP:0100398",
- "is_present": true
- },
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -8959,7 +9797,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -8967,8 +9806,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399612,
- "end": 114399613,
+ "start": 114366365,
+ "end": 114366366,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -8988,63 +9827,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.262A>T",
+ "hgvs_cdna": "NM_000192.3:c.781A>T",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Lys88Ter",
+ "hgvsp": "NP_000183.2:p.Ser261Cys",
"protein_effect_location": {
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- "end": 88
+ "start": 260,
+ "end": 261
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.112A>T",
+ "hgvs_cdna": "NM_080717.4:c.631A>T",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Lys38Ter",
+ "hgvsp": "NP_542448.1:p.Ser211Cys",
"protein_effect_location": {
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- "end": 38
+ "start": 210,
+ "end": 211
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.262A>T",
+ "hgvs_cdna": "NM_181486.4:c.781A>T",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Lys88Ter",
+ "hgvsp": "NP_852259.1:p.Ser261Cys",
"protein_effect_location": {
- "start": 87,
- "end": 88
+ "start": 260,
+ "end": 261
}
}
],
"genotypes": {
"samples": [
{
- "label": "Patient I-2",
- "meta_label": "PMID_18351627_Patient_I_2"
+ "label": "K14:II-1",
+ "meta_label": "PMID_12789647_K14_II_1"
}
],
"genotypes": [
@@ -9056,66 +9895,77 @@
},
{
"labels": {
- "label": "Patient II-1",
- "meta_label": "PMID_18351627_Patient_II_1"
+ "label": "K15:III-1",
+ "meta_label": "PMID_12789647_K15_III_1"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001634",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009623",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0010034",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
- },
- {
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -9123,7 +9973,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -9131,8 +9982,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399612,
- "end": 114399613,
+ "start": 114398681,
+ "end": 114398682,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -9142,9 +9993,9 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
- "change_length": 0
+ "ref": "C",
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -9152,63 +10003,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.262A>T",
+ "hgvs_cdna": "NM_000192.3:c.400dup",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Lys88Ter",
+ "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 87,
- "end": 88
+ "start": 133,
+ "end": 134
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.112A>T",
+ "hgvs_cdna": "NM_080717.4:c.250dup",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Lys38Ter",
+ "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
"protein_effect_location": {
- "start": 37,
- "end": 38
+ "start": 83,
+ "end": 84
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.262A>T",
+ "hgvs_cdna": "NM_181486.4:c.400dup",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Lys88Ter",
+ "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 87,
- "end": 88
+ "start": 133,
+ "end": 134
}
}
],
"genotypes": {
"samples": [
{
- "label": "Patient II-1",
- "meta_label": "PMID_18351627_Patient_II_1"
+ "label": "K15:III-1",
+ "meta_label": "PMID_12789647_K15_III_1"
}
],
"genotypes": [
@@ -9220,46 +10071,77 @@
},
{
"labels": {
- "label": "Family A V-12",
- "meta_label": "PMID_10077612_Family_A_V_12"
+ "label": "K15:III-2",
+ "meta_label": "PMID_12789647_K15_III_2"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001629",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -9267,7 +10149,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -9275,8 +10158,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114398681,
+ "end": 114398682,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -9287,8 +10170,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "T",
- "change_length": 0
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -9296,63 +10179,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.400dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 133,
+ "end": 134
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.250dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 2
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 83,
+ "end": 84
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.400dup",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 133,
+ "end": 134
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A V-12",
- "meta_label": "PMID_10077612_Family_A_V_12"
+ "label": "K15:III-2",
+ "meta_label": "PMID_12789647_K15_III_2"
}
],
"genotypes": [
@@ -9364,62 +10247,42 @@
},
{
"labels": {
- "label": "Family B IV-5",
- "meta_label": "PMID_10077612_Family_B_IV_5"
+ "label": "K15:II-2",
+ "meta_label": "PMID_12789647_K15_II_2"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0001191",
- "is_present": true
- },
{
"term_id": "HP:0001629",
- "is_present": false
- },
- {
- "term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0031546",
- "is_present": false
- },
- {
- "term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -9427,7 +10290,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -9435,8 +10299,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114398681,
+ "end": 114398682,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -9447,8 +10311,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "T",
- "change_length": 0
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -9456,63 +10320,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.400dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 133,
+ "end": 134
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.250dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 6
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 83,
+ "end": 84
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.400dup",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 133,
+ "end": 134
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B IV-5",
- "meta_label": "PMID_10077612_Family_B_IV_5"
+ "label": "K15:II-2",
+ "meta_label": "PMID_12789647_K15_II_2"
}
],
"genotypes": [
@@ -9524,66 +10388,87 @@
},
{
"labels": {
- "label": "HOS-A2",
- "meta_label": "PMID_10842287_HOS_A2"
+ "label": "K15:IV-1",
+ "meta_label": "PMID_12789647_K15_IV_1"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0002986",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003031",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -9591,7 +10476,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -9599,8 +10485,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398665,
- "end": 114398667,
+ "start": 114398681,
+ "end": 114398682,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -9610,9 +10496,9 @@
},
"strand": "POSITIVE"
},
- "ref": "TG",
- "alt": "T",
- "change_length": -1
+ "ref": "C",
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -9620,7 +10506,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.416del",
+ "hgvs_cdna": "NM_000192.3:c.400dup",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -9629,16 +10515,16 @@
5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Pro139GlnfsTer11",
+ "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 138,
- "end": 139
+ "start": 133,
+ "end": 134
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.266del",
+ "hgvs_cdna": "NM_080717.4:c.250dup",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -9647,16 +10533,16 @@
4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Pro89GlnfsTer11",
+ "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
"protein_effect_location": {
- "start": 88,
- "end": 89
+ "start": 83,
+ "end": 84
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.416del",
+ "hgvs_cdna": "NM_181486.4:c.400dup",
"is_preferred": true,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -9665,18 +10551,18 @@
5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Pro139GlnfsTer11",
+ "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 138,
- "end": 139
+ "start": 133,
+ "end": 134
}
}
],
"genotypes": {
"samples": [
{
- "label": "HOS-A2",
- "meta_label": "PMID_10842287_HOS_A2"
+ "label": "K15:IV-1",
+ "meta_label": "PMID_12789647_K15_IV_1"
}
],
"genotypes": [
@@ -9688,74 +10574,82 @@
},
{
"labels": {
- "label": "K11:III-2",
- "meta_label": "PMID_12789647_K11_III_2"
+ "label": "K15:IV-2",
+ "meta_label": "PMID_12789647_K15_IV_2"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0002984",
- "is_present": true
- },
- {
- "term_id": "HP:0003022",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -9763,7 +10657,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -9771,8 +10666,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114398681,
+ "end": 114398682,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -9783,8 +10678,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "T",
- "change_length": 0
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -9792,63 +10687,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.400dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 133,
+ "end": 134
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.250dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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- 6
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 83,
+ "end": 84
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.400dup",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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- 7
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
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- "start": 236,
- "end": 237
+ "start": 133,
+ "end": 134
}
}
],
"genotypes": {
"samples": [
{
- "label": "K11:III-2",
- "meta_label": "PMID_12789647_K11_III_2"
+ "label": "K15:IV-2",
+ "meta_label": "PMID_12789647_K15_IV_2"
}
],
"genotypes": [
@@ -9860,78 +10755,87 @@
},
{
"labels": {
- "label": "proband",
- "meta_label": "PMID_22190901_proband"
+ "label": "K16:III-3",
+ "meta_label": "PMID_12789647_K16_III_3"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0001199",
- "is_present": true
- },
- {
- "term_id": "HP:0001643",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000268",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000767",
- "is_present": true
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001688",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009622",
- "is_present": true
+ "term_id": "HP:0003022",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000954",
- "is_present": true
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000960",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011567",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011705",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -9939,7 +10843,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -9947,8 +10852,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114355783,
- "end": 114355785,
+ "start": 114398655,
+ "end": 114398656,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -9958,9 +10863,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CA",
- "alt": "C",
- "change_length": -1
+ "ref": "C",
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -9968,63 +10873,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.1304del",
+ "hgvs_cdna": "NM_000192.3:c.426dup",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 9
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Leu435ArgfsTer147",
+ "hgvsp": "NP_000183.2:p.Ala143ArgfsTer40",
"protein_effect_location": {
- "start": 434,
- "end": 435
+ "start": 141,
+ "end": 143
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.1154del",
+ "hgvs_cdna": "NM_080717.4:c.276dup",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 8
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Leu385ArgfsTer147",
+ "hgvsp": "NP_542448.1:p.Ala93ArgfsTer40",
"protein_effect_location": {
- "start": 384,
- "end": 385
+ "start": 91,
+ "end": 93
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.1304del",
+ "hgvs_cdna": "NM_181486.4:c.426dup",
"is_preferred": true,
"variant_effects": [
"FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 9
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Leu435ArgfsTer147",
+ "hgvsp": "NP_852259.1:p.Ala143ArgfsTer40",
"protein_effect_location": {
- "start": 434,
- "end": 435
+ "start": 141,
+ "end": 143
}
}
],
"genotypes": {
"samples": [
{
- "label": "proband",
- "meta_label": "PMID_22190901_proband"
+ "label": "K16:III-3",
+ "meta_label": "PMID_12789647_K16_III_3"
}
],
"genotypes": [
@@ -10036,62 +10941,92 @@
},
{
"labels": {
- "label": "Family 2:III:1",
- "meta_label": "PMID_29755943_Family_2_III_1"
+ "label": "K16:II-1",
+ "meta_label": "PMID_12789647_K16_II_1"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0002974",
+ "is_present": true,
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},
{
"term_id": "HP:0001674",
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{
"term_id": "HP:0001655",
- "is_present": false
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+ "onset": null
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{
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+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0001199",
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+ "onset": null
},
{
- "term_id": "HP:0011664",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -10099,7 +11034,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -10107,8 +11043,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403791,
- "end": 114403792,
+ "start": 114398655,
+ "end": 114398656,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -10128,58 +11064,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.106_107insC",
+ "hgvs_cdna": "NM_000192.3:c.426dup",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 2
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
+ "hgvsp": "NP_000183.2:p.Ala143ArgfsTer40",
"protein_effect_location": {
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- "end": 36
+ "start": 141,
+ "end": 143
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
+ "hgvs_cdna": "NM_080717.4:c.276dup",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "FRAMESHIFT_VARIANT"
+ ],
+ "overlapping_exons": [
+ 4
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Ala93ArgfsTer40",
+ "protein_effect_location": {
+ "start": 91,
+ "end": 93
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.106_107insC",
+ "hgvs_cdna": "NM_181486.4:c.426dup",
"is_preferred": true,
"variant_effects": [
"FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 2
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
+ "hgvsp": "NP_852259.1:p.Ala143ArgfsTer40",
"protein_effect_location": {
- "start": 35,
- "end": 36
+ "start": 141,
+ "end": 143
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family 2:III:1",
- "meta_label": "PMID_29755943_Family_2_III_1"
+ "label": "K16:II-1",
+ "meta_label": "PMID_12789647_K16_II_1"
}
],
"genotypes": [
@@ -10191,66 +11132,92 @@
},
{
"labels": {
- "label": "620-1",
- "meta_label": "PMID_16917909_620_1"
+ "label": "K16:IV-1",
+ "meta_label": "PMID_12789647_K16_IV_1"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0006394",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -10258,7 +11225,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -10266,8 +11234,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366273,
- "end": 114366274,
+ "start": 114398655,
+ "end": 114398656,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -10277,9 +11245,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "T",
- "change_length": 0
+ "ref": "C",
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -10287,63 +11255,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.873C>A",
+ "hgvs_cdna": "NM_000192.3:c.426dup",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 8
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr291Ter",
+ "hgvsp": "NP_000183.2:p.Ala143ArgfsTer40",
"protein_effect_location": {
- "start": 290,
- "end": 291
+ "start": 141,
+ "end": 143
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.723C>A",
+ "hgvs_cdna": "NM_080717.4:c.276dup",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr241Ter",
+ "hgvsp": "NP_542448.1:p.Ala93ArgfsTer40",
"protein_effect_location": {
- "start": 240,
- "end": 241
+ "start": 91,
+ "end": 93
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.873C>A",
+ "hgvs_cdna": "NM_181486.4:c.426dup",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 8
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr291Ter",
+ "hgvsp": "NP_852259.1:p.Ala143ArgfsTer40",
"protein_effect_location": {
- "start": 290,
- "end": 291
+ "start": 141,
+ "end": 143
}
}
],
"genotypes": {
"samples": [
{
- "label": "620-1",
- "meta_label": "PMID_16917909_620_1"
+ "label": "K16:IV-1",
+ "meta_label": "PMID_12789647_K16_IV_1"
}
],
"genotypes": [
@@ -10355,74 +11323,92 @@
},
{
"labels": {
- "label": "K16:IV-1",
- "meta_label": "PMID_12789647_K16_IV_1"
+ "label": "K16:IV-2",
+ "meta_label": "PMID_12789647_K16_IV_2"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003022",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0005792",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -10430,7 +11416,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -10514,8 +11501,8 @@
"genotypes": {
"samples": [
{
- "label": "K16:IV-1",
- "meta_label": "PMID_12789647_K16_IV_1"
+ "label": "K16:IV-2",
+ "meta_label": "PMID_12789647_K16_IV_2"
}
],
"genotypes": [
@@ -10527,66 +11514,92 @@
},
{
"labels": {
- "label": "Family B IV-9",
- "meta_label": "PMID_10077612_Family_B_IV_9"
+ "label": "K17:II-5",
+ "meta_label": "PMID_12789647_K17_II_5"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -10594,7 +11607,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -10602,8 +11616,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114385562,
+ "end": 114385563,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -10613,8 +11627,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -10623,7 +11637,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.668C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -10632,16 +11646,16 @@
7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Thr223Met",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 222,
+ "end": 223
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.518C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -10650,16 +11664,16 @@
6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Thr173Met",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 172,
+ "end": 173
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.668C>T",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -10668,18 +11682,18 @@
7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Thr223Met",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 222,
+ "end": 223
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B IV-9",
- "meta_label": "PMID_10077612_Family_B_IV_9"
+ "label": "K17:II-5",
+ "meta_label": "PMID_12789647_K17_II_5"
}
],
"genotypes": [
@@ -10691,66 +11705,92 @@
},
{
"labels": {
- "label": "K8:II-1",
- "meta_label": "PMID_12789647_K8_II_1"
+ "label": "K1:II-2",
+ "meta_label": "PMID_12789647_K1_II_2"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -10758,7 +11798,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -10766,8 +11807,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366311,
- "end": 114366312,
+ "start": 114398625,
+ "end": 114398627,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -10777,9 +11818,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
- "change_length": 0
+ "ref": "CG",
+ "alt": "C",
+ "change_length": -1
},
"sv_info": null
},
@@ -10787,63 +11828,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.835C>T",
+ "hgvs_cdna": "NM_000192.3:c.456del",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 8
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg279Ter",
+ "hgvsp": "NP_000183.2:p.Val153SerfsTer21",
"protein_effect_location": {
- "start": 278,
- "end": 279
+ "start": 151,
+ "end": 152
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.685C>T",
+ "hgvs_cdna": "NM_080717.4:c.306del",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg229Ter",
+ "hgvsp": "NP_542448.1:p.Val103SerfsTer21",
"protein_effect_location": {
- "start": 228,
- "end": 229
+ "start": 101,
+ "end": 102
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.835C>T",
+ "hgvs_cdna": "NM_181486.4:c.456del",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 8
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg279Ter",
+ "hgvsp": "NP_852259.1:p.Val153SerfsTer21",
"protein_effect_location": {
- "start": 278,
- "end": 279
+ "start": 151,
+ "end": 152
}
}
],
"genotypes": {
"samples": [
{
- "label": "K8:II-1",
- "meta_label": "PMID_12789647_K8_II_1"
+ "label": "K1:II-2",
+ "meta_label": "PMID_12789647_K1_II_2"
}
],
"genotypes": [
@@ -10855,94 +11896,92 @@
},
{
"labels": {
- "label": "Patient II/4 proband",
- "meta_label": "PMID_18706711_Patient_II_4_proband"
+ "label": "K2:II-1",
+ "meta_label": "PMID_12789647_K2_II_1"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001684",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030718",
- "is_present": true
+ "term_id": "HP:0000882",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011995",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000767",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009824",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001162",
- "is_present": true
- },
- {
- "term_id": "HP:0000218",
- "is_present": true
- },
- {
- "term_id": "HP:0000470",
- "is_present": true
- },
- {
- "term_id": "HP:0000914",
- "is_present": true
- },
- {
- "term_id": "HP:0010567",
- "is_present": true
- },
- {
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -10950,7 +11989,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -10958,8 +11998,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366359,
- "end": 114366360,
+ "start": 114403797,
+ "end": 114403799,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -10969,9 +12009,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
- "change_length": 0
+ "ref": "GC",
+ "alt": "G",
+ "change_length": -1
},
"sv_info": null
},
@@ -10979,63 +12019,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.787G>A",
+ "hgvs_cdna": "NM_000192.3:c.100del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 8
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Val263Met",
+ "hgvsp": "NP_000183.2:p.Ala34ProfsTer32",
"protein_effect_location": {
- "start": 262,
- "end": 263
+ "start": 33,
+ "end": 34
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.637G>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1879del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Val213Met",
- "protein_effect_location": {
- "start": 212,
- "end": 213
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.787G>A",
+ "hgvs_cdna": "NM_181486.4:c.100del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 8
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Val263Met",
+ "hgvsp": "NP_852259.1:p.Ala34ProfsTer32",
"protein_effect_location": {
- "start": 262,
- "end": 263
+ "start": 33,
+ "end": 34
}
}
],
"genotypes": {
"samples": [
{
- "label": "Patient II/4 proband",
- "meta_label": "PMID_18706711_Patient_II_4_proband"
+ "label": "K2:II-1",
+ "meta_label": "PMID_12789647_K2_II_1"
}
],
"genotypes": [
@@ -11047,62 +12082,77 @@
},
{
"labels": {
- "label": "667-1",
- "meta_label": "PMID_16917909_667_1"
+ "label": "K2:II-2",
+ "meta_label": "PMID_12789647_K2_II_2"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011709",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -11110,7 +12160,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -11119,7 +12170,7 @@
"variant_coordinates": {
"region": {
"start": 114403797,
- "end": 114403798,
+ "end": 114403799,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -11129,9 +12180,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "GC",
- "change_length": 1
+ "ref": "GC",
+ "alt": "G",
+ "change_length": -1
},
"sv_info": null
},
@@ -11139,7 +12190,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.100dup",
+ "hgvs_cdna": "NM_000192.3:c.100del",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -11148,7 +12199,7 @@
2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala34GlyfsTer27",
+ "hgvsp": "NP_000183.2:p.Ala34ProfsTer32",
"protein_effect_location": {
"start": 33,
"end": 34
@@ -11157,7 +12208,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1879dup",
+ "hgvs_cdna": "NM_080717.4:c.-3-1879del",
"is_preferred": false,
"variant_effects": [
"INTRON_VARIANT"
@@ -11170,7 +12221,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.100dup",
+ "hgvs_cdna": "NM_181486.4:c.100del",
"is_preferred": true,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -11179,7 +12230,7 @@
2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala34GlyfsTer27",
+ "hgvsp": "NP_852259.1:p.Ala34ProfsTer32",
"protein_effect_location": {
"start": 33,
"end": 34
@@ -11189,8 +12240,8 @@
"genotypes": {
"samples": [
{
- "label": "667-1",
- "meta_label": "PMID_16917909_667_1"
+ "label": "K2:II-2",
+ "meta_label": "PMID_12789647_K2_II_2"
}
],
"genotypes": [
@@ -11202,58 +12253,92 @@
},
{
"labels": {
- "label": "fetus",
- "meta_label": "PMID_27026770_fetus"
+ "label": "K2:I-1",
+ "meta_label": "PMID_12789647_K2_I_1"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0003022",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -11261,7 +12346,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -11269,8 +12355,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401826,
- "end": 114401827,
+ "start": 114403797,
+ "end": 114403799,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -11280,9 +12366,9 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
- "change_length": 0
+ "ref": "GC",
+ "alt": "G",
+ "change_length": -1
},
"sv_info": null
},
@@ -11290,66 +12376,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.241A>T",
+ "hgvs_cdna": "NM_000192.3:c.100del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg81Trp",
+ "hgvsp": "NP_000183.2:p.Ala34ProfsTer32",
"protein_effect_location": {
- "start": 80,
- "end": 81
+ "start": 33,
+ "end": 34
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.91A>T",
+ "hgvs_cdna": "NM_080717.4:c.-3-1879del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
- ],
- "overlapping_exons": [
- 2
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg31Trp",
- "protein_effect_location": {
- "start": 30,
- "end": 31
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.241A>T",
+ "hgvs_cdna": "NM_181486.4:c.100del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg81Trp",
+ "hgvsp": "NP_852259.1:p.Ala34ProfsTer32",
"protein_effect_location": {
- "start": 80,
- "end": 81
+ "start": 33,
+ "end": 34
}
}
],
"genotypes": {
"samples": [
{
- "label": "fetus",
- "meta_label": "PMID_27026770_fetus"
+ "label": "K2:I-1",
+ "meta_label": "PMID_12789647_K2_I_1"
}
],
"genotypes": [
@@ -11361,66 +12439,77 @@
},
{
"labels": {
- "label": "A III/2",
- "meta_label": "PMID_12818525_A_III_2"
+ "label": "K3:II-1",
+ "meta_label": "PMID_12789647_K3_II_1"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0030241",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0006156",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -11428,7 +12517,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -11436,8 +12526,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398674,
- "end": 114398675,
+ "start": 114403797,
+ "end": 114403798,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -11448,8 +12538,8 @@
"strand": "POSITIVE"
},
"ref": "G",
- "alt": "T",
- "change_length": 0
+ "alt": "GC",
+ "change_length": 1
},
"sv_info": null
},
@@ -11457,63 +12547,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.408C>A",
+ "hgvs_cdna": "NM_000192.3:c.100dup",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 5
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr136Ter",
+ "hgvsp": "NP_000183.2:p.Ala34GlyfsTer27",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 33,
+ "end": 34
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.258C>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1879dup",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
- ],
- "overlapping_exons": [
- 4
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr86Ter",
- "protein_effect_location": {
- "start": 85,
- "end": 86
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.408C>A",
+ "hgvs_cdna": "NM_181486.4:c.100dup",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 5
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr136Ter",
+ "hgvsp": "NP_852259.1:p.Ala34GlyfsTer27",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 33,
+ "end": 34
}
}
],
"genotypes": {
"samples": [
{
- "label": "A III/2",
- "meta_label": "PMID_12818525_A_III_2"
+ "label": "K3:II-1",
+ "meta_label": "PMID_12789647_K3_II_1"
}
],
"genotypes": [
@@ -11525,58 +12610,82 @@
},
{
"labels": {
- "label": "Family A III-3",
- "meta_label": "PMID_10077612_Family_A_III_3"
+ "label": "K4:III-2",
+ "meta_label": "PMID_12789647_K4_III_2"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -11584,7 +12693,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -11592,8 +12702,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114399513,
+ "end": 114399514,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -11603,8 +12713,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "A",
+ "alt": "C",
"change_length": 0
},
"sv_info": null
@@ -11613,63 +12723,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.361T>G",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 3
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Trp121Gly",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 120,
+ "end": 121
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.211T>G",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 2
+ 3
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Trp71Gly",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 70,
+ "end": 71
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.361T>G",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 3
+ 4
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Trp121Gly",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 120,
+ "end": 121
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A III-3",
- "meta_label": "PMID_10077612_Family_A_III_3"
+ "label": "K4:III-2",
+ "meta_label": "PMID_12789647_K4_III_2"
}
],
"genotypes": [
@@ -11681,66 +12794,62 @@
},
{
"labels": {
- "label": "K10:II-4",
- "meta_label": "PMID_12789647_K10_II_4"
+ "label": "K4:III-3",
+ "meta_label": "PMID_12789647_K4_III_3"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0011682",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": true
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0002984",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -11748,7 +12857,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -11756,8 +12866,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385521,
- "end": 114385522,
+ "start": 114399513,
+ "end": 114399514,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -11767,8 +12877,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
+ "ref": "A",
+ "alt": "C",
"change_length": 0
},
"sv_info": null
@@ -11777,63 +12887,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.709C>T",
+ "hgvs_cdna": "NM_000192.3:c.361T>G",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 7
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Trp",
+ "hgvsp": "NP_000183.2:p.Trp121Gly",
"protein_effect_location": {
- "start": 236,
- "end": 237
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.559C>T",
+ "hgvs_cdna": "NM_080717.4:c.211T>G",
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"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 6
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],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Trp",
+ "hgvsp": "NP_542448.1:p.Trp71Gly",
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- "end": 187
+ "start": 70,
+ "end": 71
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.709C>T",
+ "hgvs_cdna": "NM_181486.4:c.361T>G",
"is_preferred": true,
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- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 7
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],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Trp",
+ "hgvsp": "NP_852259.1:p.Trp121Gly",
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- "start": 236,
- "end": 237
+ "start": 120,
+ "end": 121
}
}
],
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{
- "label": "K10:II-4",
- "meta_label": "PMID_12789647_K10_II_4"
+ "label": "K4:III-3",
+ "meta_label": "PMID_12789647_K4_III_3"
}
],
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@@ -11845,66 +12958,97 @@
},
{
"labels": {
- "label": "K6:II-3",
- "meta_label": "PMID_12789647_K6_II_3"
+ "label": "K4:II-1",
+ "meta_label": "PMID_12789647_K4_II_1"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0000774",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0011623",
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},
{
- "term_id": "HP:0011623",
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+ "term_id": "HP:0011682",
+ "is_present": false,
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{
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+ "onset": null
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{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
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{
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+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
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},
{
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+ "is_present": false,
+ "onset": null
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{
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{
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},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -11912,7 +13056,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -11920,8 +13065,8 @@
"variant_info": {
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"region": {
- "start": 114366347,
- "end": 114366349,
+ "start": 114399513,
+ "end": 114399514,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -11931,9 +13076,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CT",
+ "ref": "A",
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- "change_length": -1
+ "change_length": 0
},
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},
@@ -11941,63 +13086,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.798del",
+ "hgvs_cdna": "NM_000192.3:c.361T>G",
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- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 8
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Val267TrpfsTer127",
+ "hgvsp": "NP_000183.2:p.Trp121Gly",
"protein_effect_location": {
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- "end": 266
+ "start": 120,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.648del",
+ "hgvs_cdna": "NM_080717.4:c.211T>G",
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- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 7
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],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Val217TrpfsTer127",
+ "hgvsp": "NP_542448.1:p.Trp71Gly",
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- "end": 216
+ "start": 70,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.798del",
+ "hgvs_cdna": "NM_181486.4:c.361T>G",
"is_preferred": true,
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- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 8
+ 4
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Val267TrpfsTer127",
+ "hgvsp": "NP_852259.1:p.Trp121Gly",
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- "end": 266
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}
}
],
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{
- "label": "K6:II-3",
- "meta_label": "PMID_12789647_K6_II_3"
+ "label": "K4:II-1",
+ "meta_label": "PMID_12789647_K4_II_1"
}
],
"genotypes": [
@@ -12009,74 +13157,97 @@
},
{
"labels": {
- "label": "K16:IV-2",
- "meta_label": "PMID_12789647_K16_IV_2"
+ "label": "K4:IV-1",
+ "meta_label": "PMID_12789647_K4_IV_1"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
+ "term_id": "HP:0001631",
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+ "onset": null
},
{
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- "is_present": true
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},
{
- "term_id": "HP:0011682",
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+ "term_id": "HP:0004209",
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},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0011682",
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{
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{
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{
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},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
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},
{
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{
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{
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},
{
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{
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+ "onset": null
},
{
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{
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{
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+ "onset": null
}
],
"measurements": [],
@@ -12084,7 +13255,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -12092,8 +13264,8 @@
"variant_info": {
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- "end": 114398656,
+ "start": 114399513,
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@@ -12103,9 +13275,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "CG",
- "change_length": 1
+ "ref": "A",
+ "alt": "C",
+ "change_length": 0
},
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},
@@ -12113,63 +13285,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.426dup",
+ "hgvs_cdna": "NM_000192.3:c.361T>G",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 5
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala143ArgfsTer40",
+ "hgvsp": "NP_000183.2:p.Trp121Gly",
"protein_effect_location": {
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- "end": 143
+ "start": 120,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.276dup",
+ "hgvs_cdna": "NM_080717.4:c.211T>G",
"is_preferred": false,
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- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 4
+ 3
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ala93ArgfsTer40",
+ "hgvsp": "NP_542448.1:p.Trp71Gly",
"protein_effect_location": {
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- "end": 93
+ "start": 70,
+ "end": 71
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.426dup",
+ "hgvs_cdna": "NM_181486.4:c.361T>G",
"is_preferred": true,
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- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 5
+ 4
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala143ArgfsTer40",
+ "hgvsp": "NP_852259.1:p.Trp121Gly",
"protein_effect_location": {
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- "end": 143
+ "start": 120,
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}
}
],
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{
- "label": "K16:IV-2",
- "meta_label": "PMID_12789647_K16_IV_2"
+ "label": "K4:IV-1",
+ "meta_label": "PMID_12789647_K4_IV_1"
}
],
"genotypes": [
@@ -12181,70 +13356,92 @@
},
{
"labels": {
- "label": "620-2",
- "meta_label": "PMID_16917909_620_2"
+ "label": "K4:I-2",
+ "meta_label": "PMID_12789647_K4_I_2"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0006394",
- "is_present": true
- },
- {
- "term_id": "HP:0011927",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
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},
{
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{
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{
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{
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{
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{
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+ "onset": null
},
{
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- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
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+ "onset": null
},
{
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+ "onset": null
},
{
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+ "onset": null
},
{
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- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -12252,7 +13449,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -12260,8 +13458,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366273,
- "end": 114366274,
+ "start": 114399513,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -12271,8 +13469,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "T",
+ "ref": "A",
+ "alt": "C",
"change_length": 0
},
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@@ -12281,63 +13479,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.873C>A",
+ "hgvs_cdna": "NM_000192.3:c.361T>G",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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- 8
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr291Ter",
+ "hgvsp": "NP_000183.2:p.Trp121Gly",
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- "end": 291
+ "start": 120,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.723C>A",
+ "hgvs_cdna": "NM_080717.4:c.211T>G",
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"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
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+ 3
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr241Ter",
+ "hgvsp": "NP_542448.1:p.Trp71Gly",
"protein_effect_location": {
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- "end": 241
+ "start": 70,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.873C>A",
+ "hgvs_cdna": "NM_181486.4:c.361T>G",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
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+ 4
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr291Ter",
+ "hgvsp": "NP_852259.1:p.Trp121Gly",
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- "end": 291
+ "start": 120,
+ "end": 121
}
}
],
"genotypes": {
"samples": [
{
- "label": "620-2",
- "meta_label": "PMID_16917909_620_2"
+ "label": "K4:I-2",
+ "meta_label": "PMID_12789647_K4_I_2"
}
],
"genotypes": [
@@ -12349,58 +13550,87 @@
},
{
"labels": {
- "label": "Family B II-8",
- "meta_label": "PMID_10077612_Family_B_II_8"
+ "label": "K5:III-1",
+ "meta_label": "PMID_12789647_K5_III_1"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": true,
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},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
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+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
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+ },
+ {
+ "term_id": "HP:0001674",
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+ {
+ "term_id": "HP:0001655",
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{
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{
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{
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{
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{
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{
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},
{
- "term_id": "HP:0011565",
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{
- "term_id": "HP:0031297",
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+ "term_id": "HP:0011565",
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},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0031297",
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}
],
"measurements": [],
@@ -12408,7 +13638,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -12416,8 +13647,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114385562,
+ "end": 114385563,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -12427,8 +13658,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -12437,7 +13668,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.668C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -12446,16 +13677,16 @@
7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Thr223Met",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 222,
+ "end": 223
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.518C>T",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -12464,16 +13695,16 @@
6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Thr173Met",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 172,
+ "end": 173
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.668C>T",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -12482,18 +13713,18 @@
7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Thr223Met",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 222,
+ "end": 223
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B II-8",
- "meta_label": "PMID_10077612_Family_B_II_8"
+ "label": "K5:III-1",
+ "meta_label": "PMID_12789647_K5_III_1"
}
],
"genotypes": [
@@ -12505,50 +13736,82 @@
},
{
"labels": {
- "label": "K4:III-3",
- "meta_label": "PMID_12789647_K4_III_3"
+ "label": "K5:III-2",
+ "meta_label": "PMID_12789647_K5_III_2"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
+ },
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -12556,7 +13819,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -12564,8 +13828,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399513,
- "end": 114399514,
+ "start": 114385562,
+ "end": 114385563,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -12575,8 +13839,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "C",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -12585,66 +13849,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.361T>G",
+ "hgvs_cdna": "NM_000192.3:c.668C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Trp121Gly",
+ "hgvsp": "NP_000183.2:p.Thr223Met",
"protein_effect_location": {
- "start": 120,
- "end": 121
+ "start": 222,
+ "end": 223
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.211T>G",
+ "hgvs_cdna": "NM_080717.4:c.518C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Trp71Gly",
+ "hgvsp": "NP_542448.1:p.Thr173Met",
"protein_effect_location": {
- "start": 70,
- "end": 71
+ "start": 172,
+ "end": 173
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.361T>G",
+ "hgvs_cdna": "NM_181486.4:c.668C>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Trp121Gly",
+ "hgvsp": "NP_852259.1:p.Thr223Met",
"protein_effect_location": {
- "start": 120,
- "end": 121
+ "start": 222,
+ "end": 223
}
}
],
"genotypes": {
"samples": [
{
- "label": "K4:III-3",
- "meta_label": "PMID_12789647_K4_III_3"
+ "label": "K5:III-2",
+ "meta_label": "PMID_12789647_K5_III_2"
}
],
"genotypes": [
@@ -12656,54 +13917,77 @@
},
{
"labels": {
- "label": "667-2",
- "meta_label": "PMID_16917909_667_2"
+ "label": "K5:II-1",
+ "meta_label": "PMID_12789647_K5_II_1"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001653",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0002092",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -12711,7 +13995,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -12719,8 +14004,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403797,
- "end": 114403798,
+ "start": 114385562,
+ "end": 114385563,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -12731,8 +14016,8 @@
"strand": "POSITIVE"
},
"ref": "G",
- "alt": "GC",
- "change_length": 1
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -12740,58 +14025,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.100dup",
+ "hgvs_cdna": "NM_000192.3:c.668C>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala34GlyfsTer27",
+ "hgvsp": "NP_000183.2:p.Thr223Met",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 222,
+ "end": 223
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1879dup",
+ "hgvs_cdna": "NM_080717.4:c.518C>T",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 6
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Thr173Met",
+ "protein_effect_location": {
+ "start": 172,
+ "end": 173
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.100dup",
+ "hgvs_cdna": "NM_181486.4:c.668C>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala34GlyfsTer27",
+ "hgvsp": "NP_852259.1:p.Thr223Met",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 222,
+ "end": 223
}
}
],
"genotypes": {
"samples": [
{
- "label": "667-2",
- "meta_label": "PMID_16917909_667_2"
+ "label": "K5:II-1",
+ "meta_label": "PMID_12789647_K5_II_1"
}
],
"genotypes": [
@@ -12803,58 +14093,82 @@
},
{
"labels": {
- "label": "3",
- "meta_label": "PMID_20519243_3"
+ "label": "K6:II-3",
+ "meta_label": "PMID_12789647_K6_II_3"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0004058",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003982",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -12862,7 +14176,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -12870,8 +14185,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399558,
- "end": 114399559,
+ "start": 114366347,
+ "end": 114366349,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -12881,9 +14196,9 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
+ "ref": "CT",
"alt": "C",
- "change_length": 0
+ "change_length": -1
},
"sv_info": null
},
@@ -12891,63 +14206,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.316A>G",
+ "hgvs_cdna": "NM_000192.3:c.798del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ile106Val",
+ "hgvsp": "NP_000183.2:p.Val267TrpfsTer127",
"protein_effect_location": {
- "start": 105,
- "end": 106
+ "start": 265,
+ "end": 266
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.166A>G",
+ "hgvs_cdna": "NM_080717.4:c.648del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ile56Val",
+ "hgvsp": "NP_542448.1:p.Val217TrpfsTer127",
"protein_effect_location": {
- "start": 55,
- "end": 56
+ "start": 215,
+ "end": 216
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.316A>G",
+ "hgvs_cdna": "NM_181486.4:c.798del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ile106Val",
+ "hgvsp": "NP_852259.1:p.Val267TrpfsTer127",
"protein_effect_location": {
- "start": 105,
- "end": 106
+ "start": 265,
+ "end": 266
}
}
],
"genotypes": {
"samples": [
{
- "label": "3",
- "meta_label": "PMID_20519243_3"
+ "label": "K6:II-3",
+ "meta_label": "PMID_12789647_K6_II_3"
}
],
"genotypes": [
@@ -12959,66 +14274,92 @@
},
{
"labels": {
- "label": "a 6-month-old female",
- "meta_label": "PMID_28434921_a_6_month_old_female"
+ "label": "K7:II-1",
+ "meta_label": "PMID_12789647_K7_II_1"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0002092",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0004602",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003363",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -13026,7 +14367,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -13034,8 +14376,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403858,
- "end": 114403859,
+ "start": 114394819,
+ "end": 114394820,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -13045,8 +14387,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "T",
+ "ref": "C",
+ "alt": "G",
"change_length": 0
},
"sv_info": null
@@ -13055,58 +14397,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.40C>A",
+ "hgvs_cdna": "NM_000192.3:c.584G>C",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 6
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Pro14Thr",
+ "hgvsp": "NP_000183.2:p.Gly195Ala",
"protein_effect_location": {
- "start": 13,
- "end": 14
+ "start": 194,
+ "end": 195
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1939C>A",
+ "hgvs_cdna": "NM_080717.4:c.434G>C",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 5
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Gly145Ala",
+ "protein_effect_location": {
+ "start": 144,
+ "end": 145
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.40C>A",
+ "hgvs_cdna": "NM_181486.4:c.584G>C",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 6
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Pro14Thr",
+ "hgvsp": "NP_852259.1:p.Gly195Ala",
"protein_effect_location": {
- "start": 13,
- "end": 14
+ "start": 194,
+ "end": 195
}
}
],
"genotypes": {
"samples": [
{
- "label": "a 6-month-old female",
- "meta_label": "PMID_28434921_a_6_month_old_female"
+ "label": "K7:II-1",
+ "meta_label": "PMID_12789647_K7_II_1"
}
],
"genotypes": [
@@ -13118,58 +14465,82 @@
},
{
"labels": {
- "label": "Family A III-12",
- "meta_label": "PMID_10077612_Family_A_III_12"
+ "label": "K8:II-1",
+ "meta_label": "PMID_12789647_K8_II_1"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -13177,7 +14548,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -13185,8 +14557,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114366311,
+ "end": 114366312,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -13196,8 +14568,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -13206,63 +14578,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.835C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Arg279Ter",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 278,
+ "end": 279
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.685C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Arg229Ter",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 228,
+ "end": 229
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.835C>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Arg279Ter",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 278,
+ "end": 279
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A III-12",
- "meta_label": "PMID_10077612_Family_A_III_12"
+ "label": "K8:II-1",
+ "meta_label": "PMID_12789647_K8_II_1"
}
],
"genotypes": [
@@ -13274,50 +14646,82 @@
},
{
"labels": {
- "label": "nan",
- "meta_label": "PMID_10077612_nan"
+ "label": "K9:II-3",
+ "meta_label": "PMID_12789647_K9_II_3"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001629",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001631",
- "is_present": false
+ "term_id": "HP:0003022",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -13325,7 +14729,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -13333,8 +14738,8 @@
"variant_info": {
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"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114394816,
+ "end": 114394817,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -13344,8 +14749,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "G",
+ "alt": "C",
"change_length": 0
},
"sv_info": null
@@ -13354,63 +14759,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.587C>G",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 6
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Ser196Ter",
"protein_effect_location": {
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- "end": 80
+ "start": 195,
+ "end": 196
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.437C>G",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 2
+ 5
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Ser146Ter",
"protein_effect_location": {
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- "end": 30
+ "start": 145,
+ "end": 146
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.587C>G",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 6
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Ser196Ter",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 195,
+ "end": 196
}
}
],
"genotypes": {
"samples": [
{
- "label": "nan",
- "meta_label": "PMID_10077612_nan"
+ "label": "K9:II-3",
+ "meta_label": "PMID_12789647_K9_II_3"
}
],
"genotypes": [
@@ -13422,30 +14827,82 @@
},
{
"labels": {
- "label": "Family B III-2",
- "meta_label": "PMID_10077612_Family_B_III_2"
+ "label": "A III/2",
+ "meta_label": "PMID_12818525_A_III_2"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009813",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0030241",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -13453,7 +14910,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -13461,8 +14919,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114398674,
+ "end": 114398675,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -13472,7 +14930,7 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
+ "ref": "G",
"alt": "T",
"change_length": 0
},
@@ -13482,63 +14940,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.408C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Tyr136Ter",
"protein_effect_location": {
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- "end": 237
+ "start": 135,
+ "end": 136
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.258C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 6
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Tyr86Ter",
"protein_effect_location": {
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- "end": 187
+ "start": 85,
+ "end": 86
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.408C>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Tyr136Ter",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 135,
+ "end": 136
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B III-2",
- "meta_label": "PMID_10077612_Family_B_III_2"
+ "label": "A III/2",
+ "meta_label": "PMID_12818525_A_III_2"
}
],
"genotypes": [
@@ -13550,94 +15008,82 @@
},
{
"labels": {
- "label": "Patient II/7",
- "meta_label": "PMID_18706711_Patient_II_7"
+ "label": "A III/3",
+ "meta_label": "PMID_12818525_A_III_3"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0030241",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030718",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011995",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000767",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009824",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001162",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000218",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000470",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000914",
- "is_present": true
+ "term_id": "HP:0009813",
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},
{
- "term_id": "HP:0010567",
- "is_present": true
- },
- {
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- },
- {
- "term_id": "HP:0009777",
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- {
- "term_id": "HP:0009778",
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- {
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- {
- "term_id": "HP:0009813",
- "is_present": false
- },
- {
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
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{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -13645,7 +15091,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -13653,8 +15100,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366359,
- "end": 114366360,
+ "start": 114398674,
+ "end": 114398675,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -13664,7 +15111,7 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
+ "ref": "G",
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"change_length": 0
},
@@ -13674,63 +15121,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.787G>A",
+ "hgvs_cdna": "NM_000192.3:c.408C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
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- 8
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Val263Met",
+ "hgvsp": "NP_000183.2:p.Tyr136Ter",
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- "end": 263
+ "start": 135,
+ "end": 136
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.637G>A",
+ "hgvs_cdna": "NM_080717.4:c.258C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 7
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Val213Met",
+ "hgvsp": "NP_542448.1:p.Tyr86Ter",
"protein_effect_location": {
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- "end": 213
+ "start": 85,
+ "end": 86
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.787G>A",
+ "hgvs_cdna": "NM_181486.4:c.408C>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 8
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Val263Met",
+ "hgvsp": "NP_852259.1:p.Tyr136Ter",
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- "start": 262,
- "end": 263
+ "start": 135,
+ "end": 136
}
}
],
"genotypes": {
"samples": [
{
- "label": "Patient II/7",
- "meta_label": "PMID_18706711_Patient_II_7"
+ "label": "A III/3",
+ "meta_label": "PMID_12818525_A_III_3"
}
],
"genotypes": [
@@ -13742,62 +15189,82 @@
},
{
"labels": {
- "label": "K2:II-2",
- "meta_label": "PMID_12789647_K2_II_2"
+ "label": "A IV/4 ",
+ "meta_label": "PMID_12818525_A_IV_4"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0030241",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -13805,7 +15272,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -13813,8 +15281,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
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- "end": 114403799,
+ "start": 114398674,
+ "end": 114398675,
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"genbank_acc": "CM000674.2",
@@ -13824,9 +15292,9 @@
},
"strand": "POSITIVE"
},
- "ref": "GC",
- "alt": "G",
- "change_length": -1
+ "ref": "G",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -13834,58 +15302,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.100del",
+ "hgvs_cdna": "NM_000192.3:c.408C>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 2
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala34ProfsTer32",
+ "hgvsp": "NP_000183.2:p.Tyr136Ter",
"protein_effect_location": {
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- "end": 34
+ "start": 135,
+ "end": 136
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1879del",
+ "hgvs_cdna": "NM_080717.4:c.258C>A",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "STOP_GAINED"
+ ],
+ "overlapping_exons": [
+ 4
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Tyr86Ter",
+ "protein_effect_location": {
+ "start": 85,
+ "end": 86
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.100del",
+ "hgvs_cdna": "NM_181486.4:c.408C>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 2
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala34ProfsTer32",
+ "hgvsp": "NP_852259.1:p.Tyr136Ter",
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- "end": 34
+ "start": 135,
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}
}
],
"genotypes": {
"samples": [
{
- "label": "K2:II-2",
- "meta_label": "PMID_12789647_K2_II_2"
+ "label": "A IV/4 ",
+ "meta_label": "PMID_12818525_A_IV_4"
}
],
"genotypes": [
@@ -13897,42 +15370,82 @@
},
{
"labels": {
- "label": "Family B III-11",
- "meta_label": "PMID_10077612_Family_B_III_11"
+ "label": "B III/1",
+ "meta_label": "PMID_12818525_B_III_1"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009813",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0030241",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
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+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -13940,7 +15453,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -13948,8 +15462,8 @@
"variant_info": {
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"region": {
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- "end": 114385521,
+ "start": 114398674,
+ "end": 114398675,
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"genbank_acc": "CM000674.2",
@@ -13959,7 +15473,7 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
+ "ref": "G",
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"change_length": 0
},
@@ -13969,63 +15483,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.408C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
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+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Tyr136Ter",
"protein_effect_location": {
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- "end": 237
+ "start": 135,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.258C>A",
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"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
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+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Tyr86Ter",
"protein_effect_location": {
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- "end": 187
+ "start": 85,
+ "end": 86
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.408C>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Tyr136Ter",
"protein_effect_location": {
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- "end": 237
+ "start": 135,
+ "end": 136
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B III-11",
- "meta_label": "PMID_10077612_Family_B_III_11"
+ "label": "B III/1",
+ "meta_label": "PMID_12818525_B_III_1"
}
],
"genotypes": [
@@ -14037,54 +15551,82 @@
},
{
"labels": {
- "label": "5.index",
- "meta_label": "PMID_20519243_5_index"
+ "label": "B III/2",
+ "meta_label": "PMID_12818525_B_III_2"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0030241",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -14092,7 +15634,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -14100,8 +15643,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114398674,
+ "end": 114398675,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -14111,8 +15654,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "G",
+ "ref": "G",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -14121,63 +15664,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>C",
+ "hgvs_cdna": "NM_000192.3:c.408C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Pro",
+ "hgvsp": "NP_000183.2:p.Tyr136Ter",
"protein_effect_location": {
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- "end": 237
+ "start": 135,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>C",
+ "hgvs_cdna": "NM_080717.4:c.258C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
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+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Pro",
+ "hgvsp": "NP_542448.1:p.Tyr86Ter",
"protein_effect_location": {
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- "end": 187
+ "start": 85,
+ "end": 86
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>C",
+ "hgvs_cdna": "NM_181486.4:c.408C>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
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+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Pro",
+ "hgvsp": "NP_852259.1:p.Tyr136Ter",
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- "end": 237
+ "start": 135,
+ "end": 136
}
}
],
"genotypes": {
"samples": [
{
- "label": "5.index",
- "meta_label": "PMID_20519243_5_index"
+ "label": "B III/2",
+ "meta_label": "PMID_12818525_B_III_2"
}
],
"genotypes": [
@@ -14189,66 +15732,82 @@
},
{
"labels": {
- "label": "Family 5 Patient 7",
- "meta_label": "PMID_25216260_Family_5_Patient_7"
+ "label": "B III/5",
+ "meta_label": "PMID_12818525_B_III_5"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0030241",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0011623",
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{
- "term_id": "HP:0001655",
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+ "term_id": "HP:0011682",
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+ "onset": null
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{
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+ "term_id": "HP:0001674",
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+ "onset": null
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{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001655",
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{
"term_id": "HP:0009778",
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{
"term_id": "HP:0001199",
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{
"term_id": "HP:0009813",
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{
"term_id": "HP:0011565",
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"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -14256,7 +15815,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -14264,8 +15824,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385521,
- "end": 114385522,
+ "start": 114398674,
+ "end": 114398675,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -14276,7 +15836,7 @@
"strand": "POSITIVE"
},
"ref": "G",
- "alt": "A",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -14285,63 +15845,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.709C>T",
+ "hgvs_cdna": "NM_000192.3:c.408C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Trp",
+ "hgvsp": "NP_000183.2:p.Tyr136Ter",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 135,
+ "end": 136
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.559C>T",
+ "hgvs_cdna": "NM_080717.4:c.258C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 6
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Trp",
+ "hgvsp": "NP_542448.1:p.Tyr86Ter",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 85,
+ "end": 86
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.709C>T",
+ "hgvs_cdna": "NM_181486.4:c.408C>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 7
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Trp",
+ "hgvsp": "NP_852259.1:p.Tyr136Ter",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 135,
+ "end": 136
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family 5 Patient 7",
- "meta_label": "PMID_25216260_Family_5_Patient_7"
+ "label": "B III/5",
+ "meta_label": "PMID_12818525_B_III_5"
}
],
"genotypes": [
@@ -14353,62 +15913,77 @@
},
{
"labels": {
- "label": "Family 2:II:2",
- "meta_label": "PMID_29755943_Family_2_II_2"
+ "label": "15\u2010month\u2010old male patient",
+ "meta_label": "PMID_15710732_15_month_old_male_patient"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011664",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -14416,7 +15991,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -14424,8 +16000,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403791,
- "end": 114403792,
+ "start": 114399621,
+ "end": 114399622,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -14435,9 +16011,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "CG",
- "change_length": 1
+ "ref": "G",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -14445,58 +16021,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.106_107insC",
+ "hgvs_cdna": "NM_000192.3:c.253C>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
+ "hgvsp": "NP_000183.2:p.Pro85Thr",
"protein_effect_location": {
- "start": 35,
- "end": 36
+ "start": 84,
+ "end": 85
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
+ "hgvs_cdna": "NM_080717.4:c.103C>A",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Pro35Thr",
+ "protein_effect_location": {
+ "start": 34,
+ "end": 35
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.106_107insC",
+ "hgvs_cdna": "NM_181486.4:c.253C>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 4
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
+ "hgvsp": "NP_852259.1:p.Pro85Thr",
"protein_effect_location": {
- "start": 35,
- "end": 36
+ "start": 84,
+ "end": 85
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family 2:II:2",
- "meta_label": "PMID_29755943_Family_2_II_2"
+ "label": "15\u2010month\u2010old male patient",
+ "meta_label": "PMID_15710732_15_month_old_male_patient"
}
],
"genotypes": [
@@ -14508,74 +16089,87 @@
},
{
"labels": {
- "label": "Patient II-2",
- "meta_label": "PMID_18351627_Patient_II_2"
+ "label": "370-1",
+ "meta_label": "PMID_16917909_370_1"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009623",
- "is_present": true
- },
- {
- "term_id": "HP:0004209",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009577",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0004220",
- "is_present": true
+ "term_id": "HP:0006394",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0011927",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -14583,7 +16177,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -14591,8 +16186,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399612,
- "end": 114399613,
+ "start": 114366206,
+ "end": 114366208,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -14602,9 +16197,9 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
- "change_length": 0
+ "ref": "GC",
+ "alt": "G",
+ "change_length": -1
},
"sv_info": null
},
@@ -14612,63 +16207,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.262A>T",
+ "hgvs_cdna": "NM_000192.3:c.939del",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Lys88Ter",
+ "hgvsp": "NP_000183.2:p.Gln315ArgfsTer79",
"protein_effect_location": {
- "start": 87,
- "end": 88
+ "start": 312,
+ "end": 313
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.112A>T",
+ "hgvs_cdna": "NM_080717.4:c.789del",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Lys38Ter",
+ "hgvsp": "NP_542448.1:p.Gln265ArgfsTer79",
"protein_effect_location": {
- "start": 37,
- "end": 38
+ "start": 262,
+ "end": 263
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.262A>T",
+ "hgvs_cdna": "NM_181486.4:c.939del",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Lys88Ter",
+ "hgvsp": "NP_852259.1:p.Gln315ArgfsTer79",
"protein_effect_location": {
- "start": 87,
- "end": 88
- }
+ "start": 312,
+ "end": 313
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "Patient II-2",
- "meta_label": "PMID_18351627_Patient_II_2"
+ "label": "370-1",
+ "meta_label": "PMID_16917909_370_1"
}
],
"genotypes": [
@@ -14680,58 +16275,82 @@
},
{
"labels": {
- "label": "HH17",
- "meta_label": "PMID_17534187_HH17"
+ "label": "370-2",
+ "meta_label": "PMID_16917909_370_2"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0006394",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0011927",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -14739,7 +16358,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -14747,8 +16367,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366311,
- "end": 114366312,
+ "start": 114366206,
+ "end": 114366208,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -14758,9 +16378,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
- "change_length": 0
+ "ref": "GC",
+ "alt": "G",
+ "change_length": -1
},
"sv_info": null
},
@@ -14768,63 +16388,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.835C>T",
+ "hgvs_cdna": "NM_000192.3:c.939del",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg279Ter",
+ "hgvsp": "NP_000183.2:p.Gln315ArgfsTer79",
"protein_effect_location": {
- "start": 278,
- "end": 279
+ "start": 312,
+ "end": 313
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.685C>T",
+ "hgvs_cdna": "NM_080717.4:c.789del",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg229Ter",
+ "hgvsp": "NP_542448.1:p.Gln265ArgfsTer79",
"protein_effect_location": {
- "start": 228,
- "end": 229
+ "start": 262,
+ "end": 263
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.835C>T",
+ "hgvs_cdna": "NM_181486.4:c.939del",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg279Ter",
+ "hgvsp": "NP_852259.1:p.Gln315ArgfsTer79",
"protein_effect_location": {
- "start": 278,
- "end": 279
+ "start": 312,
+ "end": 313
}
}
],
"genotypes": {
"samples": [
{
- "label": "HH17",
- "meta_label": "PMID_17534187_HH17"
+ "label": "370-2",
+ "meta_label": "PMID_16917909_370_2"
}
],
"genotypes": [
@@ -14836,58 +16456,72 @@
},
{
"labels": {
- "label": "HOS-A1",
- "meta_label": "PMID_10842287_HOS_A1"
+ "label": "603-1",
+ "meta_label": "PMID_16917909_603_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0001653",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": true
+ "term_id": "HP:0011705",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -14895,7 +16529,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -14903,8 +16538,8 @@
"variant_info": {
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- "end": 114398667,
+ "start": 114398631,
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@@ -14914,9 +16549,9 @@
},
"strand": "POSITIVE"
},
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- "change_length": -1
+ "ref": "G",
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},
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},
@@ -14924,63 +16559,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.416del",
+ "hgvs_cdna": "NM_000192.3:c.451C>T",
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+ "STOP_GAINED"
],
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],
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- "hgvsp": "NP_000183.2:p.Pro139GlnfsTer11",
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}
},
{
"gene_id": "TBX5",
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+ "STOP_GAINED"
],
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4
],
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- "hgvsp": "NP_542448.1:p.Pro89GlnfsTer11",
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}
},
{
"gene_id": "TBX5",
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- "hgvs_cdna": "NM_181486.4:c.416del",
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"is_preferred": true,
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+ "STOP_GAINED"
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],
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- "hgvsp": "NP_852259.1:p.Pro139GlnfsTer11",
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}
}
],
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{
- "label": "HOS-A1",
- "meta_label": "PMID_10842287_HOS_A1"
+ "label": "603-1",
+ "meta_label": "PMID_16917909_603_1"
}
],
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@@ -14992,74 +16627,77 @@
},
{
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- "label": "K13:II-2",
- "meta_label": "PMID_12789647_K13_II_2"
+ "label": "619-1",
+ "meta_label": "PMID_16917909_619_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
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{
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- "is_present": true
+ "is_present": true,
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},
{
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+ "term_id": "HP:0001629",
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{
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{
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{
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{
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{
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{
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{
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- },
- {
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{
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{
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{
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{
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@@ -15067,7 +16705,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -15075,8 +16714,8 @@
"variant_info": {
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- "end": 114385522,
+ "start": 114398577,
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@@ -15086,9 +16725,9 @@
},
"strand": "POSITIVE"
},
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- "change_length": 0
+ "ref": "CA",
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},
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},
@@ -15096,63 +16735,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.709C>T",
+ "hgvs_cdna": "NM_000192.3:c.504del",
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"variant_effects": [
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+ "FRAMESHIFT_VARIANT"
],
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- "hgvsp": "NP_000183.2:p.Arg237Trp",
+ "hgvsp": "NP_000183.2:p.Phe168LeufsTer6",
"protein_effect_location": {
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}
},
{
"gene_id": "TBX5",
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- "hgvs_cdna": "NM_080717.4:c.559C>T",
+ "hgvs_cdna": "NM_080717.4:c.354del",
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+ "FRAMESHIFT_VARIANT"
],
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+ "hgvsp": "NP_542448.1:p.Phe118LeufsTer6",
"protein_effect_location": {
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+ "start": 117,
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}
},
{
"gene_id": "TBX5",
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- "hgvs_cdna": "NM_181486.4:c.709C>T",
+ "hgvs_cdna": "NM_181486.4:c.504del",
"is_preferred": true,
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- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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+ "hgvsp": "NP_852259.1:p.Phe168LeufsTer6",
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}
}
],
"genotypes": {
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{
- "label": "K13:II-2",
- "meta_label": "PMID_12789647_K13_II_2"
+ "label": "619-1",
+ "meta_label": "PMID_16917909_619_1"
}
],
"genotypes": [
@@ -15164,78 +16803,107 @@
},
{
"labels": {
- "label": "K11:III-1",
- "meta_label": "PMID_12789647_K11_III_1"
+ "label": "619-2",
+ "meta_label": "PMID_16917909_619_2"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
+ "term_id": "HP:0009777",
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},
{
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+ "term_id": "HP:0009778",
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{
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+ "term_id": "HP:0001634",
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},
{
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+ "term_id": "HP:0001704",
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},
{
- "term_id": "HP:0011682",
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+ "term_id": "HP:0001653",
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},
{
- "term_id": "HP:0001674",
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+ "term_id": "HP:0006394",
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+ "onset": null
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{
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{
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+ "term_id": "HP:0001684",
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{
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+ "onset": null
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{
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+ "term_id": "HP:0011682",
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+ "onset": null
},
{
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+ "term_id": "HP:0001674",
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+ "onset": null
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{
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+ "term_id": "HP:0001655",
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+ "onset": null
},
{
- "term_id": "HP:0005792",
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+ "term_id": "HP:0002092",
+ "is_present": false,
+ "onset": null
+ },
+ {
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+ "is_present": false,
+ "onset": null
+ },
+ {
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},
{
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{
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{
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{
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}
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@@ -15243,7 +16911,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -15251,8 +16920,8 @@
"variant_info": {
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- "end": 114385521,
+ "start": 114398577,
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@@ -15262,9 +16931,9 @@
},
"strand": "POSITIVE"
},
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- "change_length": 0
+ "ref": "CA",
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+ "change_length": -1
},
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@@ -15272,63 +16941,63 @@
{
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"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.504del",
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- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Phe168LeufsTer6",
"protein_effect_location": {
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- "end": 237
+ "start": 167,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.354del",
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"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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- 6
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
+ "hgvsp": "NP_542448.1:p.Phe118LeufsTer6",
"protein_effect_location": {
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- "end": 187
+ "start": 117,
+ "end": 118
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.504del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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- 7
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Phe168LeufsTer6",
"protein_effect_location": {
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- "end": 237
+ "start": 167,
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}
}
],
"genotypes": {
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{
- "label": "K11:III-1",
- "meta_label": "PMID_12789647_K11_III_1"
+ "label": "619-2",
+ "meta_label": "PMID_16917909_619_2"
}
],
"genotypes": [
@@ -15340,70 +17009,82 @@
},
{
"labels": {
- "label": "K12:II-2",
- "meta_label": "PMID_12789647_K12_II_2"
+ "label": "620-1",
+ "meta_label": "PMID_16917909_620_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
+ "term_id": "HP:0001629",
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},
{
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
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},
{
"term_id": "HP:0002984",
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},
{
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+ "term_id": "HP:0006394",
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{
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+ "term_id": "HP:0001684",
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{
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{
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{
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- "is_present": false
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{
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{
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{
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{
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{
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}
],
"measurements": [],
@@ -15411,7 +17092,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -15419,8 +17101,8 @@
"variant_info": {
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"region": {
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- "end": 114385563,
+ "start": 114366273,
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"genbank_acc": "CM000674.2",
@@ -15431,7 +17113,7 @@
"strand": "POSITIVE"
},
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@@ -15440,63 +17122,63 @@
{
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"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.668C>T",
+ "hgvs_cdna": "NM_000192.3:c.873C>A",
"is_preferred": false,
"variant_effects": [
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+ "STOP_GAINED"
],
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+ 8
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"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr223Met",
+ "hgvsp": "NP_000183.2:p.Tyr291Ter",
"protein_effect_location": {
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+ "start": 290,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.518C>T",
+ "hgvs_cdna": "NM_080717.4:c.723C>A",
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- "MISSENSE_VARIANT"
+ "STOP_GAINED"
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- "hgvsp": "NP_542448.1:p.Thr173Met",
+ "hgvsp": "NP_542448.1:p.Tyr241Ter",
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}
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{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.668C>T",
+ "hgvs_cdna": "NM_181486.4:c.873C>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
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+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr223Met",
+ "hgvsp": "NP_852259.1:p.Tyr291Ter",
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+ "start": 290,
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}
}
],
"genotypes": {
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{
- "label": "K12:II-2",
- "meta_label": "PMID_12789647_K12_II_2"
+ "label": "620-1",
+ "meta_label": "PMID_16917909_620_1"
}
],
"genotypes": [
@@ -15508,74 +17190,87 @@
},
{
"labels": {
- "label": "K13:I-1",
- "meta_label": "PMID_12789647_K13_I_1"
+ "label": "620-2",
+ "meta_label": "PMID_16917909_620_2"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001631",
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},
{
- "term_id": "HP:0001684",
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+ "term_id": "HP:0006394",
+ "is_present": true,
+ "onset": null
+ },
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{
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},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -15583,7 +17278,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -15591,8 +17287,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385521,
- "end": 114385522,
+ "start": 114366273,
+ "end": 114366274,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -15603,7 +17299,7 @@
"strand": "POSITIVE"
},
"ref": "G",
- "alt": "A",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -15612,63 +17308,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.709C>T",
+ "hgvs_cdna": "NM_000192.3:c.873C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
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- 7
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Trp",
+ "hgvsp": "NP_000183.2:p.Tyr291Ter",
"protein_effect_location": {
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- "end": 237
+ "start": 290,
+ "end": 291
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.559C>T",
+ "hgvs_cdna": "NM_080717.4:c.723C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 6
+ 7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Trp",
+ "hgvsp": "NP_542448.1:p.Tyr241Ter",
"protein_effect_location": {
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- "end": 187
+ "start": 240,
+ "end": 241
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.709C>T",
+ "hgvs_cdna": "NM_181486.4:c.873C>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 7
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Trp",
+ "hgvsp": "NP_852259.1:p.Tyr291Ter",
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- "start": 236,
- "end": 237
+ "start": 290,
+ "end": 291
}
}
],
"genotypes": {
"samples": [
{
- "label": "K13:I-1",
- "meta_label": "PMID_12789647_K13_I_1"
+ "label": "620-2",
+ "meta_label": "PMID_16917909_620_2"
}
],
"genotypes": [
@@ -15680,58 +17376,77 @@
},
{
"labels": {
- "label": "Family A IV-11",
- "meta_label": "PMID_10077612_Family_A_IV_11"
+ "label": "649-1",
+ "meta_label": "PMID_16917909_649_1"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
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+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
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},
{
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0031546",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -15739,7 +17454,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -15747,8 +17463,8 @@
"variant_info": {
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- "end": 114401830,
+ "start": 114356063,
+ "end": 114356065,
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@@ -15758,9 +17474,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
+ "ref": "TA",
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- "change_length": 0
+ "change_length": -1
},
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},
@@ -15768,63 +17484,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.1024del",
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"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
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+ 9
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Tyr342ThrfsTer52",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 341,
+ "end": 342
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.874del",
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"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Tyr292ThrfsTer52",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 291,
+ "end": 292
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.1024del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 9
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Tyr342ThrfsTer52",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 341,
+ "end": 342
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A IV-11",
- "meta_label": "PMID_10077612_Family_A_IV_11"
+ "label": "649-1",
+ "meta_label": "PMID_16917909_649_1"
}
],
"genotypes": [
@@ -15836,70 +17552,77 @@
},
{
"labels": {
- "label": "K12:III-2",
- "meta_label": "PMID_12789647_K12_III_2"
+ "label": "666-1",
+ "meta_label": "PMID_16917909_666_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
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+ "onset": null
},
{
"term_id": "HP:0001655",
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},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
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+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
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+ "onset": null
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{
"term_id": "HP:0003974",
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- {
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- },
- {
- "term_id": "HP:0003022",
- "is_present": false
- },
- {
- "term_id": "HP:0005792",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
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+ "onset": null
},
{
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -15907,7 +17630,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -15915,8 +17639,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
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- "end": 114385563,
+ "start": 114394761,
+ "end": 114394763,
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@@ -15926,9 +17650,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
- "change_length": 0
+ "ref": "CA",
+ "alt": "C",
+ "change_length": -1
},
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},
@@ -15936,63 +17660,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.668C>T",
+ "hgvs_cdna": "NM_000192.3:c.641del",
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"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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- 7
+ 6
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr223Met",
+ "hgvsp": "NP_000183.2:p.Val214GlyfsTer12",
"protein_effect_location": {
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- "end": 223
+ "start": 213,
+ "end": 214
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.518C>T",
+ "hgvs_cdna": "NM_080717.4:c.491del",
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"variant_effects": [
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+ "FRAMESHIFT_VARIANT"
],
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+ 5
],
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- "hgvsp": "NP_542448.1:p.Thr173Met",
+ "hgvsp": "NP_542448.1:p.Val164GlyfsTer12",
"protein_effect_location": {
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- "end": 173
+ "start": 163,
+ "end": 164
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.668C>T",
+ "hgvs_cdna": "NM_181486.4:c.641del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 6
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr223Met",
+ "hgvsp": "NP_852259.1:p.Val214GlyfsTer12",
"protein_effect_location": {
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- "end": 223
+ "start": 213,
+ "end": 214
}
}
],
"genotypes": {
"samples": [
{
- "label": "K12:III-2",
- "meta_label": "PMID_12789647_K12_III_2"
+ "label": "666-1",
+ "meta_label": "PMID_16917909_666_1"
}
],
"genotypes": [
@@ -16004,94 +17728,77 @@
},
{
"labels": {
- "label": "Patient II/12",
- "meta_label": "PMID_18706711_Patient_II_12"
+ "label": "666-2 ",
+ "meta_label": "PMID_16917909_666_2"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
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- },
- {
- "term_id": "HP:0009824",
- "is_present": true
- },
- {
- "term_id": "HP:0001162",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000218",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0000470",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000914",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0010567",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
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},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
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+ "onset": null
},
{
"term_id": "HP:0001199",
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+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
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+ "onset": null
},
{
"term_id": "HP:0031297",
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+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -16099,7 +17806,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -16107,8 +17815,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
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- "end": 114366360,
+ "start": 114394761,
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"genbank_acc": "CM000674.2",
@@ -16118,9 +17826,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
- "change_length": 0
+ "ref": "CA",
+ "alt": "C",
+ "change_length": -1
},
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},
@@ -16128,63 +17836,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.787G>A",
+ "hgvs_cdna": "NM_000192.3:c.641del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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+ 6
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Val263Met",
+ "hgvsp": "NP_000183.2:p.Val214GlyfsTer12",
"protein_effect_location": {
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- "end": 263
+ "start": 213,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.637G>A",
+ "hgvs_cdna": "NM_080717.4:c.491del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Val213Met",
+ "hgvsp": "NP_542448.1:p.Val164GlyfsTer12",
"protein_effect_location": {
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+ "start": 163,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.787G>A",
+ "hgvs_cdna": "NM_181486.4:c.641del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
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+ 6
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Val263Met",
+ "hgvsp": "NP_852259.1:p.Val214GlyfsTer12",
"protein_effect_location": {
- "start": 262,
- "end": 263
+ "start": 213,
+ "end": 214
}
}
],
"genotypes": {
"samples": [
{
- "label": "Patient II/12",
- "meta_label": "PMID_18706711_Patient_II_12"
+ "label": "666-2 ",
+ "meta_label": "PMID_16917909_666_2"
}
],
"genotypes": [
@@ -16196,70 +17904,77 @@
},
{
"labels": {
- "label": "K12:II-3",
- "meta_label": "PMID_12789647_K12_II_3"
+ "label": "667-1",
+ "meta_label": "PMID_16917909_667_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0011709",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0010704",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -16267,7 +17982,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -16275,8 +17991,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385562,
- "end": 114385563,
+ "start": 114403797,
+ "end": 114403798,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -16287,8 +18003,8 @@
"strand": "POSITIVE"
},
"ref": "G",
- "alt": "A",
- "change_length": 0
+ "alt": "GC",
+ "change_length": 1
},
"sv_info": null
},
@@ -16296,63 +18012,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.668C>T",
+ "hgvs_cdna": "NM_000192.3:c.100dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr223Met",
+ "hgvsp": "NP_000183.2:p.Ala34GlyfsTer27",
"protein_effect_location": {
- "start": 222,
- "end": 223
+ "start": 33,
+ "end": 34
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.518C>T",
+ "hgvs_cdna": "NM_080717.4:c.-3-1879dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr173Met",
- "protein_effect_location": {
- "start": 172,
- "end": 173
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.668C>T",
+ "hgvs_cdna": "NM_181486.4:c.100dup",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr223Met",
+ "hgvsp": "NP_852259.1:p.Ala34GlyfsTer27",
"protein_effect_location": {
- "start": 222,
- "end": 223
+ "start": 33,
+ "end": 34
}
}
],
"genotypes": {
"samples": [
{
- "label": "K12:II-3",
- "meta_label": "PMID_12789647_K12_II_3"
+ "label": "667-1",
+ "meta_label": "PMID_16917909_667_1"
}
],
"genotypes": [
@@ -16364,66 +18075,67 @@
},
{
"labels": {
- "label": "B III/5",
- "meta_label": "PMID_12818525_B_III_5"
+ "label": "667-2",
+ "meta_label": "PMID_16917909_667_2"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030241",
- "is_present": true
+ "term_id": "HP:0001653",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -16431,7 +18143,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -16439,8 +18152,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398674,
- "end": 114398675,
+ "start": 114403797,
+ "end": 114403798,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -16451,8 +18164,8 @@
"strand": "POSITIVE"
},
"ref": "G",
- "alt": "T",
- "change_length": 0
+ "alt": "GC",
+ "change_length": 1
},
"sv_info": null
},
@@ -16460,63 +18173,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.408C>A",
+ "hgvs_cdna": "NM_000192.3:c.100dup",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 5
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr136Ter",
+ "hgvsp": "NP_000183.2:p.Ala34GlyfsTer27",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 33,
+ "end": 34
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.258C>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1879dup",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
- ],
- "overlapping_exons": [
- 4
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr86Ter",
- "protein_effect_location": {
- "start": 85,
- "end": 86
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.408C>A",
+ "hgvs_cdna": "NM_181486.4:c.100dup",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 5
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr136Ter",
+ "hgvsp": "NP_852259.1:p.Ala34GlyfsTer27",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 33,
+ "end": 34
}
}
],
"genotypes": {
"samples": [
{
- "label": "B III/5",
- "meta_label": "PMID_12818525_B_III_5"
+ "label": "667-2",
+ "meta_label": "PMID_16917909_667_2"
}
],
"genotypes": [
@@ -16528,42 +18236,62 @@
},
{
"labels": {
- "label": "Family B II-5",
- "meta_label": "PMID_10077612_Family_B_II_5"
+ "label": "667-3",
+ "meta_label": "PMID_16917909_667_3"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009813",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -16571,7 +18299,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -16579,8 +18308,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114403797,
+ "end": 114403798,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -16590,9 +18319,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
- "change_length": 0
+ "ref": "G",
+ "alt": "GC",
+ "change_length": 1
},
"sv_info": null
},
@@ -16600,63 +18329,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.100dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
+ "hgvsp": "NP_000183.2:p.Ala34GlyfsTer27",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 33,
+ "end": 34
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1879dup",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
- "protein_effect_location": {
- "start": 186,
- "end": 187
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.100dup",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
+ "hgvsp": "NP_852259.1:p.Ala34GlyfsTer27",
"protein_effect_location": {
- "start": 236,
- "end": 237
+ "start": 33,
+ "end": 34
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family B II-5",
- "meta_label": "PMID_10077612_Family_B_II_5"
+ "label": "667-3",
+ "meta_label": "PMID_16917909_667_3"
}
],
"genotypes": [
@@ -16668,66 +18392,52 @@
},
{
"labels": {
- "label": "Patient I/1",
- "meta_label": "PMID_18706711_Patient_I_1"
+ "label": "668-1 ",
+ "meta_label": "PMID_16917909_668_1"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0030718",
- "is_present": true
- },
- {
- "term_id": "HP:0011995",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0000767",
- "is_present": false
- },
- {
- "term_id": "HP:0001162",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -16735,7 +18445,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -16743,8 +18454,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366359,
- "end": 114366360,
+ "start": 114385473,
+ "end": 114385474,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -16754,8 +18465,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "A",
+ "alt": "G",
"change_length": 0
},
"sv_info": null
@@ -16764,63 +18475,48 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.787G>A",
+ "hgvs_cdna": "NM_000192.3:c.755+2T>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 8
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Val263Met",
- "protein_effect_location": {
- "start": 262,
- "end": 263
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.637G>A",
+ "hgvs_cdna": "NM_080717.4:c.605+2T>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Val213Met",
- "protein_effect_location": {
- "start": 212,
- "end": 213
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.787G>A",
+ "hgvs_cdna": "NM_181486.4:c.755+2T>C",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 8
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Val263Met",
- "protein_effect_location": {
- "start": 262,
- "end": 263
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "Patient I/1",
- "meta_label": "PMID_18706711_Patient_I_1"
+ "label": "668-1 ",
+ "meta_label": "PMID_16917909_668_1"
}
],
"genotypes": [
@@ -16832,66 +18528,82 @@
},
{
"labels": {
- "label": "370-2",
- "meta_label": "PMID_16917909_370_2"
+ "label": "668-2",
+ "meta_label": "PMID_16917909_668_2"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0011636",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0006394",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011927",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -16899,7 +18611,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -16907,8 +18620,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366206,
- "end": 114366208,
+ "start": 114385473,
+ "end": 114385474,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -16918,9 +18631,9 @@
},
"strand": "POSITIVE"
},
- "ref": "GC",
+ "ref": "A",
"alt": "G",
- "change_length": -1
+ "change_length": 0
},
"sv_info": null
},
@@ -16928,63 +18641,48 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.939del",
+ "hgvs_cdna": "NM_000192.3:c.755+2T>C",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
- ],
- "overlapping_exons": [
- 8
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gln315ArgfsTer79",
- "protein_effect_location": {
- "start": 312,
- "end": 313
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.789del",
+ "hgvs_cdna": "NM_080717.4:c.605+2T>C",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gln265ArgfsTer79",
- "protein_effect_location": {
- "start": 262,
- "end": 263
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.939del",
+ "hgvs_cdna": "NM_181486.4:c.755+2T>C",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
- ],
- "overlapping_exons": [
- 8
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gln315ArgfsTer79",
- "protein_effect_location": {
- "start": 312,
- "end": 313
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "370-2",
- "meta_label": "PMID_16917909_370_2"
+ "label": "668-2",
+ "meta_label": "PMID_16917909_668_2"
}
],
"genotypes": [
@@ -16996,58 +18694,82 @@
},
{
"labels": {
- "label": "infant",
- "meta_label": "PMID_26219450_infant"
+ "label": "706-1",
+ "meta_label": "PMID_16917909_706_1"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001643",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005180",
- "is_present": true
+ "term_id": "HP:0010035",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009486",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0000185",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -17055,7 +18777,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -17063,8 +18786,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401852,
- "end": 114401853,
+ "start": 114355722,
+ "end": 114355723,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -17075,7 +18798,7 @@
"strand": "POSITIVE"
},
"ref": "G",
- "alt": "T",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -17084,63 +18807,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.215C>A",
+ "hgvs_cdna": "NM_000192.3:c.1366C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 9
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr72Lys",
+ "hgvsp": "NP_000183.2:p.Gln456Ter",
"protein_effect_location": {
- "start": 71,
- "end": 72
+ "start": 455,
+ "end": 456
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.65C>A",
+ "hgvs_cdna": "NM_080717.4:c.1216C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 2
+ 8
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr22Lys",
+ "hgvsp": "NP_542448.1:p.Gln406Ter",
"protein_effect_location": {
- "start": 21,
- "end": 22
+ "start": 405,
+ "end": 406
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.215C>A",
+ "hgvs_cdna": "NM_181486.4:c.1366C>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 9
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr72Lys",
+ "hgvsp": "NP_852259.1:p.Gln456Ter",
"protein_effect_location": {
- "start": 71,
- "end": 72
+ "start": 455,
+ "end": 456
}
}
],
"genotypes": {
"samples": [
{
- "label": "infant",
- "meta_label": "PMID_26219450_infant"
+ "label": "706-1",
+ "meta_label": "PMID_16917909_706_1"
}
],
"genotypes": [
@@ -17152,66 +18875,72 @@
},
{
"labels": {
- "label": "a 6-year-old girl,",
- "meta_label": "PMID_27026770_a_6_year_old_girl"
+ "label": "HH17",
+ "meta_label": "PMID_17534187_HH17"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
- },
- {
- "term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -17219,7 +18948,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -17227,8 +18957,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401826,
- "end": 114401827,
+ "start": 114366311,
+ "end": 114366312,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -17238,7 +18968,7 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
+ "ref": "G",
"alt": "A",
"change_length": 0
},
@@ -17248,66 +18978,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.241A>T",
+ "hgvs_cdna": "NM_000192.3:c.835C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg81Trp",
+ "hgvsp": "NP_000183.2:p.Arg279Ter",
"protein_effect_location": {
- "start": 80,
- "end": 81
+ "start": 278,
+ "end": 279
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.91A>T",
+ "hgvs_cdna": "NM_080717.4:c.685C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg31Trp",
+ "hgvsp": "NP_542448.1:p.Arg229Ter",
"protein_effect_location": {
- "start": 30,
- "end": 31
+ "start": 228,
+ "end": 229
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.241A>T",
+ "hgvs_cdna": "NM_181486.4:c.835C>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 3
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg81Trp",
+ "hgvsp": "NP_852259.1:p.Arg279Ter",
"protein_effect_location": {
- "start": 80,
- "end": 81
+ "start": 278,
+ "end": 279
}
}
],
"genotypes": {
"samples": [
{
- "label": "a 6-year-old girl,",
- "meta_label": "PMID_27026770_a_6_year_old_girl"
+ "label": "HH17",
+ "meta_label": "PMID_17534187_HH17"
}
],
"genotypes": [
@@ -17319,58 +19046,67 @@
},
{
"labels": {
- "label": "Family A V-10",
- "meta_label": "PMID_10077612_Family_A_V_10"
+ "label": "HH20",
+ "meta_label": "PMID_17534187_HH20"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
+ },
{
"term_id": "HP:0001629",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -17378,7 +19114,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -17386,8 +19123,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114398707,
+ "end": 114398709,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -17397,9 +19134,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
- "change_length": 0
+ "ref": "GC",
+ "alt": "G",
+ "change_length": -1
},
"sv_info": null
},
@@ -17407,63 +19144,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.374del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Gly125AlafsTer25",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 124,
+ "end": 125
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.224del",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 2
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Gly75AlafsTer25",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 74,
+ "end": 75
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.374del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Gly125AlafsTer25",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 124,
+ "end": 125
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A V-10",
- "meta_label": "PMID_10077612_Family_A_V_10"
+ "label": "HH20",
+ "meta_label": "PMID_17534187_HH20"
}
],
"genotypes": [
@@ -17475,62 +19212,92 @@
},
{
"labels": {
- "label": "Family 2:IV:2",
- "meta_label": "PMID_29755943_Family_2_IV_2"
+ "label": "HH24",
+ "meta_label": "PMID_17534187_HH24"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0001199",
- "is_present": true
- },
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001653",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001642",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000878",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000882",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
- },
- {
- "term_id": "HP:0011664",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -17538,7 +19305,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -17546,8 +19314,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403791,
- "end": 114403792,
+ "start": 114385552,
+ "end": 114385553,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -17558,8 +19326,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "CG",
- "change_length": 1
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -17567,58 +19335,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.106_107insC",
+ "hgvs_cdna": "NM_000192.3:c.678G>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
+ "hgvsp": "NP_000183.2:p.Lys226Asn",
"protein_effect_location": {
- "start": 35,
- "end": 36
+ "start": 225,
+ "end": 226
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
+ "hgvs_cdna": "NM_080717.4:c.528G>T",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 6
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Lys176Asn",
+ "protein_effect_location": {
+ "start": 175,
+ "end": 176
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.106_107insC",
+ "hgvs_cdna": "NM_181486.4:c.678G>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
+ "hgvsp": "NP_852259.1:p.Lys226Asn",
"protein_effect_location": {
- "start": 35,
- "end": 36
+ "start": 225,
+ "end": 226
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family 2:IV:2",
- "meta_label": "PMID_29755943_Family_2_IV_2"
+ "label": "HH24",
+ "meta_label": "PMID_17534187_HH24"
}
],
"genotypes": [
@@ -17630,54 +19403,67 @@
},
{
"labels": {
- "label": "girl",
- "meta_label": "PMID_27552067_girl"
+ "label": "HH8",
+ "meta_label": "PMID_17534187_HH8"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001684",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0009623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0004220",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0010704",
- "is_present": true
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -17685,7 +19471,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -17693,8 +19480,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398601,
- "end": 114398602,
+ "start": 114366311,
+ "end": 114366312,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -17704,8 +19491,8 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "G",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -17714,63 +19501,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.481A>C",
+ "hgvs_cdna": "NM_000192.3:c.835C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 5
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr161Pro",
+ "hgvsp": "NP_000183.2:p.Arg279Ter",
"protein_effect_location": {
- "start": 160,
- "end": 161
+ "start": 278,
+ "end": 279
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.331A>C",
+ "hgvs_cdna": "NM_080717.4:c.685C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 4
+ 7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr111Pro",
+ "hgvsp": "NP_542448.1:p.Arg229Ter",
"protein_effect_location": {
- "start": 110,
- "end": 111
+ "start": 228,
+ "end": 229
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.481A>C",
+ "hgvs_cdna": "NM_181486.4:c.835C>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 5
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr161Pro",
+ "hgvsp": "NP_852259.1:p.Arg279Ter",
"protein_effect_location": {
- "start": 160,
- "end": 161
+ "start": 278,
+ "end": 279
}
}
],
"genotypes": {
"samples": [
{
- "label": "girl",
- "meta_label": "PMID_27552067_girl"
+ "label": "HH8",
+ "meta_label": "PMID_17534187_HH8"
}
],
"genotypes": [
@@ -17782,54 +19569,82 @@
},
{
"labels": {
- "label": "HH20",
- "meta_label": "PMID_17534187_HH20"
+ "label": "Patient II-1",
+ "meta_label": "PMID_18351627_Patient_II_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001634",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": true
+ "term_id": "HP:0009623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0010034",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -17837,7 +19652,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -17845,8 +19661,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398707,
- "end": 114398709,
+ "start": 114399612,
+ "end": 114399613,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -17856,9 +19672,9 @@
},
"strand": "POSITIVE"
},
- "ref": "GC",
- "alt": "G",
- "change_length": -1
+ "ref": "T",
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -17866,63 +19682,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.374del",
+ "hgvs_cdna": "NM_000192.3:c.262A>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 5
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly125AlafsTer25",
+ "hgvsp": "NP_000183.2:p.Lys88Ter",
"protein_effect_location": {
- "start": 124,
- "end": 125
+ "start": 87,
+ "end": 88
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.224del",
+ "hgvs_cdna": "NM_080717.4:c.112A>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 4
+ 3
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly75AlafsTer25",
+ "hgvsp": "NP_542448.1:p.Lys38Ter",
"protein_effect_location": {
- "start": 74,
- "end": 75
+ "start": 37,
+ "end": 38
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.374del",
+ "hgvs_cdna": "NM_181486.4:c.262A>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 5
+ 4
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly125AlafsTer25",
+ "hgvsp": "NP_852259.1:p.Lys88Ter",
"protein_effect_location": {
- "start": 124,
- "end": 125
+ "start": 87,
+ "end": 88
}
}
],
"genotypes": {
"samples": [
{
- "label": "HH20",
- "meta_label": "PMID_17534187_HH20"
+ "label": "Patient II-1",
+ "meta_label": "PMID_18351627_Patient_II_1"
}
],
"genotypes": [
@@ -17934,82 +19750,92 @@
},
{
"labels": {
- "label": "II-2",
- "meta_label": "PMID_34490705_II_2"
+ "label": "Patient II-2",
+ "meta_label": "PMID_18351627_Patient_II_2"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": false
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0009623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0004209",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0009577",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": false
+ "term_id": "HP:0004220",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003022",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011664",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -18017,7 +19843,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -18025,8 +19852,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385474,
- "end": 114385475,
+ "start": 114399612,
+ "end": 114399613,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -18036,8 +19863,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "T",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -18046,48 +19873,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.755+1G>A",
+ "hgvs_cdna": "NM_000192.3:c.262A>T",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "STOP_GAINED"
+ ],
+ "overlapping_exons": [
+ 4
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Lys88Ter",
+ "protein_effect_location": {
+ "start": 87,
+ "end": 88
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.605+1G>A",
+ "hgvs_cdna": "NM_080717.4:c.112A>T",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "STOP_GAINED"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Lys38Ter",
+ "protein_effect_location": {
+ "start": 37,
+ "end": 38
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.755+1G>A",
+ "hgvs_cdna": "NM_181486.4:c.262A>T",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "STOP_GAINED"
+ ],
+ "overlapping_exons": [
+ 4
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Lys88Ter",
+ "protein_effect_location": {
+ "start": 87,
+ "end": 88
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "II-2",
- "meta_label": "PMID_34490705_II_2"
+ "label": "Patient II-2",
+ "meta_label": "PMID_18351627_Patient_II_2"
}
],
"genotypes": [
@@ -18099,74 +19941,87 @@
},
{
"labels": {
- "label": "K7:II-1",
- "meta_label": "PMID_12789647_K7_II_1"
+ "label": "Patient I-2",
+ "meta_label": "PMID_18351627_Patient_I_2"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001655",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0100379",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0004602",
- "is_present": true
+ "term_id": "HP:0010035",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003363",
- "is_present": true
+ "term_id": "HP:0100398",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
- },
- {
- "term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -18174,7 +20029,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -18182,8 +20038,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114394819,
- "end": 114394820,
+ "start": 114399612,
+ "end": 114399613,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -18193,8 +20049,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "G",
+ "ref": "T",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -18203,63 +20059,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.584G>C",
+ "hgvs_cdna": "NM_000192.3:c.262A>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 6
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly195Ala",
+ "hgvsp": "NP_000183.2:p.Lys88Ter",
"protein_effect_location": {
- "start": 194,
- "end": 195
+ "start": 87,
+ "end": 88
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.434G>C",
+ "hgvs_cdna": "NM_080717.4:c.112A>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 5
+ 3
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly145Ala",
+ "hgvsp": "NP_542448.1:p.Lys38Ter",
"protein_effect_location": {
- "start": 144,
- "end": 145
+ "start": 37,
+ "end": 38
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.584G>C",
+ "hgvs_cdna": "NM_181486.4:c.262A>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "STOP_GAINED"
],
"overlapping_exons": [
- 6
+ 4
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly195Ala",
+ "hgvsp": "NP_852259.1:p.Lys88Ter",
"protein_effect_location": {
- "start": 194,
- "end": 195
+ "start": 87,
+ "end": 88
}
}
],
"genotypes": {
"samples": [
{
- "label": "K7:II-1",
- "meta_label": "PMID_12789647_K7_II_1"
+ "label": "Patient I-2",
+ "meta_label": "PMID_18351627_Patient_I_2"
}
],
"genotypes": [
@@ -18271,58 +20127,120 @@
},
{
"labels": {
- "label": "Patient II/2 (proband)",
- "meta_label": "PMID_26401820_Patient_II_2_proband"
+ "label": "Patient II/12",
+ "meta_label": "PMID_18706711_Patient_II_12"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": {
+ "days": 12783.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0002092",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0030718",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0011995",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000767",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009824",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001162",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000218",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000470",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000914",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0010567",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011664",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -18330,7 +20248,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -18338,8 +20257,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401920,
- "end": 114401921,
+ "start": 114366359,
+ "end": 114366360,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -18350,7 +20269,7 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "G",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -18359,48 +20278,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.148-1G>C",
+ "hgvs_cdna": "NM_000192.3:c.787G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_ACCEPTOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 8
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Val263Met",
+ "protein_effect_location": {
+ "start": 262,
+ "end": 263
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1G>C",
+ "hgvs_cdna": "NM_080717.4:c.637G>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_ACCEPTOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Val213Met",
+ "protein_effect_location": {
+ "start": 212,
+ "end": 213
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.148-1G>C",
+ "hgvs_cdna": "NM_181486.4:c.787G>A",
"is_preferred": true,
"variant_effects": [
- "SPLICE_ACCEPTOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 8
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Val263Met",
+ "protein_effect_location": {
+ "start": 262,
+ "end": 263
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "Patient II/2 (proband)",
- "meta_label": "PMID_26401820_Patient_II_2_proband"
+ "label": "Patient II/12",
+ "meta_label": "PMID_18706711_Patient_II_12"
}
],
"genotypes": [
@@ -18412,70 +20346,129 @@
},
{
"labels": {
- "label": "K14:III-3",
- "meta_label": "PMID_12789647_K14_III_3"
+ "label": "Patient II/4 proband",
+ "meta_label": "PMID_18706711_Patient_II_4_proband"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": {
+ "days": 14244.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001674",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0002092",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001719",
- "is_present": true
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009535",
- "is_present": true
+ "term_id": "HP:0030718",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0011995",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0000767",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0009824",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001162",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0000218",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0000470",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0000914",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0010567",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
- }
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
+ }
],
"measurements": [],
"diseases": [
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -18483,8 +20476,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366365,
- "end": 114366366,
+ "start": 114366359,
+ "end": 114366360,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -18494,8 +20487,8 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -18504,7 +20497,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.781A>T",
+ "hgvs_cdna": "NM_000192.3:c.787G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -18513,16 +20506,16 @@
8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ser261Cys",
+ "hgvsp": "NP_000183.2:p.Val263Met",
"protein_effect_location": {
- "start": 260,
- "end": 261
+ "start": 262,
+ "end": 263
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.631A>T",
+ "hgvs_cdna": "NM_080717.4:c.637G>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -18531,16 +20524,16 @@
7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ser211Cys",
+ "hgvsp": "NP_542448.1:p.Val213Met",
"protein_effect_location": {
- "start": 210,
- "end": 211
+ "start": 212,
+ "end": 213
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.781A>T",
+ "hgvs_cdna": "NM_181486.4:c.787G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
@@ -18549,18 +20542,18 @@
8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ser261Cys",
+ "hgvsp": "NP_852259.1:p.Val263Met",
"protein_effect_location": {
- "start": 260,
- "end": 261
+ "start": 262,
+ "end": 263
}
}
],
"genotypes": {
"samples": [
{
- "label": "K14:III-3",
- "meta_label": "PMID_12789647_K14_III_3"
+ "label": "Patient II/4 proband",
+ "meta_label": "PMID_18706711_Patient_II_4_proband"
}
],
"genotypes": [
@@ -18572,50 +20565,120 @@
},
{
"labels": {
- "label": "667-3",
- "meta_label": "PMID_16917909_667_3"
+ "label": "Patient II/7",
+ "meta_label": "PMID_18706711_Patient_II_7"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 12783.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0002092",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0030718",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0011995",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0000767",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009824",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001162",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000218",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000470",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000914",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0010567",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -18623,7 +20686,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -18631,8 +20695,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403797,
- "end": 114403798,
+ "start": 114366359,
+ "end": 114366360,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -18642,9 +20706,9 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "GC",
- "change_length": 1
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -18652,58 +20716,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.100dup",
+ "hgvs_cdna": "NM_000192.3:c.787G>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala34GlyfsTer27",
+ "hgvsp": "NP_000183.2:p.Val263Met",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 262,
+ "end": 263
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1879dup",
+ "hgvs_cdna": "NM_080717.4:c.637G>A",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
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],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Val213Met",
+ "protein_effect_location": {
+ "start": 212,
+ "end": 213
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.100dup",
+ "hgvs_cdna": "NM_181486.4:c.787G>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
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- 2
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala34GlyfsTer27",
+ "hgvsp": "NP_852259.1:p.Val263Met",
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- "end": 34
+ "start": 262,
+ "end": 263
}
}
],
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"samples": [
{
- "label": "667-3",
- "meta_label": "PMID_16917909_667_3"
+ "label": "Patient II/7",
+ "meta_label": "PMID_18706711_Patient_II_7"
}
],
"genotypes": [
@@ -18715,54 +20784,85 @@
},
{
"labels": {
- "label": "2",
- "meta_label": "PMID_20519243_2"
+ "label": "Patient I/1",
+ "meta_label": "PMID_18706711_Patient_I_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 25567.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0030718",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0011995",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0001684",
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},
{
- "term_id": "HP:0001655",
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+ "term_id": "HP:0001629",
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{
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- "is_present": false
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},
{
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- "is_present": false
+ "is_present": false,
+ "onset": null
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+ {
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+ "is_present": false,
+ "onset": null
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+ {
+ "term_id": "HP:0002984",
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{
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{
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+ "is_present": false,
+ "onset": null
},
{
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+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000767",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001162",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -18770,7 +20870,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -18778,8 +20879,8 @@
"variant_info": {
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"region": {
- "start": 114399593,
- "end": 114399594,
+ "start": 114366359,
+ "end": 114366360,
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"genbank_acc": "CM000674.2",
@@ -18789,8 +20890,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "C",
+ "ref": "C",
+ "alt": "T",
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},
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@@ -18799,63 +20900,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.281T>G",
+ "hgvs_cdna": "NM_000192.3:c.787G>A",
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"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
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],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Leu94Arg",
+ "hgvsp": "NP_000183.2:p.Val263Met",
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- "end": 94
+ "start": 262,
+ "end": 263
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.131T>G",
+ "hgvs_cdna": "NM_080717.4:c.637G>A",
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"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
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],
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- "hgvsp": "NP_542448.1:p.Leu44Arg",
+ "hgvsp": "NP_542448.1:p.Val213Met",
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- "end": 44
+ "start": 212,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.281T>G",
+ "hgvs_cdna": "NM_181486.4:c.787G>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
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],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Leu94Arg",
+ "hgvsp": "NP_852259.1:p.Val263Met",
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- "end": 94
+ "start": 262,
+ "end": 263
}
}
],
"genotypes": {
"samples": [
{
- "label": "2",
- "meta_label": "PMID_20519243_2"
+ "label": "Patient I/1",
+ "meta_label": "PMID_18706711_Patient_I_1"
}
],
"genotypes": [
@@ -18867,66 +20968,72 @@
},
{
"labels": {
- "label": "K4:III-2",
- "meta_label": "PMID_12789647_K4_III_2"
+ "label": "4-year old male patient",
+ "meta_label": "PMID_18828908_4_year_old_male_patient"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
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},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
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+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0000343",
+ "is_present": true,
+ "onset": null
+ },
+ {
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+ "is_present": true,
+ "onset": null
},
{
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{
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{
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{
- "term_id": "HP:0009777",
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- {
- "term_id": "HP:0003974",
- "is_present": false
- },
- {
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0009813",
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},
{
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+ "onset": null
},
{
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+ "onset": null
},
{
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+ "onset": null
}
],
"measurements": [],
@@ -18934,7 +21041,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -18942,8 +21050,8 @@
"variant_info": {
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- "end": 114399514,
+ "start": 114355754,
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@@ -18953,9 +21061,9 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "C",
- "change_length": 0
+ "ref": "TG",
+ "alt": "T",
+ "change_length": -1
},
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},
@@ -18963,66 +21071,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.361T>G",
+ "hgvs_cdna": "NM_000192.3:c.1333del",
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"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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- 4
+ 9
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Trp121Gly",
+ "hgvsp": "NP_000183.2:p.His445MetfsTer137",
"protein_effect_location": {
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- "end": 121
+ "start": 444,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.211T>G",
+ "hgvs_cdna": "NM_080717.4:c.1183del",
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"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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+ 8
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Trp71Gly",
+ "hgvsp": "NP_542448.1:p.His395MetfsTer137",
"protein_effect_location": {
- "start": 70,
- "end": 71
+ "start": 394,
+ "end": 395
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.361T>G",
+ "hgvs_cdna": "NM_181486.4:c.1333del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 9
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Trp121Gly",
+ "hgvsp": "NP_852259.1:p.His445MetfsTer137",
"protein_effect_location": {
- "start": 120,
- "end": 121
+ "start": 444,
+ "end": 445
}
}
],
"genotypes": {
"samples": [
{
- "label": "K4:III-2",
- "meta_label": "PMID_12789647_K4_III_2"
+ "label": "4-year old male patient",
+ "meta_label": "PMID_18828908_4_year_old_male_patient"
}
],
"genotypes": [
@@ -19034,74 +21139,72 @@
},
{
"labels": {
- "label": "K4:I-2",
- "meta_label": "PMID_12789647_K4_I_2"
+ "label": "1",
+ "meta_label": "PMID_20519243_1"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0004756",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
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+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
- },
- {
- "term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
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- {
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- },
- {
- "term_id": "HP:0003022",
- "is_present": false
- },
- {
- "term_id": "HP:0005792",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
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+ "is_present": false,
+ "onset": null
},
{
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- "is_present": false
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+ "onset": null
},
{
"term_id": "HP:0011565",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -19109,7 +21212,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -19117,8 +21221,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399513,
- "end": 114399514,
+ "start": 114401845,
+ "end": 114401846,
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"genbank_acc": "CM000674.2",
@@ -19128,8 +21232,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "C",
+ "ref": "C",
+ "alt": "G",
"change_length": 0
},
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@@ -19138,66 +21242,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.361T>G",
+ "hgvs_cdna": "NM_000192.3:c.222G>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Trp121Gly",
+ "hgvsp": "NP_000183.2:p.Met74Ile",
"protein_effect_location": {
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- "end": 121
+ "start": 73,
+ "end": 74
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.211T>G",
+ "hgvs_cdna": "NM_080717.4:c.72G>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
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+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Trp71Gly",
+ "hgvsp": "NP_542448.1:p.Met24Ile",
"protein_effect_location": {
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- "end": 71
+ "start": 23,
+ "end": 24
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.361T>G",
+ "hgvs_cdna": "NM_181486.4:c.222G>C",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
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+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Trp121Gly",
+ "hgvsp": "NP_852259.1:p.Met74Ile",
"protein_effect_location": {
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- "end": 121
+ "start": 73,
+ "end": 74
}
}
],
"genotypes": {
"samples": [
{
- "label": "K4:I-2",
- "meta_label": "PMID_12789647_K4_I_2"
+ "label": "1",
+ "meta_label": "PMID_20519243_1"
}
],
"genotypes": [
@@ -19209,58 +21310,67 @@
},
{
"labels": {
- "label": "603-1",
- "meta_label": "PMID_16917909_603_1"
+ "label": "2",
+ "meta_label": "PMID_20519243_2"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0001653",
- "is_present": true
- },
- {
- "term_id": "HP:0011705",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001674",
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+ "onset": null
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{
"term_id": "HP:0001655",
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},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
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+ "is_present": false,
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},
{
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+ "is_present": false,
+ "onset": null
},
{
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+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -19268,7 +21378,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -19276,8 +21387,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
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- "end": 114398632,
+ "start": 114399593,
+ "end": 114399594,
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"genbank_acc": "CM000674.2",
@@ -19287,8 +21398,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
+ "ref": "A",
+ "alt": "C",
"change_length": 0
},
"sv_info": null
@@ -19297,63 +21408,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.451C>T",
+ "hgvs_cdna": "NM_000192.3:c.281T>G",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 4
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gln151Ter",
+ "hgvsp": "NP_000183.2:p.Leu94Arg",
"protein_effect_location": {
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- "end": 151
+ "start": 93,
+ "end": 94
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.301C>T",
+ "hgvs_cdna": "NM_080717.4:c.131T>G",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
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+ 3
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gln101Ter",
+ "hgvsp": "NP_542448.1:p.Leu44Arg",
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.451C>T",
+ "hgvs_cdna": "NM_181486.4:c.281T>G",
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- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
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+ 4
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gln151Ter",
+ "hgvsp": "NP_852259.1:p.Leu94Arg",
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+ "start": 93,
+ "end": 94
}
}
],
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{
- "label": "603-1",
- "meta_label": "PMID_16917909_603_1"
+ "label": "2",
+ "meta_label": "PMID_20519243_2"
}
],
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@@ -19365,66 +21476,72 @@
},
{
"labels": {
- "label": "K9:II-3",
- "meta_label": "PMID_12789647_K9_II_3"
+ "label": "3",
+ "meta_label": "PMID_20519243_3"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
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- {
- "term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0001199",
- "is_present": true
- },
{
"term_id": "HP:0003974",
- "is_present": true
+ "is_present": true,
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},
{
- "term_id": "HP:0003022",
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+ "term_id": "HP:0004058",
+ "is_present": true,
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},
{
- "term_id": "HP:0001684",
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{
- "term_id": "HP:0001674",
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{
- "term_id": "HP:0001655",
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{
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{
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{
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}
],
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@@ -19432,7 +21549,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -19440,8 +21558,8 @@
"variant_info": {
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- "end": 114394817,
+ "start": 114399558,
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@@ -19451,7 +21569,7 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
+ "ref": "T",
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},
@@ -19461,63 +21579,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.587C>G",
+ "hgvs_cdna": "NM_000192.3:c.316A>G",
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+ "MISSENSE_VARIANT"
],
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"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ser196Ter",
+ "hgvsp": "NP_000183.2:p.Ile106Val",
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}
},
{
"gene_id": "TBX5",
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- "hgvs_cdna": "NM_080717.4:c.437C>G",
+ "hgvs_cdna": "NM_080717.4:c.166A>G",
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- "STOP_GAINED"
+ "MISSENSE_VARIANT"
],
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- "hgvsp": "NP_542448.1:p.Ser146Ter",
+ "hgvsp": "NP_542448.1:p.Ile56Val",
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}
},
{
"gene_id": "TBX5",
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- "hgvs_cdna": "NM_181486.4:c.587C>G",
+ "hgvs_cdna": "NM_181486.4:c.316A>G",
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+ "MISSENSE_VARIANT"
],
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- "hgvsp": "NP_852259.1:p.Ser196Ter",
+ "hgvsp": "NP_852259.1:p.Ile106Val",
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}
}
],
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{
- "label": "K9:II-3",
- "meta_label": "PMID_12789647_K9_II_3"
+ "label": "3",
+ "meta_label": "PMID_20519243_3"
}
],
"genotypes": [
@@ -19529,62 +21647,67 @@
},
{
"labels": {
- "label": "Family 2:III:3",
- "meta_label": "PMID_29755943_Family_2_III_3"
+ "label": "4",
+ "meta_label": "PMID_20519243_4"
},
- "sex": "FEMALE",
+ "sex": "MALE",
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+ "vital_status": null,
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{
- "term_id": "HP:0001199",
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- },
- {
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- {
- "term_id": "HP:0011623",
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+ "term_id": "HP:0001674",
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},
{
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},
{
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{
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{
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{
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{
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{
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{
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],
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@@ -19592,7 +21715,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
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@@ -19600,8 +21724,8 @@
"variant_info": {
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- "end": 114403792,
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@@ -19611,9 +21735,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "CG",
- "change_length": 1
+ "ref": "TGTG",
+ "alt": "T",
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},
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@@ -19621,58 +21745,63 @@
{
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- "hgvs_cdna": "NM_000192.3:c.106_107insC",
+ "hgvs_cdna": "NM_000192.3:c.658_660del",
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+ "INFRAME_DELETION"
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- "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
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{
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- "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
+ "hgvs_cdna": "NM_080717.4:c.508_510del",
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- "INTRON_VARIANT"
+ "INFRAME_DELETION"
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],
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"protein_id": "NP_542448.1",
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- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.His170del",
+ "protein_effect_location": {
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+ "end": 170
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},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.106_107insC",
+ "hgvs_cdna": "NM_181486.4:c.658_660del",
"is_preferred": true,
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- "FRAMESHIFT_VARIANT"
+ "INFRAME_DELETION"
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- "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
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}
}
],
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{
- "label": "Family 2:III:3",
- "meta_label": "PMID_29755943_Family_2_III_3"
+ "label": "4",
+ "meta_label": "PMID_20519243_4"
}
],
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@@ -19684,74 +21813,82 @@
},
{
"labels": {
- "label": "K16:II-1",
- "meta_label": "PMID_12789647_K16_II_1"
+ "label": "5.father",
+ "meta_label": "PMID_20519243_5_father"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
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+ "vital_status": null,
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{
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{
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+ "term_id": "HP:0001674",
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},
{
- "term_id": "HP:0001674",
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{
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{
- "term_id": "HP:0009777",
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{
- "term_id": "HP:0001199",
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{
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+ "term_id": "HP:0001655",
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{
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+ "term_id": "HP:0009777",
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{
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+ "term_id": "HP:0009778",
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{
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+ "term_id": "HP:0001199",
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{
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{
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{
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{
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],
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@@ -19759,7 +21896,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -19767,8 +21905,8 @@
"variant_info": {
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- "end": 114398656,
+ "start": 114385520,
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@@ -19779,8 +21917,8 @@
"strand": "POSITIVE"
},
"ref": "C",
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- "change_length": 1
+ "alt": "G",
+ "change_length": 0
},
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@@ -19788,63 +21926,63 @@
{
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- "hgvs_cdna": "NM_000192.3:c.426dup",
+ "hgvs_cdna": "NM_000192.3:c.710G>C",
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+ "MISSENSE_VARIANT"
],
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+ 7
],
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- "hgvsp": "NP_000183.2:p.Ala143ArgfsTer40",
+ "hgvsp": "NP_000183.2:p.Arg237Pro",
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- "end": 143
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.276dup",
+ "hgvs_cdna": "NM_080717.4:c.560G>C",
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+ "MISSENSE_VARIANT"
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- "hgvsp": "NP_542448.1:p.Ala93ArgfsTer40",
+ "hgvsp": "NP_542448.1:p.Arg187Pro",
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.426dup",
+ "hgvs_cdna": "NM_181486.4:c.710G>C",
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- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
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- "hgvsp": "NP_852259.1:p.Ala143ArgfsTer40",
+ "hgvsp": "NP_852259.1:p.Arg237Pro",
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+ "start": 236,
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}
}
],
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{
- "label": "K16:II-1",
- "meta_label": "PMID_12789647_K16_II_1"
+ "label": "5.father",
+ "meta_label": "PMID_20519243_5_father"
}
],
"genotypes": [
@@ -19856,62 +21994,67 @@
},
{
"labels": {
- "label": "Family 1:III:1",
- "meta_label": "PMID_29755943_Family_1_III_1"
+ "label": "5.index",
+ "meta_label": "PMID_20519243_5_index"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0001199",
- "is_present": true
- },
- {
- "term_id": "HP:0011623",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
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+ "term_id": "HP:0001629",
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{
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{
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{
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{
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+ "term_id": "HP:0001199",
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{
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{
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],
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@@ -19919,7 +22062,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
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}
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@@ -19927,8 +22071,8 @@
"variant_info": {
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- "end": 114398568,
+ "start": 114385520,
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@@ -19939,7 +22083,7 @@
"strand": "POSITIVE"
},
"ref": "C",
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@@ -19948,51 +22092,63 @@
{
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- "hgvs_cdna": "NM_000192.3:c.510+5G>T",
+ "hgvs_cdna": "NM_000192.3:c.710G>C",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_5TH_BASE_VARIANT",
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
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],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Arg237Pro",
+ "protein_effect_location": {
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+ "end": 237
+ }
},
{
"gene_id": "TBX5",
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- "hgvs_cdna": "NM_080717.4:c.360+5G>T",
+ "hgvs_cdna": "NM_080717.4:c.560G>C",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_5TH_BASE_VARIANT",
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
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- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Arg187Pro",
+ "protein_effect_location": {
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},
{
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- "hgvs_cdna": "NM_181486.4:c.510+5G>T",
+ "hgvs_cdna": "NM_181486.4:c.710G>C",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_5TH_BASE_VARIANT",
- "INTRON_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Arg237Pro",
+ "protein_effect_location": {
+ "start": 236,
+ "end": 237
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "Family 1:III:1",
- "meta_label": "PMID_29755943_Family_1_III_1"
+ "label": "5.index",
+ "meta_label": "PMID_20519243_5_index"
}
],
"genotypes": [
@@ -20004,62 +22160,97 @@
},
{
"labels": {
- "label": "Family A VI-1",
- "meta_label": "PMID_10077612_Family_A_VI_1"
+ "label": "proband",
+ "meta_label": "PMID_22190901_proband"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
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{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001643",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0000268",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
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+ "term_id": "HP:0000767",
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{
- "term_id": "HP:0001199",
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+ "term_id": "HP:0001688",
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{
- "term_id": "HP:0009813",
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+ "term_id": "HP:0009622",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009812",
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+ "term_id": "HP:0000954",
+ "is_present": true,
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},
{
- "term_id": "HP:0031546",
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+ "term_id": "HP:0000960",
+ "is_present": true,
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},
{
- "term_id": "HP:0005301",
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+ "term_id": "HP:0011567",
+ "is_present": true,
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},
{
- "term_id": "HP:0011565",
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+ "term_id": "HP:0011705",
+ "is_present": true,
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},
{
- "term_id": "HP:0031297",
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+ "term_id": "HP:0001674",
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},
{
- "term_id": "HP:0001643",
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+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -20067,7 +22258,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -20075,8 +22267,8 @@
"variant_info": {
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- "end": 114401830,
+ "start": 114355783,
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@@ -20086,9 +22278,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
- "change_length": 0
+ "ref": "CA",
+ "alt": "C",
+ "change_length": -1
},
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},
@@ -20096,63 +22288,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.1304del",
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"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Leu435ArgfsTer147",
"protein_effect_location": {
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- "end": 80
+ "start": 434,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.1154del",
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- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
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],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Leu385ArgfsTer147",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 384,
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}
},
{
"gene_id": "TBX5",
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- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.1304del",
"is_preferred": true,
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- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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],
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- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Leu435ArgfsTer147",
"protein_effect_location": {
- "start": 79,
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+ "start": 434,
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}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A VI-1",
- "meta_label": "PMID_10077612_Family_A_VI_1"
+ "label": "proband",
+ "meta_label": "PMID_22190901_proband"
}
],
"genotypes": [
@@ -20164,66 +22356,77 @@
},
{
"labels": {
- "label": "5.father",
- "meta_label": "PMID_20519243_5_father"
+ "label": "8-year-old male patient",
+ "meta_label": "PMID_24408148_8_year_old_male_patient"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
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+ "term_id": "HP:0009777",
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},
{
- "term_id": "HP:0005301",
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+ "term_id": "HP:0000767",
+ "is_present": true,
+ "onset": null
},
{
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+ "term_id": "HP:0003042",
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},
{
- "term_id": "HP:0011623",
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+ "term_id": "HP:0001684",
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},
{
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+ "term_id": "HP:0001674",
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{
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- },
- {
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{
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{
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{
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{
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{
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},
{
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}
],
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@@ -20231,7 +22434,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -20239,8 +22443,8 @@
"variant_info": {
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+ "start": 114401872,
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@@ -20250,9 +22454,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "G",
- "change_length": 0
+ "ref": "TA",
+ "alt": "T",
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},
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},
@@ -20260,63 +22464,63 @@
{
"gene_id": "TBX5",
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- "hgvs_cdna": "NM_000192.3:c.710G>C",
+ "hgvs_cdna": "NM_000192.3:c.194del",
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- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Pro",
+ "hgvsp": "NP_000183.2:p.Leu65GlnfsTer10",
"protein_effect_location": {
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- "end": 237
+ "start": 64,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>C",
+ "hgvs_cdna": "NM_080717.4:c.44del",
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"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
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],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Pro",
+ "hgvsp": "NP_542448.1:p.Leu15GlnfsTer10",
"protein_effect_location": {
- "start": 186,
- "end": 187
+ "start": 14,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>C",
+ "hgvs_cdna": "NM_181486.4:c.194del",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
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],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Pro",
+ "hgvsp": "NP_852259.1:p.Leu65GlnfsTer10",
"protein_effect_location": {
- "start": 236,
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}
}
],
"genotypes": {
"samples": [
{
- "label": "5.father",
- "meta_label": "PMID_20519243_5_father"
+ "label": "8-year-old male patient",
+ "meta_label": "PMID_24408148_8_year_old_male_patient"
}
],
"genotypes": [
@@ -20328,70 +22532,82 @@
},
{
"labels": {
- "label": "K15:IV-1",
- "meta_label": "PMID_12789647_K15_IV_1"
+ "label": "Family 1 Patient 1",
+ "meta_label": "PMID_25216260_Family_1_Patient_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001631",
- "is_present": true
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002092",
+ "is_present": true,
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},
{
"term_id": "HP:0001199",
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},
{
- "term_id": "HP:0011623",
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+ "term_id": "HP:0001643",
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},
{
- "term_id": "HP:0011682",
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+ "onset": null
},
{
"term_id": "HP:0001674",
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},
{
"term_id": "HP:0001655",
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+ "onset": null
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{
"term_id": "HP:0009777",
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},
{
"term_id": "HP:0009778",
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- {
- "term_id": "HP:0002984",
- "is_present": false
- },
- {
- "term_id": "HP:0003022",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
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+ "onset": null
},
{
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},
{
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+ "onset": null
},
{
"term_id": "HP:0031297",
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+ "is_present": false,
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}
],
"measurements": [],
@@ -20399,7 +22615,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -20407,8 +22624,8 @@
"variant_info": {
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- "end": 114398682,
+ "start": 114366266,
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@@ -20419,8 +22636,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "CG",
- "change_length": 1
+ "alt": "A",
+ "change_length": 0
},
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},
@@ -20428,63 +22645,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.400dup",
+ "hgvs_cdna": "NM_000192.3:c.880G>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
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- 5
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
+ "hgvsp": "NP_000183.2:p.Glu294Ter",
"protein_effect_location": {
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- "end": 134
+ "start": 293,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.250dup",
+ "hgvs_cdna": "NM_080717.4:c.730G>T",
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"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
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+ 7
],
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- "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
+ "hgvsp": "NP_542448.1:p.Glu244Ter",
"protein_effect_location": {
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- "end": 84
+ "start": 243,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.400dup",
+ "hgvs_cdna": "NM_181486.4:c.880G>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "STOP_GAINED"
],
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],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
+ "hgvsp": "NP_852259.1:p.Glu294Ter",
"protein_effect_location": {
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- "end": 134
+ "start": 293,
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}
}
],
"genotypes": {
"samples": [
{
- "label": "K15:IV-1",
- "meta_label": "PMID_12789647_K15_IV_1"
+ "label": "Family 1 Patient 1",
+ "meta_label": "PMID_25216260_Family_1_Patient_1"
}
],
"genotypes": [
@@ -20496,66 +22713,77 @@
},
{
"labels": {
- "label": "Family 1:II:2",
- "meta_label": "PMID_29755943_Family_1_II_2"
+ "label": "Family 1 Patient 2",
+ "meta_label": "PMID_25216260_Family_1_Patient_2"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011664",
- "is_present": true
+ "term_id": "HP:0009778",
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},
{
- "term_id": "HP:0001688",
- "is_present": true
+ "term_id": "HP:0001684",
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},
{
"term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
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{
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+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
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{
"term_id": "HP:0009777",
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{
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+ "term_id": "HP:0001199",
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},
{
"term_id": "HP:0009813",
- "is_present": false
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+ "onset": null
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{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
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+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -20563,7 +22791,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -20571,8 +22800,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
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- "end": 114398568,
+ "start": 114366266,
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"genbank_acc": "CM000674.2",
@@ -20592,51 +22821,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.510+5G>T",
+ "hgvs_cdna": "NM_000192.3:c.880G>T",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_5TH_BASE_VARIANT",
- "INTRON_VARIANT"
+ "STOP_GAINED"
+ ],
+ "overlapping_exons": [
+ 8
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Glu294Ter",
+ "protein_effect_location": {
+ "start": 293,
+ "end": 294
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.360+5G>T",
+ "hgvs_cdna": "NM_080717.4:c.730G>T",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_5TH_BASE_VARIANT",
- "INTRON_VARIANT"
+ "STOP_GAINED"
+ ],
+ "overlapping_exons": [
+ 7
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Glu244Ter",
+ "protein_effect_location": {
+ "start": 243,
+ "end": 244
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.510+5G>T",
+ "hgvs_cdna": "NM_181486.4:c.880G>T",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_5TH_BASE_VARIANT",
- "INTRON_VARIANT"
+ "STOP_GAINED"
+ ],
+ "overlapping_exons": [
+ 8
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Glu294Ter",
+ "protein_effect_location": {
+ "start": 293,
+ "end": 294
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "Family 1:II:2",
- "meta_label": "PMID_29755943_Family_1_II_2"
+ "label": "Family 1 Patient 2",
+ "meta_label": "PMID_25216260_Family_1_Patient_2"
}
],
"genotypes": [
@@ -20648,62 +22889,82 @@
},
{
"labels": {
- "label": "Family B II-2",
- "meta_label": "PMID_10077612_Family_B_II_2"
+ "label": "Family 2 Patient 3",
+ "meta_label": "PMID_25216260_Family_2_Patient_3"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001688",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0002092",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -20711,7 +22972,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -20719,8 +22981,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114385473,
+ "end": 114385474,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -20730,8 +22992,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "A",
+ "alt": "G",
"change_length": 0
},
"sv_info": null
@@ -20740,63 +23002,48 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.755+2T>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
- "protein_effect_location": {
- "start": 236,
- "end": 237
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.605+2T>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
- "protein_effect_location": {
- "start": 186,
- "end": 187
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.755+2T>C",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
- "protein_effect_location": {
- "start": 236,
- "end": 237
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "Family B II-2",
- "meta_label": "PMID_10077612_Family_B_II_2"
+ "label": "Family 2 Patient 3",
+ "meta_label": "PMID_25216260_Family_2_Patient_3"
}
],
"genotypes": [
@@ -20808,66 +23055,77 @@
},
{
"labels": {
- "label": "B III/2",
- "meta_label": "PMID_12818525_B_III_2"
+ "label": "Family 2 Patient 4",
+ "meta_label": "PMID_25216260_Family_2_Patient_4"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030241",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
- },
- {
- "term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0002092",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -20875,7 +23133,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -20883,8 +23142,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398674,
- "end": 114398675,
+ "start": 114385473,
+ "end": 114385474,
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"name": "12",
"genbank_acc": "CM000674.2",
@@ -20894,8 +23153,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "T",
+ "ref": "A",
+ "alt": "G",
"change_length": 0
},
"sv_info": null
@@ -20904,63 +23163,48 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.408C>A",
+ "hgvs_cdna": "NM_000192.3:c.755+2T>C",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
- ],
- "overlapping_exons": [
- 5
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr136Ter",
- "protein_effect_location": {
- "start": 135,
- "end": 136
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.258C>A",
+ "hgvs_cdna": "NM_080717.4:c.605+2T>C",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
- ],
- "overlapping_exons": [
- 4
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr86Ter",
- "protein_effect_location": {
- "start": 85,
- "end": 86
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.408C>A",
+ "hgvs_cdna": "NM_181486.4:c.755+2T>C",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
- ],
- "overlapping_exons": [
- 5
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr136Ter",
- "protein_effect_location": {
- "start": 135,
- "end": 136
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "B III/2",
- "meta_label": "PMID_12818525_B_III_2"
+ "label": "Family 2 Patient 4",
+ "meta_label": "PMID_25216260_Family_2_Patient_4"
}
],
"genotypes": [
@@ -20972,78 +23216,82 @@
},
{
"labels": {
- "label": "K4:IV-1",
- "meta_label": "PMID_12789647_K4_IV_1"
+ "label": "Family 5 Patient 7",
+ "meta_label": "PMID_25216260_Family_5_Patient_7"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0001674",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0004209",
- "is_present": true
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002092",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
- },
- {
- "term_id": "HP:0002984",
- "is_present": false
- },
- {
- "term_id": "HP:0003022",
- "is_present": false
- },
- {
- "term_id": "HP:0005792",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -21051,7 +23299,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -21059,8 +23308,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399513,
- "end": 114399514,
+ "start": 114385521,
+ "end": 114385522,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -21070,8 +23319,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "C",
+ "ref": "G",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -21080,66 +23329,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.361T>G",
+ "hgvs_cdna": "NM_000192.3:c.709C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Trp121Gly",
+ "hgvsp": "NP_000183.2:p.Arg237Trp",
"protein_effect_location": {
- "start": 120,
- "end": 121
+ "start": 236,
+ "end": 237
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.211T>G",
+ "hgvs_cdna": "NM_080717.4:c.559C>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Trp71Gly",
+ "hgvsp": "NP_542448.1:p.Arg187Trp",
"protein_effect_location": {
- "start": 70,
- "end": 71
+ "start": 186,
+ "end": 187
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.361T>G",
+ "hgvs_cdna": "NM_181486.4:c.709C>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Trp121Gly",
+ "hgvsp": "NP_852259.1:p.Arg237Trp",
"protein_effect_location": {
- "start": 120,
- "end": 121
+ "start": 236,
+ "end": 237
}
}
],
"genotypes": {
"samples": [
{
- "label": "K4:IV-1",
- "meta_label": "PMID_12789647_K4_IV_1"
+ "label": "Family 5 Patient 7",
+ "meta_label": "PMID_25216260_Family_5_Patient_7"
}
],
"genotypes": [
@@ -21151,62 +23397,92 @@
},
{
"labels": {
- "label": "K15:III-2",
- "meta_label": "PMID_12789647_K15_III_2"
+ "label": "4-month-old female infant",
+ "meta_label": "PMID_26219450_4_month_old_female_infant"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
- {
- "term_id": "HP:0001631",
- "is_present": true
- },
{
"term_id": "HP:0001629",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005180",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000347",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000185",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -21214,7 +23490,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -21222,8 +23499,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398681,
- "end": 114398682,
+ "start": 114401852,
+ "end": 114401853,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -21233,9 +23510,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "CG",
- "change_length": 1
+ "ref": "G",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -21243,63 +23520,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.400dup",
+ "hgvs_cdna": "NM_000192.3:c.215C>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
+ "hgvsp": "NP_000183.2:p.Thr72Lys",
"protein_effect_location": {
- "start": 133,
- "end": 134
+ "start": 71,
+ "end": 72
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.250dup",
+ "hgvs_cdna": "NM_080717.4:c.65C>A",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 4
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
+ "hgvsp": "NP_542448.1:p.Thr22Lys",
"protein_effect_location": {
- "start": 83,
- "end": 84
+ "start": 21,
+ "end": 22
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.400dup",
+ "hgvs_cdna": "NM_181486.4:c.215C>A",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 5
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
+ "hgvsp": "NP_852259.1:p.Thr72Lys",
"protein_effect_location": {
- "start": 133,
- "end": 134
+ "start": 71,
+ "end": 72
}
}
],
"genotypes": {
"samples": [
{
- "label": "K15:III-2",
- "meta_label": "PMID_12789647_K15_III_2"
+ "label": "4-month-old female infant",
+ "meta_label": "PMID_26219450_4_month_old_female_infant"
}
],
"genotypes": [
@@ -21311,42 +23588,75 @@
},
{
"labels": {
- "label": "668-1 ",
- "meta_label": "PMID_16917909_668_1"
+ "label": "infant",
+ "meta_label": "PMID_26219450_infant"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": {
+ "days": 121.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005180",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009486",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000185",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -21354,7 +23664,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -21362,8 +23673,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385473,
- "end": 114385474,
+ "start": 114401852,
+ "end": 114401853,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -21373,8 +23684,8 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "G",
+ "ref": "G",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -21383,48 +23694,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.755+2T>C",
+ "hgvs_cdna": "NM_000192.3:c.215C>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Thr72Lys",
+ "protein_effect_location": {
+ "start": 71,
+ "end": 72
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.605+2T>C",
+ "hgvs_cdna": "NM_080717.4:c.65C>A",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 2
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Thr22Lys",
+ "protein_effect_location": {
+ "start": 21,
+ "end": 22
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.755+2T>C",
+ "hgvs_cdna": "NM_181486.4:c.215C>A",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Thr72Lys",
+ "protein_effect_location": {
+ "start": 71,
+ "end": 72
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "668-1 ",
- "meta_label": "PMID_16917909_668_1"
+ "label": "infant",
+ "meta_label": "PMID_26219450_infant"
}
],
"genotypes": [
@@ -21436,66 +23762,72 @@
},
{
"labels": {
- "label": "HOS-B1",
- "meta_label": "PMID_10842287_HOS_B1"
+ "label": "Patient II/2 (proband)",
+ "meta_label": "PMID_26401820_Patient_II_2_proband"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
- },
- {
- "term_id": "HP:0006097",
- "is_present": true
- },
- {
- "term_id": "HP:0009460",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -21503,7 +23835,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -21511,8 +23844,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403753,
- "end": 114403754,
+ "start": 114401920,
+ "end": 114401921,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -21522,8 +23855,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "T",
+ "ref": "C",
+ "alt": "G",
"change_length": 0
},
"sv_info": null
@@ -21532,29 +23865,23 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.145C>A",
+ "hgvs_cdna": "NM_000192.3:c.148-1G>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
- ],
- "overlapping_exons": [
- 2
+ "SPLICE_ACCEPTOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gln49Lys",
- "protein_effect_location": {
- "start": 48,
- "end": 49
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1834C>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1G>C",
"is_preferred": false,
"variant_effects": [
- "INTRON_VARIANT"
+ "SPLICE_ACCEPTOR_VARIANT"
],
"overlapping_exons": null,
"protein_id": "NP_542448.1",
@@ -21564,28 +23891,22 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.145C>A",
+ "hgvs_cdna": "NM_181486.4:c.148-1G>C",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
- ],
- "overlapping_exons": [
- 2
+ "SPLICE_ACCEPTOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gln49Lys",
- "protein_effect_location": {
- "start": 48,
- "end": 49
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "HOS-B1",
- "meta_label": "PMID_10842287_HOS_B1"
+ "label": "Patient II/2 (proband)",
+ "meta_label": "PMID_26401820_Patient_II_2_proband"
}
],
"genotypes": [
@@ -21597,62 +23918,65 @@
},
{
"labels": {
- "label": "Family A IV-20",
- "meta_label": "PMID_10077612_Family_A_IV_20"
+ "label": "II-1",
+ "meta_label": "PMID_27026770_II_1"
},
"sex": "FEMALE",
+ "age": {
+ "days": 2191.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -21660,7 +23984,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -21668,8 +23993,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114401826,
+ "end": 114401827,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -21679,8 +24004,8 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
+ "ref": "T",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -21689,63 +24014,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.241A>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Arg81Trp",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 80,
+ "end": 81
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.91A>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
+ "hgvsp": "NP_542448.1:p.Arg31Trp",
"protein_effect_location": {
- "start": 29,
- "end": 30
+ "start": 30,
+ "end": 31
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.241A>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Arg81Trp",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 80,
+ "end": 81
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A IV-20",
- "meta_label": "PMID_10077612_Family_A_IV_20"
+ "label": "II-1",
+ "meta_label": "PMID_27026770_II_1"
}
],
"genotypes": [
@@ -21757,62 +24085,82 @@
},
{
"labels": {
- "label": "619-1",
- "meta_label": "PMID_16917909_619_1"
+ "label": "a 6-year-old girl,",
+ "meta_label": "PMID_27026770_a_6_year_old_girl"
},
- "sex": "MALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001684",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -21820,7 +24168,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -21828,8 +24177,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398577,
- "end": 114398579,
+ "start": 114401826,
+ "end": 114401827,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -21839,9 +24188,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CA",
- "alt": "C",
- "change_length": -1
+ "ref": "T",
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -21849,63 +24198,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.504del",
+ "hgvs_cdna": "NM_000192.3:c.241A>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 5
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Phe168LeufsTer6",
+ "hgvsp": "NP_000183.2:p.Arg81Trp",
"protein_effect_location": {
- "start": 167,
- "end": 168
+ "start": 80,
+ "end": 81
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.354del",
+ "hgvs_cdna": "NM_080717.4:c.91A>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 4
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Phe118LeufsTer6",
+ "hgvsp": "NP_542448.1:p.Arg31Trp",
"protein_effect_location": {
- "start": 117,
- "end": 118
+ "start": 30,
+ "end": 31
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.504del",
+ "hgvs_cdna": "NM_181486.4:c.241A>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 5
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Phe168LeufsTer6",
+ "hgvsp": "NP_852259.1:p.Arg81Trp",
"protein_effect_location": {
- "start": 167,
- "end": 168
+ "start": 80,
+ "end": 81
}
}
],
"genotypes": {
"samples": [
{
- "label": "619-1",
- "meta_label": "PMID_16917909_619_1"
+ "label": "a 6-year-old girl,",
+ "meta_label": "PMID_27026770_a_6_year_old_girl"
}
],
"genotypes": [
@@ -21917,66 +24269,72 @@
},
{
"labels": {
- "label": "A IV/4 ",
- "meta_label": "PMID_12818525_A_IV_4"
+ "label": "fetus",
+ "meta_label": "PMID_27026770_fetus"
},
- "sex": "FEMALE",
+ "sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0030241",
- "is_present": true
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0001191",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
- },
- {
- "term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -21984,7 +24342,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -21992,8 +24351,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114398674,
- "end": 114398675,
+ "start": 114401826,
+ "end": 114401827,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -22003,8 +24362,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "T",
+ "ref": "T",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -22013,63 +24372,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.408C>A",
+ "hgvs_cdna": "NM_000192.3:c.241A>T",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 5
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Tyr136Ter",
+ "hgvsp": "NP_000183.2:p.Arg81Trp",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 80,
+ "end": 81
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.258C>A",
+ "hgvs_cdna": "NM_080717.4:c.91A>T",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 4
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Tyr86Ter",
+ "hgvsp": "NP_542448.1:p.Arg31Trp",
"protein_effect_location": {
- "start": 85,
- "end": 86
+ "start": 30,
+ "end": 31
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.408C>A",
+ "hgvs_cdna": "NM_181486.4:c.241A>T",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "MISSENSE_VARIANT",
+ "SPLICE_REGION_VARIANT"
],
"overlapping_exons": [
- 5
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Tyr136Ter",
+ "hgvsp": "NP_852259.1:p.Arg81Trp",
"protein_effect_location": {
- "start": 135,
- "end": 136
+ "start": 80,
+ "end": 81
}
}
],
"genotypes": {
"samples": [
{
- "label": "A IV/4 ",
- "meta_label": "PMID_12818525_A_IV_4"
+ "label": "fetus",
+ "meta_label": "PMID_27026770_fetus"
}
],
"genotypes": [
@@ -22081,50 +24443,70 @@
},
{
"labels": {
- "label": "II-1",
- "meta_label": "PMID_27026770_II_1"
+ "label": "girl",
+ "meta_label": "PMID_27552067_girl"
},
"sex": "FEMALE",
+ "age": {
+ "days": 44.4375,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0003974",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001629",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0010704",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -22132,7 +24514,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -22140,8 +24523,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401826,
- "end": 114401827,
+ "start": 114398601,
+ "end": 114398602,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -22152,7 +24535,7 @@
"strand": "POSITIVE"
},
"ref": "T",
- "alt": "A",
+ "alt": "G",
"change_length": 0
},
"sv_info": null
@@ -22161,66 +24544,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.241A>T",
+ "hgvs_cdna": "NM_000192.3:c.481A>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg81Trp",
+ "hgvsp": "NP_000183.2:p.Thr161Pro",
"protein_effect_location": {
- "start": 80,
- "end": 81
+ "start": 160,
+ "end": 161
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.91A>T",
+ "hgvs_cdna": "NM_080717.4:c.331A>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 2
+ 4
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg31Trp",
+ "hgvsp": "NP_542448.1:p.Thr111Pro",
"protein_effect_location": {
- "start": 30,
- "end": 31
+ "start": 110,
+ "end": 111
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.241A>T",
+ "hgvs_cdna": "NM_181486.4:c.481A>C",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT",
- "SPLICE_REGION_VARIANT"
+ "MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 5
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg81Trp",
+ "hgvsp": "NP_852259.1:p.Thr161Pro",
"protein_effect_location": {
- "start": 80,
- "end": 81
+ "start": 160,
+ "end": 161
}
}
],
"genotypes": {
"samples": [
{
- "label": "II-1",
- "meta_label": "PMID_27026770_II_1"
+ "label": "girl",
+ "meta_label": "PMID_27552067_girl"
}
],
"genotypes": [
@@ -22232,54 +24612,80 @@
},
{
"labels": {
- "label": "K14:III-4",
- "meta_label": "PMID_12789647_K14_III_4"
+ "label": "patient",
+ "meta_label": "PMID_27652283_patient"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 456.5625,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0005180",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -22287,7 +24693,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -22295,8 +24702,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114366365,
- "end": 114366366,
+ "start": 114401852,
+ "end": 114401853,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -22306,8 +24713,8 @@
},
"strand": "POSITIVE"
},
- "ref": "T",
- "alt": "A",
+ "ref": "G",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -22316,63 +24723,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.781A>T",
+ "hgvs_cdna": "NM_000192.3:c.215C>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 3
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ser261Cys",
+ "hgvsp": "NP_000183.2:p.Thr72Lys",
"protein_effect_location": {
- "start": 260,
- "end": 261
+ "start": 71,
+ "end": 72
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.631A>T",
+ "hgvs_cdna": "NM_080717.4:c.65C>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ser211Cys",
+ "hgvsp": "NP_542448.1:p.Thr22Lys",
"protein_effect_location": {
- "start": 210,
- "end": 211
+ "start": 21,
+ "end": 22
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.781A>T",
+ "hgvs_cdna": "NM_181486.4:c.215C>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 8
+ 3
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ser261Cys",
+ "hgvsp": "NP_852259.1:p.Thr72Lys",
"protein_effect_location": {
- "start": 260,
- "end": 261
+ "start": 71,
+ "end": 72
}
}
],
"genotypes": {
"samples": [
{
- "label": "K14:III-4",
- "meta_label": "PMID_12789647_K14_III_4"
+ "label": "patient",
+ "meta_label": "PMID_27652283_patient"
}
],
"genotypes": [
@@ -22384,58 +24791,85 @@
},
{
"labels": {
- "label": "Family A V-7",
- "meta_label": "PMID_10077612_Family_A_V_7"
+ "label": "a 6-month-old female",
+ "meta_label": "PMID_28434921_a_6_month_old_female"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0002092",
+ "is_present": true,
+ "onset": {
+ "days": 273.9375,
+ "timeline": "POSTNATAL"
+ }
},
{
- "term_id": "HP:0009777",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -22443,7 +24877,11 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 0.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -22451,8 +24889,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114403858,
+ "end": 114403859,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -22462,7 +24900,7 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
+ "ref": "G",
"alt": "T",
"change_length": 0
},
@@ -22472,63 +24910,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.40C>A",
"is_preferred": false,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Pro14Thr",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 13,
+ "end": 14
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1939C>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 2
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
- "protein_effect_location": {
- "start": 29,
- "end": 30
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.40C>A",
"is_preferred": true,
"variant_effects": [
"MISSENSE_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Pro14Thr",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 13,
+ "end": 14
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A V-7",
- "meta_label": "PMID_10077612_Family_A_V_7"
+ "label": "a 6-month-old female",
+ "meta_label": "PMID_28434921_a_6_month_old_female"
}
],
"genotypes": [
@@ -22540,58 +24973,77 @@
},
{
"labels": {
- "label": "Family B III-5",
- "meta_label": "PMID_10077612_Family_B_III_5"
+ "label": "Family 1:III:1",
+ "meta_label": "PMID_29755943_Family_1_III_1"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011565",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031297",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001643",
- "is_present": false
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -22599,7 +25051,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -22607,8 +25060,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114398567,
+ "end": 114398568,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -22619,7 +25072,7 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "T",
+ "alt": "A",
"change_length": 0
},
"sv_info": null
@@ -22628,63 +25081,51 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.510+5G>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_5TH_BASE_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
- "protein_effect_location": {
- "start": 236,
- "end": 237
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.360+5G>T",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "SPLICE_DONOR_5TH_BASE_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
- "protein_effect_location": {
- "start": 186,
- "end": 187
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.510+5G>T",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_5TH_BASE_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
- "protein_effect_location": {
- "start": 236,
- "end": 237
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "Family B III-5",
- "meta_label": "PMID_10077612_Family_B_III_5"
+ "label": "Family 1:III:1",
+ "meta_label": "PMID_29755943_Family_1_III_1"
}
],
"genotypes": [
@@ -22696,62 +25137,82 @@
},
{
"labels": {
- "label": "666-1",
- "meta_label": "PMID_16917909_666_1"
+ "label": "Family 1:II:2",
+ "meta_label": "PMID_29755943_Family_1_II_2"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011664",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001688",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -22759,7 +25220,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -22767,8 +25229,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114394761,
- "end": 114394763,
+ "start": 114398567,
+ "end": 114398568,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -22778,9 +25240,9 @@
},
"strand": "POSITIVE"
},
- "ref": "CA",
- "alt": "C",
- "change_length": -1
+ "ref": "C",
+ "alt": "A",
+ "change_length": 0
},
"sv_info": null
},
@@ -22788,63 +25250,51 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.641del",
+ "hgvs_cdna": "NM_000192.3:c.510+5G>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "SPLICE_DONOR_5TH_BASE_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Val214GlyfsTer12",
- "protein_effect_location": {
- "start": 213,
- "end": 214
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.491del",
+ "hgvs_cdna": "NM_080717.4:c.360+5G>T",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
- ],
- "overlapping_exons": [
- 5
+ "SPLICE_DONOR_5TH_BASE_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Val164GlyfsTer12",
- "protein_effect_location": {
- "start": 163,
- "end": 164
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.641del",
+ "hgvs_cdna": "NM_181486.4:c.510+5G>T",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "SPLICE_DONOR_5TH_BASE_VARIANT",
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Val214GlyfsTer12",
- "protein_effect_location": {
- "start": 213,
- "end": 214
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "666-1",
- "meta_label": "PMID_16917909_666_1"
+ "label": "Family 1:II:2",
+ "meta_label": "PMID_29755943_Family_1_II_2"
}
],
"genotypes": [
@@ -22856,18 +25306,77 @@
},
{
"labels": {
- "label": "father II:1",
- "meta_label": "PMID_36444245_father_II_1"
+ "label": "Family 2:III:1",
+ "meta_label": "PMID_29755943_Family_2_III_1"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011565",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031297",
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -22875,7 +25384,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -22883,8 +25393,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385549,
- "end": 114385550,
+ "start": 114403791,
+ "end": 114403792,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -22894,9 +25404,9 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "AATTATTCTCAG",
- "change_length": 11
+ "ref": "C",
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -22904,66 +25414,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.680_681insCTGAGAATAAT",
+ "hgvs_cdna": "NM_000192.3:c.106_107insC",
"is_preferred": false,
"variant_effects": [
- "INFRAME_INSERTION",
- "STOP_RETAINED_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ile227_Glu228insTer",
+ "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 226,
- "end": 227
+ "start": 35,
+ "end": 36
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.530_531insCTGAGAATAAT",
+ "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
"is_preferred": false,
"variant_effects": [
- "INFRAME_INSERTION",
- "STOP_RETAINED_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ile177_Glu178insTer",
- "protein_effect_location": {
- "start": 176,
- "end": 177
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.680_681insCTGAGAATAAT",
+ "hgvs_cdna": "NM_181486.4:c.106_107insC",
"is_preferred": true,
"variant_effects": [
- "INFRAME_INSERTION",
- "STOP_RETAINED_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 7
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ile227_Glu228insTer",
+ "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 226,
- "end": 227
+ "start": 35,
+ "end": 36
}
}
],
"genotypes": {
"samples": [
{
- "label": "father II:1",
- "meta_label": "PMID_36444245_father_II_1"
+ "label": "Family 2:III:1",
+ "meta_label": "PMID_29755943_Family_2_III_1"
}
],
"genotypes": [
@@ -22975,54 +25477,77 @@
},
{
"labels": {
- "label": "4",
- "meta_label": "PMID_20519243_4"
+ "label": "Family 2:III:3",
+ "meta_label": "PMID_29755943_Family_2_III_3"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001674",
- "is_present": true
- },
- {
- "term_id": "HP:0000878",
- "is_present": true
- },
- {
- "term_id": "HP:0004762",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -23030,7 +25555,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -23038,8 +25564,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114394742,
- "end": 114394746,
+ "start": 114403791,
+ "end": 114403792,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -23049,73 +25575,68 @@
},
"strand": "POSITIVE"
},
- "ref": "TGTG",
- "alt": "T",
- "change_length": -3
- },
- "sv_info": null
+ "ref": "C",
+ "alt": "CG",
+ "change_length": 1
+ },
+ "sv_info": null
},
"tx_annotations": [
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.658_660del",
+ "hgvs_cdna": "NM_000192.3:c.106_107insC",
"is_preferred": false,
"variant_effects": [
- "INFRAME_DELETION"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.His220del",
+ "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 219,
- "end": 220
+ "start": 35,
+ "end": 36
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.508_510del",
+ "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
"is_preferred": false,
"variant_effects": [
- "INFRAME_DELETION"
- ],
- "overlapping_exons": [
- 5
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.His170del",
- "protein_effect_location": {
- "start": 169,
- "end": 170
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.658_660del",
+ "hgvs_cdna": "NM_181486.4:c.106_107insC",
"is_preferred": true,
"variant_effects": [
- "INFRAME_DELETION"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 6
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.His220del",
+ "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 219,
- "end": 220
+ "start": 35,
+ "end": 36
}
}
],
"genotypes": {
"samples": [
{
- "label": "4",
- "meta_label": "PMID_20519243_4"
+ "label": "Family 2:III:3",
+ "meta_label": "PMID_29755943_Family_2_III_3"
}
],
"genotypes": [
@@ -23127,74 +25648,77 @@
},
{
"labels": {
- "label": "K2:I-1",
- "meta_label": "PMID_12789647_K2_I_1"
+ "label": "Family 2:II:2",
+ "meta_label": "PMID_29755943_Family_2_II_2"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009777",
- "is_present": true
- },
- {
- "term_id": "HP:0002984",
- "is_present": true
- },
- {
- "term_id": "HP:0003022",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005792",
- "is_present": true
+ "term_id": "HP:0011664",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001684",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011623",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011682",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0003974",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -23202,7 +25726,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -23210,8 +25735,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114403797,
- "end": 114403799,
+ "start": 114403791,
+ "end": 114403792,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -23221,9 +25746,9 @@
},
"strand": "POSITIVE"
},
- "ref": "GC",
- "alt": "G",
- "change_length": -1
+ "ref": "C",
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -23231,7 +25756,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.100del",
+ "hgvs_cdna": "NM_000192.3:c.106_107insC",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -23240,16 +25765,16 @@
2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ala34ProfsTer32",
+ "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 35,
+ "end": 36
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.-3-1879del",
+ "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
"is_preferred": false,
"variant_effects": [
"INTRON_VARIANT"
@@ -23262,7 +25787,7 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.100del",
+ "hgvs_cdna": "NM_181486.4:c.106_107insC",
"is_preferred": true,
"variant_effects": [
"FRAMESHIFT_VARIANT"
@@ -23271,18 +25796,18 @@
2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ala34ProfsTer32",
+ "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 33,
- "end": 34
+ "start": 35,
+ "end": 36
}
}
],
"genotypes": {
"samples": [
{
- "label": "K2:I-1",
- "meta_label": "PMID_12789647_K2_I_1"
+ "label": "Family 2:II:2",
+ "meta_label": "PMID_29755943_Family_2_II_2"
}
],
"genotypes": [
@@ -23294,58 +25819,77 @@
},
{
"labels": {
- "label": "Family A IV-21",
- "meta_label": "PMID_10077612_Family_A_IV_21"
+ "label": "Family 2:IV:1",
+ "meta_label": "PMID_29755943_Family_2_IV_1"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": false
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -23353,7 +25897,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -23361,8 +25906,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114403791,
+ "end": 114403792,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -23373,8 +25918,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "T",
- "change_length": 0
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -23382,63 +25927,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.106_107insC",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 35,
+ "end": 36
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 2
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
- "protein_effect_location": {
- "start": 29,
- "end": 30
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.106_107insC",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 35,
+ "end": 36
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A IV-21",
- "meta_label": "PMID_10077612_Family_A_IV_21"
+ "label": "Family 2:IV:1",
+ "meta_label": "PMID_29755943_Family_2_IV_1"
}
],
"genotypes": [
@@ -23450,62 +25990,77 @@
},
{
"labels": {
- "label": "Family A IV-4",
- "meta_label": "PMID_10077612_Family_A_IV_4"
+ "label": "Family 2:IV:2",
+ "meta_label": "PMID_29755943_Family_2_IV_2"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -23513,7 +26068,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -23521,8 +26077,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114401829,
- "end": 114401830,
+ "start": 114403791,
+ "end": 114403792,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -23533,8 +26089,8 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "T",
- "change_length": 0
+ "alt": "CG",
+ "change_length": 1
},
"sv_info": null
},
@@ -23542,63 +26098,58 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.238G>A",
+ "hgvs_cdna": "NM_000192.3:c.106_107insC",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Gly80Arg",
+ "hgvsp": "NP_000183.2:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 35,
+ "end": 36
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.88G>A",
+ "hgvs_cdna": "NM_080717.4:c.-3-1873_-3-1872insC",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 2
+ "INTRON_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Gly30Arg",
- "protein_effect_location": {
- "start": 29,
- "end": 30
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.238G>A",
+ "hgvs_cdna": "NM_181486.4:c.106_107insC",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
+ "FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 2
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Gly80Arg",
+ "hgvsp": "NP_852259.1:p.Ser36ThrfsTer25",
"protein_effect_location": {
- "start": 79,
- "end": 80
+ "start": 35,
+ "end": 36
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family A IV-4",
- "meta_label": "PMID_10077612_Family_A_IV_4"
+ "label": "Family 2:IV:2",
+ "meta_label": "PMID_29755943_Family_2_IV_2"
}
],
"genotypes": [
@@ -23610,62 +26161,85 @@
},
{
"labels": {
- "label": "Family B III-9",
- "meta_label": "PMID_10077612_Family_B_III_9"
+ "label": "patient",
+ "meta_label": "PMID_30538526_patient"
},
"sex": "FEMALE",
+ "age": {
+ "days": 730.5,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011623",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002092",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": true
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": true
+ "term_id": "HP:0003022",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": true
+ "term_id": "HP:0005792",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009777",
- "is_present": false
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
- },
- {
- "term_id": "HP:0005301",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -23673,7 +26247,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -23681,8 +26256,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114399632,
+ "end": 114399633,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -23693,7 +26268,7 @@
"strand": "POSITIVE"
},
"ref": "C",
- "alt": "T",
+ "alt": "G",
"change_length": 0
},
"sv_info": null
@@ -23702,63 +26277,48 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.243-1G>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_ACCEPTOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
- "protein_effect_location": {
- "start": 236,
- "end": 237
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.93-1G>C",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "SPLICE_ACCEPTOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
- "protein_effect_location": {
- "start": 186,
- "end": 187
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.243-1G>C",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_ACCEPTOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
- "protein_effect_location": {
- "start": 236,
- "end": 237
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "Family B III-9",
- "meta_label": "PMID_10077612_Family_B_III_9"
+ "label": "patient",
+ "meta_label": "PMID_30538526_patient"
}
],
"genotypes": [
@@ -23770,94 +26330,75 @@
},
{
"labels": {
- "label": "III-1",
- "meta_label": "PMID_34490705_III_1"
+ "label": "Individual A",
+ "meta_label": "PMID_33866394_Individual_A"
},
- "sex": "FEMALE",
+ "sex": "MALE",
+ "age": {
+ "days": 14244.75,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001684",
- "is_present": true
- },
- {
- "term_id": "HP:0001629",
- "is_present": true
+ "term_id": "HP:0009813",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": true
+ "term_id": "HP:0009812",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0010704",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0005180",
- "is_present": true
+ "term_id": "HP:0001709",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0031134",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0010035",
- "is_present": true
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0010704",
- "is_present": true
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
- },
- {
- "term_id": "HP:0009777",
- "is_present": false
- },
- {
- "term_id": "HP:0001199",
- "is_present": false
- },
- {
- "term_id": "HP:0003974",
- "is_present": false
- },
- {
- "term_id": "HP:0002984",
- "is_present": false
- },
- {
- "term_id": "HP:0003022",
- "is_present": false
- },
- {
- "term_id": "HP:0005792",
- "is_present": false
- },
- {
- "term_id": "HP:0011664",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
- },
- {
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0002092",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -23865,7 +26406,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -23873,8 +26415,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385474,
- "end": 114385475,
+ "start": 114399624,
+ "end": 114399629,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -23884,9 +26426,9 @@
},
"strand": "POSITIVE"
},
- "ref": "C",
- "alt": "T",
- "change_length": 0
+ "ref": "ACATC",
+ "alt": "A",
+ "change_length": -4
},
"sv_info": null
},
@@ -23894,48 +26436,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.755+1G>A",
+ "hgvs_cdna": "NM_000192.3:c.246_249del",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "FRAMESHIFT_VARIANT"
+ ],
+ "overlapping_exons": [
+ 4
],
- "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_000183.2:p.Met83PhefsTer6",
+ "protein_effect_location": {
+ "start": 81,
+ "end": 83
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.605+1G>A",
+ "hgvs_cdna": "NM_080717.4:c.96_99del",
"is_preferred": false,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "FRAMESHIFT_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
],
- "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_542448.1:p.Met33PhefsTer6",
+ "protein_effect_location": {
+ "start": 31,
+ "end": 33
+ }
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.755+1G>A",
+ "hgvs_cdna": "NM_181486.4:c.246_249del",
"is_preferred": true,
"variant_effects": [
- "SPLICE_DONOR_VARIANT"
+ "FRAMESHIFT_VARIANT"
+ ],
+ "overlapping_exons": [
+ 4
],
- "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": null,
- "protein_effect_location": null
+ "hgvsp": "NP_852259.1:p.Met83PhefsTer6",
+ "protein_effect_location": {
+ "start": 81,
+ "end": 83
+ }
}
],
"genotypes": {
"samples": [
{
- "label": "III-1",
- "meta_label": "PMID_34490705_III_1"
+ "label": "Individual A",
+ "meta_label": "PMID_33866394_Individual_A"
}
],
"genotypes": [
@@ -23947,58 +26504,80 @@
},
{
"labels": {
- "label": "Individual A",
- "meta_label": "PMID_33866394_Individual_A"
+ "label": "Individual B",
+ "meta_label": "PMID_33866394_Individual_B"
},
"sex": "MALE",
+ "age": {
+ "days": 29585.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0009813",
- "is_present": true
+ "term_id": "HP:0001631",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": true
+ "term_id": "HP:0001199",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0010704",
- "is_present": true
+ "term_id": "HP:0003834",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001709",
- "is_present": true
+ "term_id": "HP:0001377",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0001233",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0009778",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001674",
- "is_present": false
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001655",
- "is_present": false
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0002092",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -24006,7 +26585,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -24014,8 +26594,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114399624,
- "end": 114399629,
+ "start": 114366240,
+ "end": 114366242,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -24025,9 +26605,9 @@
},
"strand": "POSITIVE"
},
- "ref": "ACATC",
- "alt": "A",
- "change_length": -4
+ "ref": "CT",
+ "alt": "C",
+ "change_length": -1
},
"sv_info": null
},
@@ -24035,63 +26615,63 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.246_249del",
+ "hgvs_cdna": "NM_000192.3:c.905del",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Met83PhefsTer6",
+ "hgvsp": "NP_000183.2:p.Gln302ArgfsTer92",
"protein_effect_location": {
- "start": 81,
- "end": 83
+ "start": 301,
+ "end": 302
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.96_99del",
+ "hgvs_cdna": "NM_080717.4:c.755del",
"is_preferred": false,
"variant_effects": [
"FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 3
+ 7
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Met33PhefsTer6",
+ "hgvsp": "NP_542448.1:p.Gln252ArgfsTer92",
"protein_effect_location": {
- "start": 31,
- "end": 33
+ "start": 251,
+ "end": 252
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.246_249del",
+ "hgvs_cdna": "NM_181486.4:c.905del",
"is_preferred": true,
"variant_effects": [
"FRAMESHIFT_VARIANT"
],
"overlapping_exons": [
- 4
+ 8
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Met83PhefsTer6",
+ "hgvsp": "NP_852259.1:p.Gln302ArgfsTer92",
"protein_effect_location": {
- "start": 81,
- "end": 83
+ "start": 301,
+ "end": 302
}
}
],
"genotypes": {
"samples": [
{
- "label": "Individual A",
- "meta_label": "PMID_33866394_Individual_A"
+ "label": "Individual B",
+ "meta_label": "PMID_33866394_Individual_B"
}
],
"genotypes": [
@@ -24103,66 +26683,117 @@
},
{
"labels": {
- "label": "K5:III-2",
- "meta_label": "PMID_12789647_K5_III_2"
+ "label": "III-1",
+ "meta_label": "PMID_34490705_III_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011623",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0001199",
- "is_present": true
+ "term_id": "HP:0002092",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0002984",
- "is_present": true
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0011682",
- "is_present": false
+ "term_id": "HP:0005180",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0031134",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0010035",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0010704",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001674",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001655",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009778",
- "is_present": false
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009813",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009812",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -24170,7 +26801,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -24178,8 +26810,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385562,
- "end": 114385563,
+ "start": 114385474,
+ "end": 114385475,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -24189,8 +26821,8 @@
},
"strand": "POSITIVE"
},
- "ref": "G",
- "alt": "A",
+ "ref": "C",
+ "alt": "T",
"change_length": 0
},
"sv_info": null
@@ -24199,63 +26831,48 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.668C>T",
+ "hgvs_cdna": "NM_000192.3:c.755+1G>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Thr223Met",
- "protein_effect_location": {
- "start": 222,
- "end": 223
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.518C>T",
+ "hgvs_cdna": "NM_080717.4:c.605+1G>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Thr173Met",
- "protein_effect_location": {
- "start": 172,
- "end": 173
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.668C>T",
+ "hgvs_cdna": "NM_181486.4:c.755+1G>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Thr223Met",
- "protein_effect_location": {
- "start": 222,
- "end": 223
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "K5:III-2",
- "meta_label": "PMID_12789647_K5_III_2"
+ "label": "III-1",
+ "meta_label": "PMID_34490705_III_1"
}
],
"genotypes": [
@@ -24267,30 +26884,112 @@
},
{
"labels": {
- "label": "proband III:1",
- "meta_label": "PMID_36444245_proband_III_1"
+ "label": "III-2",
+ "meta_label": "PMID_34490705_III_2"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
+ {
+ "term_id": "HP:0001684",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002092",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009778",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005301",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001643",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005180",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
{
"term_id": "HP:0009777",
- "is_present": true
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001199",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0003974",
- "is_present": true
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": true
+ "term_id": "HP:0002984",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": true
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": true
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -24298,7 +26997,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -24306,8 +27006,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385549,
- "end": 114385550,
+ "start": 114385474,
+ "end": 114385475,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -24317,9 +27017,9 @@
},
"strand": "POSITIVE"
},
- "ref": "A",
- "alt": "AATTATTCTCAG",
- "change_length": 11
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
},
"sv_info": null
},
@@ -24327,66 +27027,48 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.680_681insCTGAGAATAAT",
+ "hgvs_cdna": "NM_000192.3:c.755+1G>A",
"is_preferred": false,
"variant_effects": [
- "INFRAME_INSERTION",
- "STOP_RETAINED_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Ile227_Glu228insTer",
- "protein_effect_location": {
- "start": 226,
- "end": 227
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.530_531insCTGAGAATAAT",
+ "hgvs_cdna": "NM_080717.4:c.605+1G>A",
"is_preferred": false,
"variant_effects": [
- "INFRAME_INSERTION",
- "STOP_RETAINED_VARIANT"
- ],
- "overlapping_exons": [
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+ "SPLICE_DONOR_VARIANT"
],
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"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Ile177_Glu178insTer",
- "protein_effect_location": {
- "start": 176,
- "end": 177
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.680_681insCTGAGAATAAT",
+ "hgvs_cdna": "NM_181486.4:c.755+1G>A",
"is_preferred": true,
"variant_effects": [
- "INFRAME_INSERTION",
- "STOP_RETAINED_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Ile227_Glu228insTer",
- "protein_effect_location": {
- "start": 226,
- "end": 227
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "proband III:1",
- "meta_label": "PMID_36444245_proband_III_1"
+ "label": "III-2",
+ "meta_label": "PMID_34490705_III_2"
}
],
"genotypes": [
@@ -24398,66 +27080,102 @@
},
{
"labels": {
- "label": "Family B IV-1",
- "meta_label": "PMID_10077612_Family_B_IV_1"
+ "label": "II-2",
+ "meta_label": "PMID_34490705_II_2"
},
- "sex": "MALE",
+ "sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001631",
- "is_present": true
+ "term_id": "HP:0001684",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001629",
- "is_present": false
+ "term_id": "HP:0011623",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0011682",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001674",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001655",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002092",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009777",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0009778",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0001199",
- "is_present": false
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0003974",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0002984",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0003022",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005792",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0001191",
- "is_present": false
+ "term_id": "HP:0011664",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0031546",
- "is_present": false
+ "term_id": "HP:0009813",
+ "is_present": false,
+ "onset": null
},
{
- "term_id": "HP:0005301",
- "is_present": false
+ "term_id": "HP:0009812",
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011565",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0031297",
- "is_present": false
- },
- {
- "term_id": "HP:0001643",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -24465,7 +27183,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -24473,8 +27192,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
- "start": 114385520,
- "end": 114385521,
+ "start": 114385474,
+ "end": 114385475,
"contig": {
"name": "12",
"genbank_acc": "CM000674.2",
@@ -24494,63 +27213,48 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.710G>A",
+ "hgvs_cdna": "NM_000192.3:c.755+1G>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
+ "overlapping_exons": null,
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg237Gln",
- "protein_effect_location": {
- "start": 236,
- "end": 237
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.560G>A",
+ "hgvs_cdna": "NM_080717.4:c.605+1G>A",
"is_preferred": false,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 6
+ "SPLICE_DONOR_VARIANT"
],
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"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg187Gln",
- "protein_effect_location": {
- "start": 186,
- "end": 187
- }
+ "hgvsp": null,
+ "protein_effect_location": null
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.710G>A",
+ "hgvs_cdna": "NM_181486.4:c.755+1G>A",
"is_preferred": true,
"variant_effects": [
- "MISSENSE_VARIANT"
- ],
- "overlapping_exons": [
- 7
+ "SPLICE_DONOR_VARIANT"
],
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"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg237Gln",
- "protein_effect_location": {
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- "end": 237
- }
+ "hgvsp": null,
+ "protein_effect_location": null
}
],
"genotypes": {
"samples": [
{
- "label": "Family B IV-1",
- "meta_label": "PMID_10077612_Family_B_IV_1"
+ "label": "II-2",
+ "meta_label": "PMID_34490705_II_2"
}
],
"genotypes": [
@@ -24562,62 +27266,22 @@
},
{
"labels": {
- "label": "Family 1 Patient 2",
- "meta_label": "PMID_25216260_Family_1_Patient_2"
+ "label": "father II:1",
+ "meta_label": "PMID_36444245_father_II_1"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0011682",
- "is_present": true
- },
- {
- "term_id": "HP:0009778",
- "is_present": true
+ "term_id": "HP:0001629",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0001684",
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- {
- "term_id": "HP:0011565",
- "is_present": false
- },
- {
- "term_id": "HP:0031297",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -24625,7 +27289,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -24633,8 +27298,8 @@
"variant_info": {
"variant_coordinates": {
"region": {
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- "end": 114366267,
+ "start": 114385549,
+ "end": 114385550,
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@@ -24644,9 +27309,9 @@
},
"strand": "POSITIVE"
},
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- "alt": "A",
- "change_length": 0
+ "ref": "A",
+ "alt": "AATTATTCTCAG",
+ "change_length": 11
},
"sv_info": null
},
@@ -24654,63 +27319,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.880G>T",
+ "hgvs_cdna": "NM_000192.3:c.680_681insCTGAGAATAAT",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "INFRAME_INSERTION",
+ "STOP_RETAINED_VARIANT"
],
"overlapping_exons": [
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+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Glu294Ter",
+ "hgvsp": "NP_000183.2:p.Ile227_Glu228insTer",
"protein_effect_location": {
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- "end": 294
+ "start": 226,
+ "end": 227
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.730G>T",
+ "hgvs_cdna": "NM_080717.4:c.530_531insCTGAGAATAAT",
"is_preferred": false,
"variant_effects": [
- "STOP_GAINED"
+ "INFRAME_INSERTION",
+ "STOP_RETAINED_VARIANT"
],
"overlapping_exons": [
- 7
+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Glu244Ter",
+ "hgvsp": "NP_542448.1:p.Ile177_Glu178insTer",
"protein_effect_location": {
- "start": 243,
- "end": 244
+ "start": 176,
+ "end": 177
}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.880G>T",
+ "hgvs_cdna": "NM_181486.4:c.680_681insCTGAGAATAAT",
"is_preferred": true,
"variant_effects": [
- "STOP_GAINED"
+ "INFRAME_INSERTION",
+ "STOP_RETAINED_VARIANT"
],
"overlapping_exons": [
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+ 7
],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Glu294Ter",
+ "hgvsp": "NP_852259.1:p.Ile227_Glu228insTer",
"protein_effect_location": {
- "start": 293,
- "end": 294
+ "start": 226,
+ "end": 227
}
}
],
"genotypes": {
"samples": [
{
- "label": "Family 1 Patient 2",
- "meta_label": "PMID_25216260_Family_1_Patient_2"
+ "label": "father II:1",
+ "meta_label": "PMID_36444245_father_II_1"
}
],
"genotypes": [
@@ -24722,34 +27390,40 @@
},
{
"labels": {
- "label": "K15:II-2",
- "meta_label": "PMID_12789647_K15_II_2"
+ "label": "proband III:1",
+ "meta_label": "PMID_36444245_proband_III_1"
},
- "sex": "UNKNOWN_SEX",
+ "sex": "MALE",
+ "age": {
+ "days": 1826.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
"phenotypes": [
{
- "term_id": "HP:0001629",
- "is_present": true
- },
- {
- "term_id": "HP:0001684",
- "is_present": false
+ "term_id": "HP:0009777",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009813",
- "is_present": false
+ "term_id": "HP:0003974",
+ "is_present": true,
+ "onset": null
},
{
- "term_id": "HP:0009812",
- "is_present": false
+ "term_id": "HP:0005301",
+ "is_present": true,
+ "onset": null
},
{
"term_id": "HP:0011565",
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},
{
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+ "is_present": true,
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}
],
"measurements": [],
@@ -24757,7 +27431,8 @@
{
"term_id": "OMIM:142900",
"name": "Holt-Oram syndrome",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
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@@ -24765,8 +27440,8 @@
"variant_info": {
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"region": {
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- "end": 114398682,
+ "start": 114385549,
+ "end": 114385550,
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@@ -24776,9 +27451,9 @@
},
"strand": "POSITIVE"
},
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- "change_length": 1
+ "ref": "A",
+ "alt": "AATTATTCTCAG",
+ "change_length": 11
},
"sv_info": null
},
@@ -24786,63 +27461,66 @@
{
"gene_id": "TBX5",
"transcript_id": "NM_000192.3",
- "hgvs_cdna": "NM_000192.3:c.400dup",
+ "hgvs_cdna": "NM_000192.3:c.680_681insCTGAGAATAAT",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "INFRAME_INSERTION",
+ "STOP_RETAINED_VARIANT"
],
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+ 7
],
"protein_id": "NP_000183.2",
- "hgvsp": "NP_000183.2:p.Arg134ProfsTer49",
+ "hgvsp": "NP_000183.2:p.Ile227_Glu228insTer",
"protein_effect_location": {
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- "end": 134
+ "start": 226,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_080717.4",
- "hgvs_cdna": "NM_080717.4:c.250dup",
+ "hgvs_cdna": "NM_080717.4:c.530_531insCTGAGAATAAT",
"is_preferred": false,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "INFRAME_INSERTION",
+ "STOP_RETAINED_VARIANT"
],
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+ 6
],
"protein_id": "NP_542448.1",
- "hgvsp": "NP_542448.1:p.Arg84ProfsTer49",
+ "hgvsp": "NP_542448.1:p.Ile177_Glu178insTer",
"protein_effect_location": {
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+ "start": 176,
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}
},
{
"gene_id": "TBX5",
"transcript_id": "NM_181486.4",
- "hgvs_cdna": "NM_181486.4:c.400dup",
+ "hgvs_cdna": "NM_181486.4:c.680_681insCTGAGAATAAT",
"is_preferred": true,
"variant_effects": [
- "FRAMESHIFT_VARIANT"
+ "INFRAME_INSERTION",
+ "STOP_RETAINED_VARIANT"
],
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],
"protein_id": "NP_852259.1",
- "hgvsp": "NP_852259.1:p.Arg134ProfsTer49",
+ "hgvsp": "NP_852259.1:p.Ile227_Glu228insTer",
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+ "start": 226,
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}
}
],
"genotypes": {
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{
- "label": "K15:II-2",
- "meta_label": "PMID_12789647_K15_II_2"
+ "label": "proband III:1",
+ "meta_label": "PMID_36444245_proband_III_1"
}
],
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diff --git a/docs/cohort-data/UMOD.0.1.20.json b/docs/cohort-data/UMOD.0.1.20.json
new file mode 100644
index 00000000..853ee4f9
--- /dev/null
+++ b/docs/cohort-data/UMOD.0.1.20.json
@@ -0,0 +1,48491 @@
+{
+ "members": [
+ {
+ "labels": {
+ "label": "F524 individual II-1",
+ "meta_label": "PMID_14531790_F524_individual_II_1"
+ },
+ "sex": "MALE",
+ "age": {
+ "days": 10592.25,
+ "timeline": "POSTNATAL"
+ },
+ "vital_status": null,
+ "phenotypes": [
+ {
+ "term_id": "HP:0003774",
+ "is_present": true,
+ "onset": {
+ "days": 10592.25,
+ "timeline": "POSTNATAL"
+ }
+ },
+ {
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+ "is_present": true,
+ "onset": null
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+ {
+ "term_id": "HP:0032948",
+ "is_present": true,
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+ {
+ "term_id": "HP:0001997",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0002149",
+ "is_present": true,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0004722",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000096",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000822",
+ "is_present": false,
+ "onset": null
+ }
+ ],
+ "measurements": [],
+ "diseases": [
+ {
+ "term_id": "OMIM:162000",
+ "name": "Tubulointerstitial kidney disease, autosomal dominant, 1",
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
+ }
+ ],
+ "variants": [
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+ "end": 20348627,
+ "contig": {
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+ "genbank_acc": "CM000678.2",
+ "refseq_name": "NC_000016.10",
+ "ucsc_name": "chr16",
+ "length": 90338345
+ },
+ "strand": "POSITIVE"
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+ "ref": "G",
+ "alt": "T",
+ "change_length": 0
+ },
+ "sv_info": null
+ },
+ "tx_annotations": [
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_001008389.3",
+ "hgvs_cdna": "NM_001008389.3:c.674C>A",
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+ "timeline": "POSTNATAL"
+ }
+ },
+ {
+ "term_id": "HP:0003165",
+ "is_present": true,
+ "onset": {
+ "days": 4383.0,
+ "timeline": "POSTNATAL"
+ }
+ },
+ {
+ "term_id": "HP:0003158",
+ "is_present": true,
+ "onset": {
+ "days": 4383.0,
+ "timeline": "POSTNATAL"
+ }
+ },
+ {
+ "term_id": "HP:0003774",
+ "is_present": true,
+ "onset": {
+ "days": 5113.5,
+ "timeline": "POSTNATAL"
+ }
+ },
+ {
+ "term_id": "HP:0000108",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000794",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0001997",
+ "is_present": false,
+ "onset": null
+ },
+ {
+ "term_id": "HP:0000822",
+ "is_present": false,
+ "onset": null
+ }
+ ],
+ "measurements": [],
+ "diseases": [
+ {
+ "term_id": "OMIM:162000",
+ "name": "Tubulointerstitial kidney disease, autosomal dominant, 1",
+ "is_observed": true,
+ "onset": {
+ "days": 1095.75,
+ "timeline": "POSTNATAL"
+ }
+ }
+ ],
+ "variants": [
+ {
+ "variant_info": {
+ "variant_coordinates": {
+ "region": {
+ "start": 20348716,
+ "end": 20348717,
+ "contig": {
+ "name": "16",
+ "genbank_acc": "CM000678.2",
+ "refseq_name": "NC_000016.10",
+ "ucsc_name": "chr16",
+ "length": 90338345
+ },
+ "strand": "POSITIVE"
+ },
+ "ref": "C",
+ "alt": "T",
+ "change_length": 0
+ },
+ "sv_info": null
+ },
+ "tx_annotations": [
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_001008389.3",
+ "hgvs_cdna": "NM_001008389.3:c.584G>A",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
+ ],
+ "protein_id": "NP_001008390.1",
+ "hgvsp": "NP_001008390.1:p.Cys195Tyr",
+ "protein_effect_location": {
+ "start": 194,
+ "end": 195
+ }
+ },
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_001278614.2",
+ "hgvs_cdna": "NM_001278614.2:c.683G>A",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 4
+ ],
+ "protein_id": "NP_001265543.1",
+ "hgvsp": "NP_001265543.1:p.Cys228Tyr",
+ "protein_effect_location": {
+ "start": 227,
+ "end": 228
+ }
+ },
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_001378232.1",
+ "hgvs_cdna": "NM_001378232.1:c.584G>A",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 4
+ ],
+ "protein_id": "NP_001365161.1",
+ "hgvsp": "NP_001365161.1:p.Cys195Tyr",
+ "protein_effect_location": {
+ "start": 194,
+ "end": 195
+ }
+ },
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_001378233.1",
+ "hgvs_cdna": "NM_001378233.1:c.584G>A",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 4
+ ],
+ "protein_id": "NP_001365162.1",
+ "hgvsp": "NP_001365162.1:p.Cys195Tyr",
+ "protein_effect_location": {
+ "start": 194,
+ "end": 195
+ }
+ },
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_001378234.1",
+ "hgvs_cdna": "NM_001378234.1:c.584G>A",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
+ ],
+ "protein_id": "NP_001365163.1",
+ "hgvsp": "NP_001365163.1:p.Cys195Tyr",
+ "protein_effect_location": {
+ "start": 194,
+ "end": 195
+ }
+ },
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_001378235.1",
+ "hgvs_cdna": "NM_001378235.1:c.584G>A",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
+ ],
+ "protein_id": "NP_001365164.1",
+ "hgvsp": "NP_001365164.1:p.Cys195Tyr",
+ "protein_effect_location": {
+ "start": 194,
+ "end": 195
+ }
+ },
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_001378237.1",
+ "hgvs_cdna": "NM_001378237.1:c.584G>A",
+ "is_preferred": false,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 4
+ ],
+ "protein_id": "NP_001365166.1",
+ "hgvsp": "NP_001365166.1:p.Cys195Tyr",
+ "protein_effect_location": {
+ "start": 194,
+ "end": 195
+ }
+ },
+ {
+ "gene_id": "UMOD",
+ "transcript_id": "NM_003361.4",
+ "hgvs_cdna": "NM_003361.4:c.584G>A",
+ "is_preferred": true,
+ "variant_effects": [
+ "MISSENSE_VARIANT"
+ ],
+ "overlapping_exons": [
+ 3
+ ],
+ "protein_id": "NP_003352.2",
+ "hgvsp": "NP_003352.2:p.Cys195Tyr",
+ "protein_effect_location": {
+ "start": 194,
+ "end": 195
+ }
+ }
+ ],
+ "genotypes": {
+ "samples": [
+ {
+ "label": "patient",
+ "meta_label": "PMID_37487849_patient"
+ }
+ ],
+ "genotypes": [
+ "HETEROZYGOUS"
+ ]
+ }
+ }
+ ]
+ }
+ ],
+ "excluded_patient_count": 0
+}
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 96f34f9a..c49324de 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -60,9 +60,9 @@
# built documents.
#
# The short X.Y version.
-version = u'0.5'
+version = u'0.6'
# The full version, including alpha/beta/rc tags.
-release = u'0.5.0'
+release = u'0.6.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/docs/report/tbx5_frameshift_vs_missense.csv b/docs/report/tbx5_frameshift_vs_missense.csv
index 68eba0b7..2b37d5d4 100644
--- a/docs/report/tbx5_frameshift_vs_missense.csv
+++ b/docs/report/tbx5_frameshift_vs_missense.csv
@@ -1,36 +1,18 @@
Allele group,Missense,Missense,Frameshift,Frameshift,,
,Count,Percent,Count,Percent,Corrected p values,p values
-Ventricular septal defect [HP:0001629],31/60,52%,19/19,100%,0.0019104918312468707,5.6190936213143254e-05
-Absent thumb [HP:0009777],12/71,17%,14/31,45%,0.095684672664751,0.005628510156750059
-Patent ductus arteriosus [HP:0001643],3/37,8%,2/2,100%,0.15294646873594242,0.01349527665317139
-Triphalangeal thumb [HP:0001199],13/72,18%,13/32,41%,0.2176138034868934,0.02560162393963452
-Cardiac conduction abnormality [HP:0031546],14/36,39%,3/3,100%,0.5059634533318744,0.07440639019586388
-Secundum atrial septal defect [HP:0001684],14/35,40%,4/22,18%,0.8072294637445331,0.1424522583078588
-Muscular ventricular septal defect [HP:0011623],6/59,10%,6/25,24%,0.8196217102808717,0.1687456462342971
+Ventricular septal defect [HP:0001629],31/60,52%,19/19,100%,0.0008990549794102921,5.6190936213143254e-05
+Absent thumb [HP:0009777],12/71,17%,14/31,45%,0.04502808125400047,0.005628510156750059
+Triphalangeal thumb [HP:0001199],13/72,18%,13/32,41%,0.13654199434471745,0.02560162393963452
Hypoplasia of the radius [HP:0002984],30/62,48%,6/14,43%,1.0,0.7735491022101784
-Abnormal ventricular septum morphology [HP:0010438],31/31,100%,19/19,100%,1.0,1.0
Abnormal cardiac septum morphology [HP:0001671],62/62,100%,28/28,100%,1.0,1.0
Abnormal hand morphology [HP:0005922],53/53,100%,20/20,100%,1.0,1.0
Atrial septal defect [HP:0001631],42/44,95%,20/20,100%,1.0,1.0
Abnormal atrial septum morphology [HP:0011994],43/43,100%,20/20,100%,1.0,1.0
Abnormal cardiac atrium morphology [HP:0005120],43/43,100%,20/20,100%,1.0,1.0
Abnormal appendicular skeleton morphology [HP:0011844],64/64,100%,34/34,100%,1.0,1.0
-Upper limb undergrowth [HP:0009824],33/33,100%,7/7,100%,1.0,1.0
Aplasia/hypoplasia of the extremities [HP:0009815],55/55,100%,22/22,100%,1.0,1.0
Aplasia/hypoplasia involving the skeleton [HP:0009115],56/56,100%,23/23,100%,1.0,1.0
Aplasia/hypoplasia involving bones of the upper limbs [HP:0006496],55/55,100%,22/22,100%,1.0,1.0
Aplasia/hypoplasia involving bones of the extremities [HP:0045060],55/55,100%,22/22,100%,1.0,1.0
-Aplasia/hypoplasia involving forearm bones [HP:0006503],37/37,100%,12/12,100%,1.0,1.0
-Abnormal forearm bone morphology [HP:0040072],37/37,100%,14/14,100%,1.0,1.0
-Short long bone [HP:0003026],35/35,100%,9/9,100%,1.0,1.0
-Abnormal long bone morphology [HP:0011314],44/44,100%,13/13,100%,1.0,1.0
-Aplasia/Hypoplasia of the radius [HP:0006501],37/37,100%,11/11,100%,1.0,1.0
-Abnormal morphology of the radius [HP:0002818],37/37,100%,13/13,100%,1.0,1.0
-Short thumb [HP:0009778],11/41,27%,8/30,27%,1.0,1.0
-Aplasia/Hypoplasia of the thumb [HP:0009601],20/20,100%,19/19,100%,1.0,1.0
-Aplasia/Hypoplasia of fingers [HP:0006265],22/22,100%,19/19,100%,1.0,1.0
-Aplasia/hypoplasia involving bones of the hand [HP:0005927],22/22,100%,19/19,100%,1.0,1.0
Abnormal finger morphology [HP:0001167],36/36,100%,31/31,100%,1.0,1.0
Abnormal digit morphology [HP:0011297],38/38,100%,33/33,100%,1.0,1.0
-Abnormal thumb morphology [HP:0001172],30/30,100%,31/31,100%,1.0,1.0
-Absent radius [HP:0003974],7/32,22%,6/25,24%,1.0,1.0
diff --git a/docs/report/tbx5_frameshift_vs_missense.mtc_report.html b/docs/report/tbx5_frameshift_vs_missense.mtc_report.html
index 57eec9a2..96984566 100644
--- a/docs/report/tbx5_frameshift_vs_missense.mtc_report.html
+++ b/docs/report/tbx5_frameshift_vs_missense.mtc_report.html
@@ -48,9 +48,9 @@
Phenotype testing report
Phenotype MTC filter: HPO MTC filter
Multiple testing correction: fdr_bh
- Performed statistical tests for 34 out of the total of 260 HPO terms.
+ Performed statistical tests for 16 out of the total of 369 HPO terms.
- Using HPO MTC filter, 226 term(s) were omitted from statistical analysis.
+ Using HPO MTC filter, 353 term(s) were omitted from statistical analysis.
| Code |
@@ -60,26 +60,20 @@ Phenotype testing report
| HMF01 |
- Skipping term with maximum frequency that was less than threshold 0.2 |
- 51 |
-
-
-
- | HMF03 |
- Skipping term because of a child term with the same individual counts |
- 2 |
+ Skipping term with maximum frequency that was less than threshold 0.4 |
+ 94 |
| HMF08 |
Skipping general term |
- 44 |
+ 48 |
| HMF09 |
- Skipping term with maximum annotation frequency that was less than threshold 0.25 |
- 129 |
+ Skipping term with maximum annotation frequency that was less than threshold 0.4 |
+ 211 |
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
index 27717477..33056c03 100644
--- a/docs/tutorial.rst
+++ b/docs/tutorial.rst
@@ -110,10 +110,10 @@ GPSEA helps with gaining insight into the cohort by providing
Show cohort summary
-------------------
-The summary report provides an overview about the HPO terms, variants, diseases, and variant effects that occurr most frequently:
+The summary report provides an overview about the HPO terms, variants, diseases, and variant effects that occur most frequently:
->>> from gpsea.view import CohortViewable
->>> viewer = CohortViewable(hpo)
+>>> from gpsea.view import CohortViewer
+>>> viewer = CohortViewer(hpo)
>>> report = viewer.process(cohort=cohort, transcript_id=tx_id)
>>> report # doctest: +SKIP
@@ -204,7 +204,7 @@ in the individuals of the *TBX5* cohort.
>>> gt_predicate = monoallelic_predicate(
... a_predicate=VariantPredicates.variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id),
... b_predicate=VariantPredicates.variant_effect(VariantEffect.FRAMESHIFT_VARIANT, tx_id),
-... names=('Missense', 'Frameshift')
+... a_label="Missense", b_label="Frameshift",
... )
>>> gt_predicate.display_question()
'Allele group: Missense, Frameshift'
@@ -230,11 +230,9 @@ was excluded):
>>> pheno_predicates = prepare_predicates_for_terms_of_interest(
... cohort=cohort,
... hpo=hpo,
-... min_n_of_patients_with_term=2,
... )
-By default, GPSEA will perform one hypothesis test for each HPO term used to annotate two or more individuals in the cohort
-(see ``min_n_of_patients_with_term=2`` above).
+By default, GPSEA will perform one hypothesis test for each HPO term used to annotate at least one individual in the cohort.
Testing multiple hypothesis on the same dataset increases the chance of receiving false positive result.
However, GPSEA simplifies the application of an appropriate multiple testing correction.
@@ -252,7 +250,7 @@ with Benjamini-Hochberg procedure (``mtc_correction='fdr_bh'``)
with a false discovery control level at (``mtc_alpha=0.05``):
>>> from gpsea.analysis.mtc_filter import HpoMtcFilter
->>> mtc_filter = HpoMtcFilter.default_filter(hpo, term_frequency_threshold=0.2)
+>>> mtc_filter = HpoMtcFilter.default_filter(hpo)
>>> mtc_correction = 'fdr_bh'
>>> mtc_alpha = 0.05
@@ -281,15 +279,15 @@ Now we can perform the analysis and investigate the results.
... pheno_predicates=pheno_predicates,
... )
>>> result.total_tests
-34
+16
-We only tested 34 HPO terms. This is despite the individuals being collectively annotated with
-260 direct and indirect HPO terms
+We only tested 16 HPO terms. This is despite the individuals being collectively annotated with
+369 direct and indirect HPO terms
>>> len(result.phenotypes)
-260
+369
-We can show the reasoning behind *not* testing 226 (`260 - 34`) HPO terms
+We can show the reasoning behind *not* testing 353 (`369 - 16`) HPO terms
by exploring the phenotype MTC filtering report.
>>> from gpsea.view import MtcStatsViewer
@@ -328,4 +326,4 @@ was observed in 31/60 (52%) patients with a missense variant
but it was observed in 19/19 (100%) patients with a frameshift variant.
Fisher exact test computed a p value of `~0.0000562`
and the p value corrected by Benjamini-Hochberg procedure
-is `~0.001910`.
+is `~0.000899`.
diff --git a/docs/user-guide/analyses/index.rst b/docs/user-guide/analyses/index.rst
index 85a8700d..39f86254 100644
--- a/docs/user-guide/analyses/index.rst
+++ b/docs/user-guide/analyses/index.rst
@@ -18,3 +18,4 @@ and explanations of how they are implemented by our software.
phenotype-groups
phenotype-scores
measurements
+ survival
diff --git a/docs/user-guide/analyses/measurements.rst b/docs/user-guide/analyses/measurements.rst
index 856ee79f..0d9f0509 100644
--- a/docs/user-guide/analyses/measurements.rst
+++ b/docs/user-guide/analyses/measurements.rst
@@ -66,7 +66,7 @@ Assuming AR inheritance, we compare missense vs. rest:
>>> gt_predicate = biallelic_predicate(
... a_predicate=is_missense,
... b_predicate=~is_missense,
-... names=('Missense', 'Other'),
+... a_label="Missense", b_label="Other",
... partitions=({0,}, {1, 2}),
... )
>>> gt_predicate.display_question()
diff --git a/docs/user-guide/analyses/phenotype-groups.rst b/docs/user-guide/analyses/phenotype-groups.rst
index a2377423..21300a91 100644
--- a/docs/user-guide/analyses/phenotype-groups.rst
+++ b/docs/user-guide/analyses/phenotype-groups.rst
@@ -159,13 +159,12 @@ and then we can create the predicates
>>> pheno_predicates = prepare_predicates_for_terms_of_interest(
... cohort=cohort,
... hpo=hpo,
-... min_n_of_patients_with_term=2,
... )
>>> len(pheno_predicates)
-260
+369
-The function finds all HPO terms that annotate at least *n* (``min_n_of_patients_with_term=2`` above) individuals,
-including the *indirect* annotations whose presence is implied by the true path rule.
+The function finds 369 HPO terms that annotate at least one individual,
+including the *indirect* annotations whose presence is implied by the :ref:`true-path-rule`.
Statistical test
@@ -228,12 +227,12 @@ We can now execute the analysis:
... pheno_predicates=pheno_predicates,
... )
>>> len(result.phenotypes)
-260
+369
>>> result.total_tests
-38
+24
-Thanks to phenotype MTC filter, we only tested 38 out of 260 terms.
+Thanks to phenotype MTC filter, we only tested 24 out of 369 terms.
We can learn more by showing the MTC filter report:
>>> from gpsea.view import MtcStatsViewer
@@ -273,9 +272,9 @@ ordered by the corrected p value (Benjamini-Hochberg FDR):
The table shows that several HPO terms are significantly associated
with presence of a heterozygous (`Monoallelic`) frameshift variant in *TBX5*.
For example, `Ventricular septal defect `_
-was observed in 42/71 (59%) patients with a missense variant
-but it was observed in 19/19 (100%) patients with a frameshift variant.
+was observed in 42/71 (59%) patients with no frameshift allele (`No allele`)
+but it was observed in 19/19 (100%) patients with a frameshift allele (`Monoallelic`).
Fisher exact test computed a p value of `~0.000242`
and the p value corrected by Benjamini-Hochberg procedure
-is `~0.00919`.
+is `~0.005806`.
diff --git a/docs/user-guide/analyses/phenotype-scores.rst b/docs/user-guide/analyses/phenotype-scores.rst
index 1db43195..91525d5d 100644
--- a/docs/user-guide/analyses/phenotype-scores.rst
+++ b/docs/user-guide/analyses/phenotype-scores.rst
@@ -128,7 +128,7 @@ The genotype predicate will bin the patient into two groups: a point mutation gr
>>> gt_predicate = monoallelic_predicate(
... a_predicate=point_mutation,
... b_predicate=lof_mutation,
-... names=('Point', 'LoF'),
+... a_label="Point", b_label="LoF",
... )
>>> gt_predicate.display_question()
'Allele group: Point, LoF'
diff --git a/docs/user-guide/analyses/report/tbx5_frameshift.csv b/docs/user-guide/analyses/report/tbx5_frameshift.csv
index f9e20f85..f02767d1 100644
--- a/docs/user-guide/analyses/report/tbx5_frameshift.csv
+++ b/docs/user-guide/analyses/report/tbx5_frameshift.csv
@@ -1,40 +1,26 @@
What is the genotype group,No allele,No allele,Monoallelic,Monoallelic,,
,Count,Percent,Count,Percent,Corrected p values,p values
-Ventricular septal defect [HP:0001629],42/71,59%,19/19,100%,0.009193214651997994,0.00024192670136836825
-Absent thumb [HP:0009777],18/100,18%,14/31,45%,0.07055975880437862,0.003713671516019927
-Patent ductus arteriosus [HP:0001643],6/40,15%,2/2,100%,0.4119241192411924,0.03252032520325203
-Secundum atrial septal defect [HP:0001684],23/55,42%,4/22,18%,0.45983847234923847,0.06544319142266644
-Triphalangeal thumb [HP:0001199],23/99,23%,13/32,41%,0.45983847234923847,0.06932119159387057
-Cardiac conduction abnormality [HP:0031546],15/37,41%,3/3,100%,0.45983847234923847,0.08259109311740892
-Muscular ventricular septal defect [HP:0011623],8/84,10%,6/25,24%,0.45983847234923847,0.08470708701170182
+Ventricular septal defect [HP:0001629],42/71,59%,19/19,100%,0.005806240832840839,0.00024192670136836825
+Absent thumb [HP:0009777],18/100,18%,14/31,45%,0.044564058192239124,0.003713671516019927
+Secundum atrial septal defect [HP:0001684],23/55,42%,4/22,18%,0.4065940176561687,0.06544319142266644
+Triphalangeal thumb [HP:0001199],23/99,23%,13/32,41%,0.4065940176561687,0.06932119159387057
+Muscular ventricular septal defect [HP:0011623],8/84,10%,6/25,24%,0.4065940176561687,0.08470708701170182
Short thumb [HP:0009778],25/69,36%,8/30,27%,1.0,0.48700997145537483
Absent radius [HP:0003974],9/43,21%,6/25,24%,1.0,0.7703831604944444
-Abnormal ventricular septum morphology [HP:0010438],42/42,100%,19/19,100%,1.0,1.0
-Abnormal cardiac ventricle morphology [HP:0001713],43/43,100%,19/19,100%,1.0,1.0
Abnormal cardiac septum morphology [HP:0001671],89/89,100%,28/28,100%,1.0,1.0
Abnormal hand morphology [HP:0005922],75/75,100%,20/20,100%,1.0,1.0
-Abnormal joint morphology [HP:0001367],33/33,100%,6/6,100%,1.0,1.0
Atrial septal defect [HP:0001631],63/65,97%,20/20,100%,1.0,1.0
Abnormal atrial septum morphology [HP:0011994],64/64,100%,20/20,100%,1.0,1.0
Abnormal cardiac atrium morphology [HP:0005120],64/64,100%,20/20,100%,1.0,1.0
Hypoplasia of the radius [HP:0002984],34/75,45%,6/14,43%,1.0,1.0
-Forearm undergrowth [HP:0009821],35/35,100%,7/7,100%,1.0,1.0
Abnormal appendicular skeleton morphology [HP:0011844],93/93,100%,34/34,100%,1.0,1.0
-Upper limb undergrowth [HP:0009824],38/38,100%,7/7,100%,1.0,1.0
Aplasia/hypoplasia of the extremities [HP:0009815],78/78,100%,22/22,100%,1.0,1.0
Aplasia/hypoplasia involving the skeleton [HP:0009115],80/80,100%,23/23,100%,1.0,1.0
Aplasia/hypoplasia involving bones of the upper limbs [HP:0006496],78/78,100%,22/22,100%,1.0,1.0
Aplasia/hypoplasia involving bones of the extremities [HP:0045060],78/78,100%,22/22,100%,1.0,1.0
-Aplasia/hypoplasia involving forearm bones [HP:0006503],43/43,100%,12/12,100%,1.0,1.0
-Abnormal forearm bone morphology [HP:0040072],43/43,100%,14/14,100%,1.0,1.0
-Short long bone [HP:0003026],41/41,100%,9/9,100%,1.0,1.0
Abnormal long bone morphology [HP:0011314],50/50,100%,13/13,100%,1.0,1.0
-Aplasia/Hypoplasia of the radius [HP:0006501],43/43,100%,11/11,100%,1.0,1.0
-Abnormal morphology of the radius [HP:0002818],43/43,100%,13/13,100%,1.0,1.0
-Aplasia/Hypoplasia of the thumb [HP:0009601],40/40,100%,19/19,100%,1.0,1.0
Aplasia/Hypoplasia of fingers [HP:0006265],44/44,100%,19/19,100%,1.0,1.0
Aplasia/hypoplasia involving bones of the hand [HP:0005927],44/44,100%,19/19,100%,1.0,1.0
Abnormal finger morphology [HP:0001167],64/64,100%,31/31,100%,1.0,1.0
Abnormal digit morphology [HP:0011297],67/67,100%,33/33,100%,1.0,1.0
Abnormal thumb morphology [HP:0001172],58/58,100%,31/31,100%,1.0,1.0
-Abnormality of thumb phalanx [HP:0009602],26/26,100%,13/13,100%,1.0,1.0
diff --git a/docs/user-guide/analyses/report/tbx5_frameshift.mtc_report.html b/docs/user-guide/analyses/report/tbx5_frameshift.mtc_report.html
index 01be462a..15fe3cd5 100644
--- a/docs/user-guide/analyses/report/tbx5_frameshift.mtc_report.html
+++ b/docs/user-guide/analyses/report/tbx5_frameshift.mtc_report.html
@@ -48,9 +48,9 @@
Phenotype testing report
Phenotype MTC filter: HPO MTC filter
Multiple testing correction: fdr_bh
- Performed statistical tests for 38 out of the total of 260 HPO terms.
+ Performed statistical tests for 24 out of the total of 369 HPO terms.
- Using HPO MTC filter, 222 term(s) were omitted from statistical analysis.
+ Using HPO MTC filter, 345 term(s) were omitted from statistical analysis.
| Code |
@@ -64,22 +64,16 @@ Phenotype testing report
10 |
-
- | HMF03 |
- Skipping term because of a child term with the same individual counts |
- 1 |
-
-
| HMF08 |
Skipping general term |
- 44 |
+ 48 |
| HMF09 |
- Skipping term with maximum annotation frequency that was less than threshold 0.25 |
- 167 |
+ Skipping term with maximum annotation frequency that was less than threshold 0.4 |
+ 287 |
diff --git a/docs/user-guide/analyses/survival.rst b/docs/user-guide/analyses/survival.rst
new file mode 100644
index 00000000..109ec55d
--- /dev/null
+++ b/docs/user-guide/analyses/survival.rst
@@ -0,0 +1,155 @@
+.. _survival:
+
+=================
+Survival analysis
+=================
+
+
+****************
+Example analysis
+****************
+
+We will analyze the time until end stage renal disease in 207 individuals with mutations in *UMOD*.
+Specifically, we will test for difference between the onset of the end stage renal disease in the individuals with mutation
+in exon 3 of *UMOD* vs. individuals with other *UMOD* mutation.
+
+
+Load cohort
+===========
+
+For the purpose of this analysis, we will load the :class:`~gpsea.model.Cohort`
+from a `JSON file `_.
+The cohort was prepared from phenopackets as described in :ref:`create-cohort-from-phenopackets` section,
+and then serialized as a JSON file following the instructions in :ref:`cohort-persistence` section.
+
+..
+ Prepare the JSON file by running the tests in `tests/tests/test_generate_doc_cohorts.py`.
+
+>>> import json
+>>> from gpsea.io import GpseaJSONDecoder
+>>> fpath_cohort_json = 'docs/cohort-data/UMOD.0.1.20.json'
+>>> with open(fpath_cohort_json) as fh:
+... cohort = json.load(fh, cls=GpseaJSONDecoder)
+>>> len(cohort)
+207
+
+
+Configure analysis
+==================
+
+*MANE* transcript of *UMOD*.
+
+>>> tx_id = 'NM_003361.4'
+
+Genotype predicate
+------------------
+
+One allele of exon 3 vs. one allele of elsewhere.
+
+>>> from gpsea.analysis.predicate.genotype import VariantPredicates
+>>> is_in_exon3 = VariantPredicates.exon(exon=3, tx_id=tx_id)
+>>> is_in_exon3.get_question()
+'variant affects exon 3 on NM_003361.4'
+
+Monoallelic predicate to compare one allele of *UMOD* exon 3 variant
+versus one allele of other *UMOD* variant:
+
+>>> from gpsea.analysis.predicate.genotype import monoallelic_predicate
+>>> gt_predicate = monoallelic_predicate(
+... a_predicate=is_in_exon3,
+... b_predicate=~is_in_exon3,
+... a_label="Exon 3", b_label="Other",
+... )
+>>> gt_predicate.display_question()
+'Allele group: Exon 3, Other'
+
+
+Survival endpoint
+-----------------
+
+The endpoint of our study is defined as development of end stage renal disease.
+In the *UMOD* cohort, this is encoded with
+`Stage 5 chronic kidney disease `_
+(`HP:0003774`) HPO term.
+We need to leverage the HPO hierarchy when computing
+the onset of an HPO term. Let's load HPO:
+
+>>> import hpotk
+>>> store = hpotk.configure_ontology_store()
+>>> hpo = store.load_minimal_hpo(release='v2024-07-01')
+
+and now we can create an :class:`~gpsea.analysis.temporal.Endpoint`
+to compute the time until an individual develops end stage renal disease:
+
+>>> from gpsea.analysis.temporal.endpoint import hpo_onset
+>>> term_id = "HP:0003774" # Stage 5 chronic kidney disease
+>>> endpoint = hpo_onset(hpo=hpo, term_id=term_id)
+>>> endpoint.display_question()
+'Compute time until postnatal onset of Stage 5 chronic kidney disease'
+
+
+Statistical test
+----------------
+
+We will use Log rank test to compare the age until the endpoint between
+the genotype groups:
+
+>>> from gpsea.analysis.temporal.stats import LogRankTest
+>>> survival_statistic = LogRankTest()
+
+Final analysis
+--------------
+
+We will put the final analysis together into :class:`~gpsea.analysis.temporal.PhenotypeScoreAnalysis`.
+
+>>> from gpsea.analysis.temporal import SurvivalAnalysis
+>>> survival_analysis = SurvivalAnalysis(
+... statistic=survival_statistic,
+... )
+
+Analysis
+========
+
+We execute the analysis by running
+
+>>> result = survival_analysis.compare_genotype_vs_survival(
+... cohort=cohort,
+... gt_predicate=gt_predicate,
+... endpoint=endpoint,
+... )
+
+>>> result.pval
+0.06200425830044376
+
+
+Kaplan-Meier curves
+-------------------
+
+
+We can plot Kaplan-Meier curves:
+
+TODO: implement!
+
+
+Raw data
+--------
+
+The `result` includes the survival values for all cohort members:
+
+>>> survivals = result.data.sort_index()
+>>> survivals.head() # doctest: +NORMALIZE_WHITESPACE
+ genotype survival
+patient_id
+AII.1[PMID_22034507_AII_1] 0 Survival(value=18262.5, is_censored=True)
+AII.2[PMID_22034507_AII_2] 0 None
+AII.3[PMID_22034507_AII_3] 0 Survival(value=16436.25, is_censored=True)
+AII.5[PMID_22034507_AII_5] 0 Survival(value=22280.25, is_censored=False)
+AIII.4[PMID_22034507_AIII_4] 0 Survival(value=19723.5, is_censored=False)
+
+Each line corresponeds to an individual and the dataframe is indexed by the individual's identifier/label.
+The `genotype` column contains the genotype group code,
+and `survival` column includes a :class:`~gpsea.analysis.temporal.Survival` value
+or `None` if computing the survival was impossible (see :func:`~gpsea.analysis.temporal.endpoint.hpo_onset` for details).
+The `Survival` reports the number of days until attaining the endpoint,
+here defined as end stage renal disease (`is_censored=False`),
+or until the individual dropped out of the analysis (`is_censored=True`).
diff --git a/docs/user-guide/exploratory.rst b/docs/user-guide/exploratory.rst
index 1f80500e..568e7cb0 100644
--- a/docs/user-guide/exploratory.rst
+++ b/docs/user-guide/exploratory.rst
@@ -89,7 +89,7 @@ Interactive exploration
We designed GPSEA to integrate with interactive Python with a widespread use
in contemporary scientific workflows.
-The code for exploration is located in :mod:`gpsea.view` module.
+The code for exploration is located in :mod:`gpsea.view` module.
As a rule of thumb, the reports are provided as :class:`~gpsea.view.GpseaReport`
which leverages IPython's "magic" to integrate with environments such as Jupyter notebook.
@@ -98,10 +98,10 @@ Cohort summary
--------------
We recommend that users start be generating a cohort summary
-with an overview about the HPO terms, variants, diseases, and variant effects that occurr most frequently:
+with an overview about the HPO terms, variants, diseases, and variant effects that occur most frequently:
->>> from gpsea.view import CohortViewable
->>> viewer = CohortViewable(hpo)
+>>> from gpsea.view import CohortViewer
+>>> viewer = CohortViewer(hpo)
>>> report = viewer.process(cohort=cohort, transcript_id=tx_id)
>>> report # doctest: +SKIP
@@ -178,3 +178,4 @@ We use Matplotlib to plot the distribution of variants on a protein diagram:
>>> fig.tight_layout()
>>> fig.savefig('docs/user-guide/img/TBX5_protein_diagram.png') # doctest: +SKIP
+
diff --git a/docs/user-guide/mtc.rst b/docs/user-guide/mtc.rst
index d797a709..ffae4ded 100644
--- a/docs/user-guide/mtc.rst
+++ b/docs/user-guide/mtc.rst
@@ -165,6 +165,8 @@ we pass an iterable (e.g. a tuple) with these two terms as an argument:
... "HP:0002339", # Abnormal caudate nucleus morphology
... )
... )
+>>> len(specified_terms.terms_to_test)
+2
.. _hpo-mtc-filter-strategy:
@@ -182,15 +184,12 @@ The strategy needs access to HPO:
and it is implemented in the :class:`~gpsea.analysis.mtc_filter.HpoMtcFilter` class:
>>> from gpsea.analysis.mtc_filter import HpoMtcFilter
->>> hpo_mtc = HpoMtcFilter.default_filter(
-... hpo=hpo,
-... term_frequency_threshold=0.2,
-... )
+>>> hpo_mtc = HpoMtcFilter.default_filter(hpo=hpo)
We use static constructor :func:`~gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter`
for creating :class:`~gpsea.analysis.mtc_filter.HpoMtcFilter`.
-The constructor takes a threshold as an argument (e.g. 20% in the example above)
+The constructor takes a ``term_frequency_threshold`` option (40% by default)
and the method's logic is made up of 8 individual heuristics
designed to skip testing the HPO terms that are unlikely to yield significant or interesting results.
@@ -276,4 +275,21 @@ that if there is a signal from the nervous system,
it will lead to at least one of the descendents of
*Abnormality of the nervous system* being significant.
+
+`HMF09` - Skipping terms that are rare on the cohort level
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+We skip terms that occur in less than a certain percentage of cohort members.
+The purpose of this threshold is to omit terms for which we simply
+do not have much data overall.
+
+For instance, if the cohort consists of 100 individuals,
+and we have explicit observed observations for 20 and excluded for 10 individuals,
+then the annotation frequency is `0.3`.
+
+The threshold is set as ``annotation_frequency_threshold`` option
+of the :func:`~gpsea.analysis.mtc_filter.HpoMtcFilter.default_filter` constructor,
+with the default value of `0.4` (40%).
+
+
See :ref:`general-hpo-terms` section for details.
diff --git a/docs/user-guide/predicates/allele_count_predicates.rst b/docs/user-guide/predicates/allele_count_predicates.rst
index 54e1ff80..b358c481 100644
--- a/docs/user-guide/predicates/allele_count_predicates.rst
+++ b/docs/user-guide/predicates/allele_count_predicates.rst
@@ -65,7 +65,8 @@ and frameshift (`B`) variants:
Monoallelic predicate lets us customize the category names.
Let's use `Missense` and `Frameshift` instead of the defaults `A` and `B`:
->>> names = ("Missense", "Frameshift")
+>>> a_label = "Missense"
+>>> b_label = "Frameshift"
Now we have all we need to create the monoallelic predicate:
@@ -73,7 +74,7 @@ Now we have all we need to create the monoallelic predicate:
>>> gt_predicate = monoallelic_predicate(
... a_predicate=is_missense,
... b_predicate=is_frameshift,
-... names=names,
+... a_label=a_label, b_label=b_label,
... )
>>> gt_predicate.display_question()
'Allele group: Missense, Frameshift'
@@ -154,7 +155,7 @@ and we will use the same allele group names as before - `Missense` and `Frameshi
>>> gt_predicate = biallelic_predicate(
... a_predicate=is_missense,
... b_predicate=is_frameshift,
-... names=names,
+... a_label=a_label, b_label=b_label,
... )
>>> gt_predicate.display_question()
'Allele group: Missense/Missense, Missense/Frameshift, Frameshift/Frameshift'
@@ -191,7 +192,7 @@ to the :func:`~gpsea.analysis.predicate.genotype.biallelic_predicate` function:
>>> gt_predicate = biallelic_predicate(
... a_predicate=is_missense,
... b_predicate=is_frameshift,
-... names=names,
+... a_label=a_label, b_label=b_label,
... partitions=partitions,
... )
>>> gt_predicate.display_question()
diff --git a/docs/user-guide/predicates/hpo_predicate.rst b/docs/user-guide/predicates/hpo_predicate.rst
index 177170cf..5da37b1f 100644
--- a/docs/user-guide/predicates/hpo_predicate.rst
+++ b/docs/user-guide/predicates/hpo_predicate.rst
@@ -74,7 +74,7 @@ processed into a cohort
Individuals Processed: ...
-we can create HPO predicates for testing all 260 HPO terms used in the cohort
+we can create HPO predicates for testing all 369 HPO terms used in the cohort
>>> from gpsea.analysis.predicate.phenotype import prepare_predicates_for_terms_of_interest
>>> pheno_predicates = prepare_predicates_for_terms_of_interest(
@@ -82,6 +82,6 @@ we can create HPO predicates for testing all 260 HPO terms used in the cohort
... hpo=hpo,
... )
>>> len(pheno_predicates)
-260
+369
and subject the predicates into further analysis, such as :class:`~gpsea.analysis.pcats.HpoTermAnalysis`.
diff --git a/src/gpsea/__init__.py b/src/gpsea/__init__.py
index aa5b1a9a..717151dc 100644
--- a/src/gpsea/__init__.py
+++ b/src/gpsea/__init__.py
@@ -2,4 +2,4 @@
GPSEA is a library for analyzing genotype-phenotype correlations in cohorts of rare disease patients.
"""
-__version__ = "0.5.0"
+__version__ = "0.6.0"
diff --git a/src/gpsea/analysis/mtc_filter/_impl.py b/src/gpsea/analysis/mtc_filter/_impl.py
index 6255ce5a..f9415288 100644
--- a/src/gpsea/analysis/mtc_filter/_impl.py
+++ b/src/gpsea/analysis/mtc_filter/_impl.py
@@ -5,7 +5,6 @@
from collections import deque
import hpotk
-import numpy as np
import pandas as pd
from ..predicate.genotype import GenotypePolyPredicate
@@ -191,17 +190,21 @@ class SpecifiedTermsMtcFilter(PhenotypeMtcFilter[hpotk.TermId]):
NON_SPECIFIED_TERM = PhenotypeMtcResult.fail(code="ST1", reason="Non-specified term")
"""
The MTC filtering result returned when an HPO term does not belong among the selection of terms to be tested.
+
+ :param terms_to_test: an iterable of items of CURIE `str` or :class:`~hpotk.TermId` representing the terms to test.
"""
def __init__(
self,
- terms_to_test: typing.Iterable[hpotk.TermId],
+ terms_to_test: typing.Iterable[typing.Union[str, hpotk.TermId]],
):
- """
- Args:
- terms_to_test: an iterable of TermIds representing the terms to test
- """
- self._terms_to_test_set = set(terms_to_test)
+ self._terms_to_test = tuple(
+ SpecifiedTermsMtcFilter.verify_term_id(val) for val in terms_to_test
+ )
+
+ @property
+ def terms_to_test(self) -> typing.Collection[hpotk.TermId]:
+ return self._terms_to_test
def filter(
self,
@@ -212,7 +215,7 @@ def filter(
) -> typing.Sequence[PhenotypeMtcResult]:
results = []
for predicate in ph_predicates:
- if predicate.phenotype in self._terms_to_test_set:
+ if predicate.phenotype in self._terms_to_test:
results.append(SpecifiedTermsMtcFilter.OK)
else:
results.append(SpecifiedTermsMtcFilter.NON_SPECIFIED_TERM)
@@ -226,6 +229,15 @@ def possible_results(self) -> typing.Collection[PhenotypeMtcResult]:
def filter_method_name(self) -> str:
return "Specified terms MTC filter"
+
+ @staticmethod
+ def verify_term_id(val: typing.Union[str, hpotk.TermId]) -> hpotk.TermId:
+ if isinstance(val, str):
+ return hpotk.TermId.from_curie(val)
+ elif isinstance(val, hpotk.TermId):
+ return val
+ else:
+ raise ValueError(f"{val} is neither `str` nor `hpotk.TermId`")
class HpoMtcFilter(PhenotypeMtcFilter[hpotk.TermId]):
@@ -253,8 +265,8 @@ class HpoMtcFilter(PhenotypeMtcFilter[hpotk.TermId]):
@staticmethod
def default_filter(
hpo: hpotk.MinimalOntology,
- term_frequency_threshold: float = 0.2,
- annotation_frequency_threshold: float = 0.25,
+ term_frequency_threshold: float = 0.4,
+ annotation_frequency_threshold: float = 0.4,
phenotypic_abnormality: hpotk.TermId = hpotk.constants.hpo.base.PHENOTYPIC_ABNORMALITY,
):
"""
@@ -263,12 +275,13 @@ def default_filter(
term_frequency_threshold: a `float` in range :math:`(0, 1]` with the minimum frequency
for an HPO term to have in at least one of the genotype groups
(e.g., 22% in missense and 3% in nonsense genotypes would be OK,
- but not 13% missense and 10% nonsense genotypes if the threshold is 0.2)
+ but not 13% missense and 10% nonsense genotypes if the threshold is 0.2).
+ The default threshold is `0.4` (40%).
annotation_frequency_threshold: a `float` in range :math:`(0, 1) with the minimum frequency of
annotation in the cohort. For instance, if the cohort consists of 100 individuals, and
we have explicit observed observations for 20 and excluded for 10 individuals, then the
- annotation frequency is 0.3. By default, we set a threshold of 25%. The purpose of this
- threshold is to omit terms for which we simply do not have much data overall.
+ annotation frequency is `0.3`. The purpose of this threshold is to omit terms for which
+ we simply do not have much data overall. By default, we set a threshold to `0.4` (40%).
phenotypic_abnormality: a :class:`~hpotk.TermId` corresponding to the root of HPO phenotype hierarchy.
Having to specify this option should be very rarely, if ever.
"""
@@ -325,15 +338,6 @@ def __init__(
annotation_frequency_threshold: float,
general_hpo_terms: typing.Iterable[hpotk.TermId],
):
- """
- Args:
- hpo: reference to HPO ontology object
- term_frequency_threshold: a `float` in range :math:`(0, 1]` with the minimum frequency
- for an HPO term to have in at least one of the genotype groups
- (e.g., 22% in missense and 3% in nonsense genotypes would be OK,
- but not 13% missense and 10% nonsense genotypes if the threshold is 0.2)
- annotation_frequency_threshold: a `float` in range :math:`(0, 1) with the minimum frequency of annotation
- """
self._hpo = hpo
self._hpo_term_frequency_filter = term_frequency_threshold
self._hpo_annotation_frequency_threshold = annotation_frequency_threshold
diff --git a/src/gpsea/analysis/predicate/genotype/_gt_predicates.py b/src/gpsea/analysis/predicate/genotype/_gt_predicates.py
index 4f2d34c1..61323b27 100644
--- a/src/gpsea/analysis/predicate/genotype/_gt_predicates.py
+++ b/src/gpsea/analysis/predicate/genotype/_gt_predicates.py
@@ -165,7 +165,8 @@ def qc_partitions(
def build_count_to_cat(
- names: typing.Tuple[str, str],
+ a_label: str,
+ b_label: str,
partitions: typing.Iterable[typing.Iterable[int]],
) -> typing.Mapping[typing.Tuple[int, int], Categorization]:
# NOT PART OF THE PUBLIC API
@@ -176,9 +177,9 @@ def build_count_to_cat(
)
partition2label = (
- f"{names[0]}/{names[0]}",
- f"{names[0]}/{names[1]}",
- f"{names[1]}/{names[1]}",
+ f"{a_label}/{a_label}",
+ f"{a_label}/{b_label}",
+ f"{b_label}/{b_label}",
)
ac2cat = {}
@@ -211,17 +212,18 @@ class PolyCountingGenotypePredicate(GenotypePolyPredicate):
def monoallelic(
a_predicate: VariantPredicate,
b_predicate: VariantPredicate,
- names: typing.Tuple[str, str],
+ a_label: str,
+ b_label: str,
) -> "PolyCountingGenotypePredicate":
count2cat = {
(1, 0): Categorization(
PatientCategory(
- cat_id=0, name=names[0], description=f"Monoallelic {names[0]}"
+ cat_id=0, name=a_label, description=f"Monoallelic {a_label}"
)
),
(0, 1): Categorization(
PatientCategory(
- cat_id=1, name=names[1], description=f"Monoallelic {names[1]}"
+ cat_id=1, name=b_label, description=f"Monoallelic {b_label}"
)
),
}
@@ -236,10 +238,15 @@ def monoallelic(
def biallelic(
a_predicate: VariantPredicate,
b_predicate: VariantPredicate,
- names: typing.Tuple[str, str],
+ a_label: str,
+ b_label: str,
partitions: typing.Iterable[typing.Iterable[int]],
) -> "PolyCountingGenotypePredicate":
- count2cat = build_count_to_cat(names, partitions=partitions)
+ count2cat = build_count_to_cat(
+ a_label=a_label,
+ b_label=b_label,
+ partitions=partitions,
+ )
return PolyCountingGenotypePredicate.for_predicates_and_categories(
count2cat=count2cat,
@@ -314,7 +321,8 @@ def __hash__(self) -> int:
def monoallelic_predicate(
a_predicate: VariantPredicate,
b_predicate: VariantPredicate,
- names: typing.Tuple[str, str] = ("A", "B"),
+ a_label: str = "A",
+ b_label: str = "B",
) -> GenotypePolyPredicate:
"""
The predicate bins patient into one of two groups, `A` and `B`,
@@ -327,19 +335,25 @@ def monoallelic_predicate(
meet the criteria of the first group (named `A` by default).
:param b_predicate: predicate to test if the variants
meet the criteria of the second group (named `B` by default).
- :param names: group names (default ``('A', 'B')``).
+ :param a_label: display name of the `a_predicate` (default ``"A"``).
+ :param b_label: display name of the `b_predicate` (default ``"B"``).
"""
+ assert isinstance(a_label, str)
+ assert isinstance(b_label, str)
+
return PolyCountingGenotypePredicate.monoallelic(
a_predicate=a_predicate,
b_predicate=b_predicate,
- names=names,
+ a_label=a_label,
+ b_label=b_label,
)
def biallelic_predicate(
a_predicate: VariantPredicate,
b_predicate: VariantPredicate,
- names: typing.Tuple[str, str] = ("A", "B"),
+ a_label: str = "A",
+ b_label: str = "B",
partitions: typing.Collection[typing.Collection[int]] = ((0,), (1,), (2,)),
) -> GenotypePolyPredicate:
"""
@@ -352,18 +366,22 @@ def biallelic_predicate(
:param a_predicate: predicate to test if the variants meet the criteria of the first group (named `A` by default).
:param b_predicate: predicate to test if the variants meet the criteria of the second group (named `B` by default).
- :param names: group names (default ``('A', 'B')``).
+ :param a_label: display name of the `a_predicate` (default ``"A"``).
+ :param b_label: display name of the `b_predicate` (default ``"B"``).
:param partitions: a sequence with partition identifiers (default ``((0,), (1,), (2,))``).
"""
# Q/C
- assert len(names) == 2
+ assert isinstance(a_label, str)
+ assert isinstance(b_label, str)
+
partitions = fixate_partitions(partitions)
qc_partitions(partitions)
return PolyCountingGenotypePredicate.biallelic(
a_predicate=a_predicate,
b_predicate=b_predicate,
- names=names,
+ a_label=a_label,
+ b_label=b_label,
partitions=partitions,
)
diff --git a/src/gpsea/analysis/predicate/genotype/_test__gt_predicates.py b/src/gpsea/analysis/predicate/genotype/_test__gt_predicates.py
index 1bb7ff13..4c7f3d25 100644
--- a/src/gpsea/analysis/predicate/genotype/_test__gt_predicates.py
+++ b/src/gpsea/analysis/predicate/genotype/_test__gt_predicates.py
@@ -48,9 +48,8 @@ def test_build_count_to_cat(
partitions: typing.Sequence[typing.Sequence[int]],
ac2cat_name: typing.Mapping[typing.Tuple[int, int], str],
):
- names = ("A", "B")
ac2cat = build_count_to_cat(
- names=names,
+ a_label="A", b_label="B",
partitions=partitions,
)
diff --git a/src/gpsea/analysis/predicate/genotype/_variant.py b/src/gpsea/analysis/predicate/genotype/_variant.py
index 4f0ec35b..a35b7e08 100644
--- a/src/gpsea/analysis/predicate/genotype/_variant.py
+++ b/src/gpsea/analysis/predicate/genotype/_variant.py
@@ -164,8 +164,8 @@ def exon(
Well, at least the genome variants of the *Homo sapiens sapiens* taxon...
Args:
- exon: a non-negative `int` with the index of the target exon
- (e.g. `0` for the 1st exon, `1` for the 2nd, ...)
+ exon: a positive `int` with the index of the target exon
+ (e.g. `1` for the 1st exon, `2` for the 2nd, ...)
tx_id: a `str` with the accession ID of the target transcript (e.g. `NM_123.4`)
"""
return VariantExonPredicate(exon, tx_id)
diff --git a/src/gpsea/analysis/predicate/phenotype/_util.py b/src/gpsea/analysis/predicate/phenotype/_util.py
index 1a0e33d5..7d3e4626 100644
--- a/src/gpsea/analysis/predicate/phenotype/_util.py
+++ b/src/gpsea/analysis/predicate/phenotype/_util.py
@@ -11,9 +11,8 @@
def prepare_predicates_for_terms_of_interest(
cohort: typing.Iterable[Patient],
- hpo: hpotk.graph.GraphAware,
+ hpo: hpotk.MinimalOntology,
missing_implies_excluded: bool = False,
- min_n_of_patients_with_term: int = 2,
) -> typing.Sequence[PhenotypePolyPredicate[hpotk.TermId]]:
"""
A convenience method for creating a battery of :class:`PropagatingPhenotypePredicate` predicates
@@ -22,8 +21,6 @@ def prepare_predicates_for_terms_of_interest(
:param cohort: a cohort of individuals to investigate.
:param hpo: an entity with an HPO graph (e.g. :class:`~hpotk.MinimalOntology`).
:param missing_implies_excluded: `True` if absence of an annotation should be counted as its explicit exclusion.
- :param min_n_of_patients_with_term: the minimum number of patients that must feature an HPO term
- (either directly or indirectly) for the term to be included in the analysis.
"""
return tuple(
HpoPredicate(
@@ -31,15 +28,14 @@ def prepare_predicates_for_terms_of_interest(
query=term,
missing_implies_phenotype_excluded=missing_implies_excluded,
) for term in prepare_hpo_terms_of_interest(
- cohort, hpo, min_n_of_patients_with_term,
+ cohort, hpo,
)
)
def prepare_hpo_terms_of_interest(
cohort: typing.Iterable[Patient],
- hpo: hpotk.graph.GraphAware,
- min_n_of_patients_with_term: int = 2,
+ hpo: hpotk.MinimalOntology,
) -> typing.Sequence[hpotk.TermId]:
"""
Prepare a collection of HPO terms to test.
@@ -48,9 +44,7 @@ def prepare_hpo_terms_of_interest(
as well as the ancestors of the present terms and the descendants of the excluded terms.
:param cohort: a cohort of individuals to investigate.
- :param hpo: an entity with an HPO graph (e.g. :class:`~hpotk.MinimalOntology`).
- :param min_n_of_patients_with_term: the minimum number of patients that must feature an HPO term
- (either directly or indirectly) for the term to be included in the analysis.
+ :param hpo: HPO as :class:`~hpotk.MinimalOntology`.
"""
present_count = Counter()
excluded_count = Counter()
@@ -82,7 +76,7 @@ def prepare_hpo_terms_of_interest(
# Keep the term if it is mentioned at least *n* times (incl. being excluded)
# in the cohort
n_all = total_count[term_id]
- if n_all >= min_n_of_patients_with_term:
+ if n_all >= 1:
final_hpo.append(term_id)
return tuple(final_hpo)
diff --git a/src/gpsea/analysis/pscore/_api.py b/src/gpsea/analysis/pscore/_api.py
index 299ecd60..dc203347 100644
--- a/src/gpsea/analysis/pscore/_api.py
+++ b/src/gpsea/analysis/pscore/_api.py
@@ -78,7 +78,10 @@ def __init__(
pval: float,
):
self._genotype_phenotype_scores = genotype_phenotype_scores
- self._pval = float(pval)
+ if isinstance(pval, float) and 0. <= pval <= 1.:
+ self._pval = float(pval)
+ else:
+ raise ValueError(f"`p_val` must be a finite float in range [0, 1] but it was {pval}")
@property
def genotype_phenotype_scores(self) -> pd.DataFrame:
@@ -125,7 +128,8 @@ def plot_boxplots(
:param colors: a tuple with colors to use for coloring the box patches of the box plot.
"""
# skip the patients with unassigned genotype group
- not_na_gts = self._genotype_phenotype_scores["genotype"].notna()
+ bla = self._genotype_phenotype_scores.notna()
+ not_na_gts = bla.all(axis='columns')
data = self._genotype_phenotype_scores.loc[not_na_gts]
# Check that the provided genotype predicate defines the same categories
diff --git a/src/gpsea/analysis/temporal/__init__.py b/src/gpsea/analysis/temporal/__init__.py
new file mode 100644
index 00000000..c70df99e
--- /dev/null
+++ b/src/gpsea/analysis/temporal/__init__.py
@@ -0,0 +1,16 @@
+"""
+The `gpsea.analysis.temporal` package implements comparison of survivals
+between genotype groups.
+
+See :ref:`survival` for an example.
+"""
+
+from ._base import Survival
+from ._api import SurvivalAnalysis, SurvivalAnalysisResult, Endpoint
+
+__all__ = [
+ "Endpoint",
+ "SurvivalAnalysis",
+ "SurvivalAnalysisResult",
+ "Survival",
+]
diff --git a/src/gpsea/analysis/temporal/_api.py b/src/gpsea/analysis/temporal/_api.py
new file mode 100644
index 00000000..6d00841c
--- /dev/null
+++ b/src/gpsea/analysis/temporal/_api.py
@@ -0,0 +1,197 @@
+import abc
+import math
+import typing
+
+from collections import defaultdict
+
+import pandas as pd
+
+from gpsea.model import Patient
+from ..predicate.genotype import GenotypePolyPredicate
+
+from ._base import Survival
+from .stats import SurvivalStatistic
+
+
+class Endpoint(metaclass=abc.ABCMeta):
+ """
+ `Endpoint` computes survival for the analyzed individual.
+
+ An example endpoint includes :func:`~gpsea.analysis.survival.endpoint.death`,
+ :func:`~gpsea.analysis.survival.endpoint.disease_onset`,
+ or onset of a phenotypic feature (:func:`~gpsea.analysis.survival.endpoint.hpo_onset`).
+ """
+
+ @abc.abstractmethod
+ def compute_survival(
+ self,
+ patient: Patient,
+ ) -> typing.Optional[Survival]:
+ """
+ Compute a survival for a given `patient` or `None` if the `patient` lacks the required
+ data (e.g. age of death or age at last investigation).
+ """
+ pass
+
+ @abc.abstractmethod
+ def display_question(self) -> str:
+ pass
+
+
+class SurvivalAnalysisResult:
+ """
+ `SurvivalAnalysisResult` includes the results of a :class:`~gpsea.analysis.temporal.SurvivalAnalysis`.
+ """
+
+ def __init__(
+ self,
+ gt_predicate: GenotypePolyPredicate,
+ data: pd.DataFrame,
+ pval: float,
+ ):
+ assert isinstance(gt_predicate, GenotypePolyPredicate)
+ self._gt_predicate = gt_predicate
+
+ assert isinstance(data, pd.DataFrame) and all(
+ col in data for col in ("genotype", "survival")
+ )
+ self._data = data
+
+ if isinstance(pval, float) and math.isfinite(pval) and 0.0 <= pval <= 1.0:
+ self._pval = float(pval)
+ else:
+ raise ValueError(
+ f"`p_val` must be a finite float in range [0, 1] but it was {pval}"
+ )
+
+ @property
+ def gt_predicate(self) -> GenotypePolyPredicate:
+ """
+ Get the genotype predicate used in the survival analysis that produced this result.
+ """
+ return self._gt_predicate
+
+ @property
+ def data(self) -> pd.DataFrame:
+ """
+ Get the data frame with the genotype group
+ and the corresponding :class:`~gpsea.analysis.tempo.Survival`.
+
+ The DataFrame has the following structure:
+
+ ========== ========== ============================================
+ patient_id genotype survival
+ ========== ========== ============================================
+ patient_1 0 `Survival(value=123.4, is_censored=False)`
+ patient_2 0 `None`
+ patient_3 `None` `Survival(value=456.7, is_censored=True)`
+ patient_4 1 `None`
+ ... ... ...
+ ========== ========== ============================================
+
+ The index includes the individual IDs (`patient_id`), and then there are 2 columns
+ with the `genotype` group id (:attr:`~gpsea.analysis.predicate.PatientCategory.cat_id`)
+ and the `survival` encoded as :class:`~gpsea.analysis.tempo.Survival` object.
+
+ A `genotype` value may be missing (`None`) if the individual cannot be assigned
+ into a genotype category.
+ Similarly, a `survival` may be `None` if computing the survival is impossible for
+ the individual in question.
+ """
+ return self._data
+
+ def complete_records(self) -> pd.DataFrame:
+ """
+ Get the :meth:`~gpsea.analysis.temporal.SurvivalAnalysisResult.data` rows
+ where both `genotype` and `survival` columns are available (i.e. not `None`).
+ """
+ return self._data.loc[
+ self._data["genotype"].notna() & self._data["survival"].notna()
+ ]
+
+ @property
+ def pval(self) -> float:
+ """
+ Get the p value of the test.
+ """
+ return self._pval
+
+ def __eq__(self, value: object) -> bool:
+ return (
+ isinstance(value, SurvivalAnalysisResult)
+ and self._gt_predicate == value._gt_predicate
+ and self._data.equals(value._data)
+ and self._pval == value._pval
+ )
+
+ def __hash__(self) -> int:
+ return hash((self._gt_predicate, self._data, self._pval))
+
+ def __str__(self) -> str:
+ return (
+ "SurvivalAnalysisResult("
+ "gt_predicate={self._gt_predicate}, "
+ "data={self._data}, "
+ "pval={self._pval})"
+ )
+
+ def __repr__(self) -> str:
+ return str(self)
+
+
+class SurvivalAnalysis:
+ """
+ `SurvivalAnalysis` compares the survivals of genotype groups with respect
+ to an :class:`~gpsea.analysis.temporal.Endpoint`.
+
+ The cohort is partitioned into groups using a genotype predicate
+ and survival is computed for each cohort member. The difference between
+ survivals is tested with selected :class:`~gpsea.analysis.temporal.stats.SurvivalStatistic`.
+ """
+
+ def __init__(
+ self,
+ statistic: SurvivalStatistic,
+ ):
+ assert isinstance(statistic, SurvivalStatistic)
+ self._statistic = statistic
+
+ def compare_genotype_vs_survival(
+ self,
+ cohort: typing.Iterable[Patient],
+ gt_predicate: GenotypePolyPredicate,
+ endpoint: Endpoint,
+ ) -> SurvivalAnalysisResult:
+ """
+ Execute the survival analysis on a given `cohort`.
+ """
+
+ idx = pd.Index((patient.patient_id for patient in cohort), name="patient_id")
+ data = pd.DataFrame(
+ None,
+ index=idx,
+ columns=["genotype", "survival"],
+ )
+ survivals = defaultdict(list)
+ # Apply the predicate and the survival metric on the cohort
+ for patient in cohort:
+ gt_cat = gt_predicate.test(patient)
+ if gt_cat is None:
+ data.loc[patient.patient_id, "genotype"] = None
+ else:
+ data.loc[patient.patient_id, "genotype"] = gt_cat.category.cat_id
+
+ survival = endpoint.compute_survival(patient)
+ data.loc[patient.patient_id, "survival"] = survival # type: ignore
+
+ if gt_cat is not None and survival is not None:
+ survivals[gt_cat].append(survival)
+
+ vals = tuple(survivals[gt_cat] for gt_cat in gt_predicate.get_categorizations())
+ pval = self._statistic.compute_pval(vals)
+
+ return SurvivalAnalysisResult(
+ gt_predicate=gt_predicate,
+ data=data,
+ pval=pval,
+ )
diff --git a/src/gpsea/analysis/temporal/_base.py b/src/gpsea/analysis/temporal/_base.py
new file mode 100644
index 00000000..e196e83d
--- /dev/null
+++ b/src/gpsea/analysis/temporal/_base.py
@@ -0,0 +1,27 @@
+import math
+
+from dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class Survival:
+ """
+ Information regarding individual's survival.
+ """
+
+ value: float
+ """
+ The survival value, expressed as a `float`.
+
+ The `value` must be finite and non-`NaN`.
+ """
+
+ is_censored: bool
+ """
+ `True` if the survival has been censored and `False` otherwise.
+ """
+
+ def __post_init__(self):
+ assert math.isfinite(
+ self.value
+ ), f"`value` must be finite and non-NaN, but was {self.value}"
diff --git a/src/gpsea/analysis/temporal/endpoint/__init__.py b/src/gpsea/analysis/temporal/endpoint/__init__.py
new file mode 100644
index 00000000..80b20956
--- /dev/null
+++ b/src/gpsea/analysis/temporal/endpoint/__init__.py
@@ -0,0 +1,12 @@
+"""
+The `gpsea.analysis.temporal.endpoint` package provides endpoints
+for comparing survivals between genotype groups.
+"""
+
+from ._impl import death, disease_onset, hpo_onset
+
+__all__ = [
+ "death",
+ "disease_onset",
+ "hpo_onset",
+]
diff --git a/src/gpsea/analysis/temporal/endpoint/_impl.py b/src/gpsea/analysis/temporal/endpoint/_impl.py
new file mode 100644
index 00000000..4d10cadf
--- /dev/null
+++ b/src/gpsea/analysis/temporal/endpoint/_impl.py
@@ -0,0 +1,315 @@
+import abc
+import typing
+
+import hpotk
+
+from gpsea.model import Patient, Age, Timeline
+from .._api import Endpoint
+from .._base import Survival
+
+
+class EndpointBase(Endpoint, metaclass=abc.ABCMeta):
+
+ def __init__(
+ self,
+ timeline: Timeline,
+ ):
+ self._timeline = timeline
+
+ def _compute_survival(
+ self,
+ age: typing.Optional[Age],
+ is_censored: bool,
+ ) -> typing.Optional[Survival]:
+ if age is None or age.timeline != self._timeline:
+ return None
+ else:
+ return Survival(
+ value=age.days,
+ is_censored=is_censored,
+ )
+
+
+class Death(EndpointBase):
+
+ def compute_survival(
+ self,
+ patient: Patient,
+ ) -> typing.Optional[Survival]:
+ # If the patient is alive we use the current age as `value` and `censored=True`
+ # If the patient is deceased, we use the age at death as a `value` and `censored=False`
+ if patient.vital_status is None:
+ # Absence of the vital status prevents reasoning about death.
+ return None
+
+ if patient.vital_status.is_deceased:
+ return self._compute_survival(
+ age=patient.vital_status.age_of_death,
+ is_censored=False,
+ )
+ else:
+ # In absence of an explicit information regarding death,
+ # we assume the individual was alive at the reported age.
+ return self._compute_survival(
+ age=patient.age,
+ is_censored=True,
+ )
+
+ def display_question(self) -> str:
+ return f"Compute time until {self._timeline.name.lower()} death"
+
+ def __eq__(self, value: object) -> bool:
+ return isinstance(value, Death) and self._timeline == value._timeline
+
+ def __hash__(self) -> int:
+ return hash((self._timeline,))
+
+ def __str__(self) -> str:
+ return f"Death(timeline={self._timeline})"
+
+ def __repr__(self) -> str:
+ return str(self)
+
+
+class PhenotypicFeatureOnset(EndpointBase):
+
+ def __init__(
+ self,
+ timeline: Timeline,
+ hpo: hpotk.MinimalOntology,
+ term_id: hpotk.TermId,
+ ):
+ super().__init__(timeline)
+
+ assert isinstance(hpo, hpotk.MinimalOntology)
+ self._hpo = hpo
+
+ assert isinstance(term_id, hpotk.TermId)
+ self._term_id = term_id
+
+ assert term_id in hpo, f"`term_id` {term_id.value} is not in HPO {hpo.version}"
+
+ def compute_survival(
+ self,
+ patient: Patient,
+ ) -> typing.Optional[Survival]:
+ # Search the present phenotypes. If the individual is annotated with multiple present descendants
+ # (e.g. Focal seizure, Clonic seizure) of the target term (e.g. Seizure) then choose
+ # the earliest onset, because the onset of the ancestor should be observable
+ # since the onset of the first descendant.
+
+ earliest_onset = None
+ for present in patient.present_phenotypes():
+ # Check if the onset is available ...
+ if present.onset is not None and present.onset.timeline == self._timeline:
+ # ... and if the individual is annotated with the target HPO or its descendant.
+ if present.identifier == self._term_id or any(
+ anc == self._term_id
+ for anc in self._hpo.graph.get_ancestors(present)
+ ):
+ if earliest_onset is None:
+ earliest_onset = present.onset
+ else:
+ earliest_onset = min(earliest_onset, present.onset)
+
+ if earliest_onset is None:
+ # Phenotype was not found, use the age of the individual and right-censor
+ return self._compute_survival(
+ age=patient.age,
+ is_censored=True,
+ )
+ else:
+ # Phenotype was found, use the earliest onset.
+ return self._compute_survival(
+ age=earliest_onset,
+ is_censored=False,
+ )
+
+ def display_question(self) -> str:
+ label = self._hpo.get_term_name(self._term_id)
+ return f"Compute time until {self._timeline.name.lower()} onset of {label}"
+
+ def __eq__(self, value: object) -> bool:
+ return (
+ isinstance(value, PhenotypicFeatureOnset)
+ and self._timeline == value._timeline
+ and self._term_id == value._term_id
+ and self._hpo.version == value._hpo.version
+ )
+
+ def __hash__(self) -> int:
+ return hash((self._timeline, self._term_id, self._hpo.version))
+
+ def __str__(self) -> str:
+ return (
+ "PhenotypicFeatureOnset("
+ f"timeline={self._timeline}, "
+ f"onset={self._term_id}, "
+ f"hpo={self._hpo.version})"
+ )
+
+ def __repr__(self) -> str:
+ return str(self)
+
+
+class DiseaseOnset(EndpointBase):
+
+ def __init__(
+ self,
+ timeline: Timeline,
+ disease_id: hpotk.TermId,
+ ):
+ super().__init__(timeline)
+
+ assert isinstance(disease_id, hpotk.TermId)
+ self._disease_id = disease_id
+
+ def compute_survival(
+ self,
+ patient: Patient,
+ ) -> typing.Optional[Survival]:
+ for disease in patient.present_diseases():
+ if disease.identifier == self._disease_id:
+ return self._compute_survival(
+ age=disease.onset,
+ is_censored=False,
+ )
+
+ return self._compute_survival(
+ age=patient.age,
+ is_censored=True,
+ )
+
+ def display_question(self) -> str:
+ return f"Compute time until {self._timeline.name.lower()} diagnosis of {self._disease_id.value}"
+
+ def __eq__(self, value: object) -> bool:
+ return (
+ isinstance(value, DiseaseOnset)
+ and self._timeline == value._timeline
+ and self._disease_id == value._disease_id
+ )
+
+ def __hash__(self) -> int:
+ return hash((self._timeline, self._disease_id))
+
+ def __str__(self) -> str:
+ return "DiseaseOnset(" \
+ f"timeline={self._timeline}, " \
+ f"disease_id={self._disease_id})"
+
+ def __repr__(self) -> str:
+ return str(self)
+
+
+GESTATIONAL_DEATH = Death(timeline=Timeline.GESTATIONAL)
+POSTNATAL_DEATH = Death(timeline=Timeline.POSTNATAL)
+
+
+def death(
+ timeline: typing.Literal["gestational", "postnatal"] = "postnatal",
+) -> Endpoint:
+ """
+ Get :class:`~gpsea.analysis.temporal.Endpoint` for computing time
+ until death of an individual or until the individual is lost from the study
+ without knowing about the time of death.
+
+ The time of death is computed from individual's vital status with the following rules:
+
+ * If the individual is labeled as :attr:`~gpsea.model.Status.DECEASED`,
+ we compute the survival from the age of death.
+ * If the individual is :attr:`~gpsea.model.Status.ALIVE` or the status is missing,
+ we use the age at last encounter as the censored survival.
+ * If the age at last encounter is missing or if the age does not match the target timeline
+ (e.g. `timeline==postnatal` but the individual has `gestational` age) then we cannot compute the survival
+ and the endpoint returns `None`.
+ """
+ age_timeline = _decode_timeline(timeline)
+ if age_timeline == Timeline.GESTATIONAL:
+ return GESTATIONAL_DEATH
+ elif age_timeline == Timeline.POSTNATAL:
+ return POSTNATAL_DEATH
+ else:
+ raise ValueError(f"Unsupported timeline {timeline}")
+
+
+def disease_onset(
+ disease_id: typing.Union[str, hpotk.TermId],
+ timeline: typing.Literal["gestational", "postnatal"] = "postnatal",
+) -> Endpoint:
+ """
+ Get :class:`~gpsea.analysis.temporal.Endpoint` to compute time
+ until onset of a disease or until the individual is lost from the study.
+
+ The onset of diagnosis is computed from the onset field of
+ a :class:`~gpsea.model.Disease` with the following rules:
+
+ * If the individual is diagnosed with the target disease and its onset is known,
+ then the survival is computed from the disease onset.
+ * If the individual is *not* diagnosed with the disease and the age at last encounter is known,
+ this age is used as censored survival.
+ * If the age at last encounter is missing or if the age does not match the target timeline
+ (e.g. `timeline==postnatal` but the individual's age is on gestational timeline) then we cannot compute
+ the time until disease onset and the endpoint returns `None`.
+ """
+ age_timeline = _decode_timeline(timeline)
+ disease_id = _validate_term_id(disease_id)
+
+ return DiseaseOnset(
+ timeline=age_timeline,
+ disease_id=disease_id,
+ )
+
+
+def hpo_onset(
+ hpo: hpotk.MinimalOntology,
+ term_id: typing.Union[str, hpotk.TermId],
+ timeline: typing.Literal["gestational", "postnatal"] = "postnatal",
+) -> Endpoint:
+ """
+ Get :class:`~gpsea.analysis.temporal.Endpoint` to compute time
+ until onset of an HPO term or until the individual is lost from the study.
+
+ The HPO term onset is computed from the onset field of
+ a :class:`~gpsea.model.Phenotype` with the following rules:
+
+ * If the individual is annotated with the target HPO term and its onset is known,
+ then the survival is computed from the term's onset.
+ * If the individual is *not* diagnosed with the term and the age at last encounter is known,
+ this age is used as censored survival.
+ * If the age at last encounter is missing or if the age does not match the target timeline
+ (e.g. `timeline==postnatal` but the individual has `gestational` age) then we cannot compute
+ time until phenotype onset and the endpoint returns `None`.
+ """
+ age_timeline = _decode_timeline(timeline)
+ term_id = _validate_term_id(term_id)
+
+ return PhenotypicFeatureOnset(
+ timeline=age_timeline,
+ hpo=hpo,
+ term_id=term_id,
+ )
+
+
+def _decode_timeline(
+ timeline: typing.Literal["gestational", "postnatal"] = "postnatal",
+) -> Timeline:
+ if timeline == "gestational":
+ return Timeline.GESTATIONAL
+ elif timeline == "postnatal":
+ return Timeline.POSTNATAL
+ else:
+ raise ValueError(f"Unsupported timeline {timeline}")
+
+
+def _validate_term_id(
+ term_id: typing.Union[str, hpotk.TermId],
+) -> hpotk.TermId:
+ if isinstance(term_id, str):
+ return hpotk.TermId.from_curie(term_id)
+ elif isinstance(term_id, hpotk.TermId):
+ return term_id
+ else:
+ raise ValueError(
+ f"`term_id` must be a `str` or `hpotk.TermId` but was {term_id}"
+ )
diff --git a/src/gpsea/analysis/temporal/stats/__init__.py b/src/gpsea/analysis/temporal/stats/__init__.py
new file mode 100644
index 00000000..ee6406ba
--- /dev/null
+++ b/src/gpsea/analysis/temporal/stats/__init__.py
@@ -0,0 +1,11 @@
+"""
+`gpsea.analysis.temporal.stats` provides statistical tests for the survival analysis in GPSEA.
+"""
+
+from ._api import SurvivalStatistic
+from ._impl import LogRankTest
+
+__all__ = [
+ "SurvivalStatistic",
+ "LogRankTest",
+]
diff --git a/src/gpsea/analysis/temporal/stats/_api.py b/src/gpsea/analysis/temporal/stats/_api.py
new file mode 100644
index 00000000..79ef01d9
--- /dev/null
+++ b/src/gpsea/analysis/temporal/stats/_api.py
@@ -0,0 +1,23 @@
+import abc
+import typing
+
+from .._base import Survival
+
+
+class SurvivalStatistic(metaclass=abc.ABCMeta):
+ """
+ `SurvivalStatistic` calculates a p value
+ for 2 or more survival groups
+ computed by a :class:`~gpsea.analysis.tempo.SurvivalMetric`.
+ """
+
+ @abc.abstractmethod
+ def compute_pval(
+ self,
+ scores: typing.Collection[typing.Sequence[Survival]],
+ ) -> float:
+ """
+ Compute p value for the collection of survivals being sampled from
+ the same source distribution.
+ """
+ pass
diff --git a/src/gpsea/analysis/temporal/stats/_impl.py b/src/gpsea/analysis/temporal/stats/_impl.py
new file mode 100644
index 00000000..814df5d0
--- /dev/null
+++ b/src/gpsea/analysis/temporal/stats/_impl.py
@@ -0,0 +1,54 @@
+import typing
+
+from scipy import stats
+
+from .._base import Survival
+from ._api import SurvivalStatistic
+
+
+class LogRankTest(SurvivalStatistic):
+ """
+ Log Rank test compares survivals of individual groups.
+
+ The class is a wrapper around Scipy's :func:`~scipy.stats.logrank` function.
+ A two-sided alternative hypothesis is tested.
+ """
+
+ def compute_pval(
+ self,
+ scores: typing.Collection[typing.Iterable[Survival]],
+ ) -> float:
+ """
+ Compute p value for survivals being sourced from the same distribution.
+
+ :param scores: a pair of survival groups
+ """
+ assert len(scores) == 2, "Log rank test only supports 2 groups at this time"
+ x, y = tuple(scores)
+
+ xc = LogRankTest._prepare_censored_data(x)
+ yc = LogRankTest._prepare_censored_data(y)
+
+ result = stats.logrank(
+ x=xc,
+ y=yc,
+ alternative="two-sided",
+ )
+
+ return float(result.pvalue)
+
+ @staticmethod
+ def _prepare_censored_data(
+ survivals: typing.Iterable[Survival],
+ ) -> stats.CensoredData:
+ uncensored = []
+ right_censored = []
+ for survival in survivals:
+ if survival.is_censored:
+ right_censored.append(survival.value)
+ else:
+ uncensored.append(survival.value)
+ return stats.CensoredData(
+ uncensored=uncensored,
+ right=right_censored,
+ )
diff --git a/src/gpsea/io.py b/src/gpsea/io.py
index 7eba1ca2..5bfa220c 100644
--- a/src/gpsea/io.py
+++ b/src/gpsea/io.py
@@ -25,7 +25,11 @@
Measurement,
Disease,
Phenotype,
+ Age,
+ Timeline,
Sex,
+ Status,
+ VitalStatus,
)
from gpsea.model.genome import Contig, Region, GenomicRegion, Strand
@@ -109,19 +113,26 @@ def default(self, o):
"label": o.label,
"meta_label": o.meta_label,
}
- elif isinstance(o, (Sex, Genotype, VariantEffect, Strand, VariantClass)):
+ elif isinstance(o, (Sex, Timeline, Genotype, VariantEffect, Strand, VariantClass, Status)):
# enums
return o.name
elif isinstance(o, Phenotype):
return {
"term_id": o.identifier.value,
"is_present": o.is_present,
+ "onset": o.onset,
+ }
+ elif isinstance(o, Age):
+ return {
+ "days": o.days,
+ "timeline": o.timeline,
}
elif isinstance(o, Disease):
return {
"term_id": o.identifier.value,
"name": o.name,
"is_observed": o.is_present,
+ "onset": o.onset,
}
elif isinstance(o, Measurement):
return {
@@ -134,11 +145,18 @@ def default(self, o):
return {
"labels": o.labels,
"sex": o.sex,
+ "age": o.age,
+ "vital_status": o.vital_status,
"phenotypes": o.phenotypes,
"measurements": o.measurements,
"diseases": o.diseases,
"variants": o.variants,
}
+ elif isinstance(o, VitalStatus):
+ return {
+ "status": o.status,
+ "age_of_death": o.age_of_death,
+ }
elif isinstance(o, Cohort):
return {
"members": o.all_patients,
@@ -201,10 +219,12 @@ def default(self, o):
_PROTEIN_METADATA = ("protein_id", "label", "protein_features", "protein_length")
_PROTEIN_FEATURE = ("info", "feature_type")
_FEATURE_INFO = ("name", "region")
-_PHENOTYPE_FIELDS = ("term_id", "is_present")
-_DISEASE_FIELDS = ("term_id", "name", "is_observed")
+_PHENOTYPE_FIELDS = ("term_id", "is_present", "onset")
+_AGE_FIELDS = ("days", "timeline")
+_DISEASE_FIELDS = ("term_id", "name", "is_observed", "onset")
_MEASUREMENT_FIELDS = ("test_term_id", "test_name", "test_result", "unit")
-_PATIENT_FIELDS = ("labels", "sex", "phenotypes", "diseases", "variants")
+_PATIENT_FIELDS = ("labels", "sex", "age", "vital_status", "phenotypes", "diseases", "variants")
+_VITAL_STATUS_FIELDS = ("status", "age_of_death")
_COHORT_FIELDS = ("members", "excluded_patient_count")
@@ -317,12 +337,19 @@ def object_hook(obj: typing.Dict[typing.Any, typing.Any]) -> typing.Any:
return Phenotype(
term_id=hpotk.TermId.from_curie(obj["term_id"]),
is_observed=obj["is_present"],
+ onset=obj["onset"],
+ )
+ elif GpseaJSONDecoder._has_all_fields(obj, _AGE_FIELDS):
+ return Age(
+ days=obj["days"],
+ timeline=Timeline[obj["timeline"]],
)
elif GpseaJSONDecoder._has_all_fields(obj, _DISEASE_FIELDS):
return Disease(
term_id=hpotk.TermId.from_curie(obj["term_id"]),
name=obj["name"],
is_observed=obj["is_observed"],
+ onset=obj["onset"],
)
elif GpseaJSONDecoder._has_all_fields(obj, _MEASUREMENT_FIELDS):
return Measurement(
@@ -335,11 +362,18 @@ def object_hook(obj: typing.Dict[typing.Any, typing.Any]) -> typing.Any:
return Patient(
labels=obj["labels"],
sex=Sex[obj["sex"]],
+ age=obj["age"],
+ vital_status=obj["vital_status"],
phenotypes=obj["phenotypes"],
measurements=obj["measurements"],
diseases=obj["diseases"],
variants=obj["variants"],
)
+ elif GpseaJSONDecoder._has_all_fields(obj, _VITAL_STATUS_FIELDS):
+ return VitalStatus(
+ status=Status[obj["status"]],
+ age_of_death=obj["age_of_death"],
+ )
elif GpseaJSONDecoder._has_all_fields(obj, _TX_COORDINATES):
return TranscriptCoordinates(
identifier=obj["identifier"],
diff --git a/src/gpsea/model/__init__.py b/src/gpsea/model/__init__.py
index a3de6a9d..91300dc9 100644
--- a/src/gpsea/model/__init__.py
+++ b/src/gpsea/model/__init__.py
@@ -6,17 +6,19 @@
"""
from ._base import SampleLabels, Sex
-from ._cohort import Cohort, Patient
+from ._cohort import Cohort, Patient, VitalStatus, Status
from ._gt import Genotype, Genotypes, Genotyped
from ._phenotype import Phenotype, Disease, Measurement
from ._protein import FeatureInfo, FeatureType, ProteinFeature, ProteinMetadata
+from ._temporal import Age, Timeline
from ._tx import TranscriptCoordinates
from ._variant import VariantCoordinates, ImpreciseSvInfo, VariantInfo, VariantInfoAware, VariantClass, Variant
from ._variant import TranscriptAnnotation, TranscriptInfoAware, FunctionalAnnotationAware
from ._variant_effects import VariantEffect
__all__ = [
- 'Cohort', 'Patient', 'SampleLabels', 'Sex',
+ 'Cohort', 'Patient', 'SampleLabels', 'Sex', 'VitalStatus', 'Status',
+ 'Age', 'Timeline',
'Phenotype', 'Disease', 'Measurement',
'Variant', 'VariantClass', 'VariantCoordinates', 'ImpreciseSvInfo', 'VariantInfo', 'VariantInfoAware',
'Genotype', 'Genotypes', 'Genotyped',
diff --git a/src/gpsea/model/_cohort.py b/src/gpsea/model/_cohort.py
index fc4068c3..2483b0b2 100644
--- a/src/gpsea/model/_cohort.py
+++ b/src/gpsea/model/_cohort.py
@@ -1,19 +1,59 @@
+import enum
import itertools
import typing
from collections import Counter
+from dataclasses import dataclass
import hpotk
from ._base import SampleLabels, Sex
from ._phenotype import Phenotype, Disease, Measurement
+from ._temporal import Age
from ._variant import Variant
+class Status(enum.Enum):
+ UNKNOWN = 0
+ ALIVE = 1
+ DECEASED = 2
+
+
+@dataclass(frozen=True)
+class VitalStatus:
+ status: Status
+ age_of_death: typing.Optional[Age]
+
+ @property
+ def is_alive(self) -> bool:
+ return self.status == Status.ALIVE
+
+ @property
+ def is_deceased(self) -> bool:
+ return self.status == Status.DECEASED
+
+ @property
+ def is_unknown(self) -> bool:
+ return self.status == Status.UNKNOWN
+
+
class Patient:
"""
`Patient` represents a single investigated individual.
+ We need to know about the following attributes:
+
+ * identifier(s) formatted as :class:`~gpsea.model.SampleLabels`
+ * :class:`~gpsea.model.Sex`
+ * age of last clinical encounter (optional) formatted as :class:`~gpsea.model.Age` or `None` if not available.
+ * vital status (optional) formatted as :class:`~gpsea.model.VitalStatus`, which reports if the individual is alive
+ or deceased plus (optional) age of death
+ * HPO terms to represent the phenotype information, each HPO formatted
+ as an instance of :class:`~gpsea.model.Phenotype`
+ * numerical measurements
+ * disease diagnoses formatted as :class:`~gpsea.model.Disease`
+ * genotype information as one or more :class:`~gpsea.model.Variant`
+
.. note::
We strongly recommend using the :func:`from_raw_parts` static constructor
@@ -22,22 +62,29 @@ class Patient:
@staticmethod
def from_raw_parts(
- labels: SampleLabels,
- sex: typing.Optional[Sex],
- phenotypes: typing.Iterable[Phenotype],
- measurements: typing.Iterable[Measurement],
- diseases: typing.Iterable[Disease],
- variants: typing.Iterable[Variant]
+ labels: typing.Union[str, SampleLabels],
+ sex: typing.Optional[Sex] = None,
+ age: typing.Optional[Age] = None,
+ vital_status: typing.Optional[VitalStatus] = None,
+ phenotypes: typing.Iterable[Phenotype] = (),
+ measurements: typing.Iterable[Measurement] = (),
+ diseases: typing.Iterable[Disease] = (),
+ variants: typing.Iterable[Variant] = (),
) -> "Patient":
"""
Create `Patient` from the primary data.
"""
+ if isinstance(labels, str):
+ labels = SampleLabels(label=labels)
+
if sex is None:
sex = Sex.UNKNOWN_SEX
return Patient(
labels=labels,
sex=sex,
+ age=age,
+ vital_status=vital_status,
phenotypes=phenotypes,
measurements=measurements,
diseases=diseases,
@@ -48,6 +95,8 @@ def __init__(
self,
labels: SampleLabels,
sex: Sex,
+ age: typing.Optional[Age],
+ vital_status: typing.Optional[VitalStatus],
phenotypes: typing.Iterable[Phenotype],
measurements: typing.Iterable[Measurement],
diseases: typing.Iterable[Disease],
@@ -58,6 +107,14 @@ def __init__(
assert isinstance(sex, Sex)
self._sex = sex
+
+ if age is not None:
+ assert isinstance(age, Age)
+ self._age = age
+
+ if vital_status is not None:
+ assert isinstance(vital_status, VitalStatus)
+ self._vital_status = vital_status
self._phenotypes = tuple(phenotypes)
self._measurements = tuple(measurements)
@@ -85,6 +142,20 @@ def sex(self) -> Sex:
"""
return self._sex
+ @property
+ def age(self) -> typing.Optional[Age]:
+ """
+ Get age of the individual or `None` if not available.
+ """
+ return self._age
+
+ @property
+ def vital_status(self) -> typing.Optional[VitalStatus]:
+ """
+ Get the vital status information for the individual or `None` if not available.
+ """
+ return self._vital_status
+
@property
def phenotypes(self) -> typing.Sequence[Phenotype]:
"""
@@ -165,10 +236,12 @@ def __str__(self) -> str:
return (f"Patient("
f"labels:{self._labels}, "
f"sex:{self._sex}, "
- f"variants:{self.variants}, "
- f"phenotypes:{[pheno.identifier for pheno in self.phenotypes]}, "
- f"measurements:{[m.name for m in self.measurements]}, "
- f"diseases:{[dis.identifier for dis in self.diseases]}")
+ f"age:{self._age}, "
+ f"vital_status:{self._vital_status}, "
+ f"variants:{self._variants}, "
+ f"phenotypes:{[pheno.identifier for pheno in self._phenotypes]}, "
+ f"measurements:{[m.name for m in self._measurements]}, "
+ f"diseases:{[dis.identifier for dis in self._diseases]}")
def __repr__(self) -> str:
return str(self)
@@ -177,13 +250,20 @@ def __eq__(self, other) -> bool:
return (isinstance(other, Patient)
and self._labels == other._labels
and self._sex == other._sex
+ and self._age == other._age
+ and self._vital_status == other._vital_status
and self._variants == other._variants
and self._phenotypes == other._phenotypes
and self._measurements == other._measurements
and self._diseases == other._diseases)
def __hash__(self) -> int:
- return hash((self._labels, self._sex, self._variants, self._phenotypes, self._measurements, self._diseases))
+ return hash((
+ self._labels, self._sex, self._age,
+ self._vital_status,
+ self._variants, self._phenotypes,
+ self._measurements, self._diseases,
+ ))
class Cohort(typing.Sized, typing.Iterable[Patient]):
diff --git a/src/gpsea/model/_phenotype.py b/src/gpsea/model/_phenotype.py
index 171bb607..3f2a9ede 100644
--- a/src/gpsea/model/_phenotype.py
+++ b/src/gpsea/model/_phenotype.py
@@ -1,10 +1,29 @@
+import abc
import typing
import warnings
import hpotk
+from ._temporal import Age
-class Phenotype(hpotk.model.Identified, hpotk.model.ObservableFeature):
+
+class OnsetAware(metaclass=abc.ABCMeta):
+ """
+ A mixin for classes which may know about their :class:`~gpsea.model.Age` or onset.
+
+ For instance, the onset of a phenotype or a disease in an individual.
+ """
+
+ @property
+ @abc.abstractmethod
+ def onset(self) -> typing.Optional[Age]:
+ """
+ Get the age of onset or `None` if unknown or otherwise not available.
+ """
+ pass
+
+
+class Phenotype(hpotk.model.Identified, hpotk.model.ObservableFeature, OnsetAware):
"""
`Phenotype` represents a clinical sign or symptom represented as an HPO term.
@@ -19,12 +38,15 @@ def from_term(term: hpotk.model.MinimalTerm, is_observed: bool):
def from_raw_parts(
term_id: typing.Union[str, hpotk.TermId],
is_observed: bool,
+ onset: typing.Optional[Age] = None,
) -> "Phenotype":
"""
Create `Phenotype` from a term ID and observation state.
:param term_id: a `str` with CURIE (e.g. `HP:0001250`) or a :class:`~hpotk.TermId`.
:param is_observed: `True` if the term ID was observed in patient or `False` if it was explicitly excluded.
+ :param onset: the :class:`~gpsea.model.Age` when the phenotype was first observed in patient
+ or `None` if not available.
"""
if isinstance(term_id, str):
term_id = hpotk.TermId.from_curie(term_id)
@@ -35,16 +57,19 @@ def from_raw_parts(
return Phenotype(
term_id,
- is_observed,
+ is_observed=is_observed,
+ onset=onset,
)
def __init__(
self,
term_id: hpotk.TermId,
- is_observed: bool
+ is_observed: bool,
+ onset: typing.Optional[Age],
):
self._term_id = hpotk.util.validate_instance(term_id, hpotk.TermId, 'term_id')
self._observed = hpotk.util.validate_instance(is_observed, bool, 'is_observed')
+ self._onset = hpotk.util.validate_optional_instance(onset, Age, "onset")
@property
def identifier(self) -> hpotk.TermId:
@@ -71,6 +96,13 @@ def observed(self) -> typing.Optional[bool]:
'Use `is_present` instead', DeprecationWarning, stacklevel=2)
return self.is_present
+ @property
+ def onset(self) -> typing.Optional[Age]:
+ """
+ Get the age of onset of the phenotype or `None` if unknown or otherwise not available.
+ """
+ return self._onset
+
@property
def is_observed(self) -> bool:
"""
@@ -83,34 +115,55 @@ def is_observed(self) -> bool:
def __eq__(self, other):
return isinstance(other, Phenotype) \
and self._term_id == other._term_id \
- and self._observed == other._observed
+ and self._observed == other._observed \
+ and self._onset == other._onset
def __hash__(self):
- return hash((self._term_id, self._observed))
+ return hash((self._term_id, self._observed, self._onset))
def __str__(self):
return f"Phenotype(" \
f"identifier={self._term_id}, " \
- f"is_present={self._observed})"
+ f"is_present={self._observed}, " \
+ f"onset={self._onset})"
def __repr__(self):
return str(self)
-class Disease(hpotk.model.Identified, hpotk.model.ObservableFeature, hpotk.model.Named):
+class Disease(hpotk.model.Identified, hpotk.model.ObservableFeature, hpotk.model.Named, OnsetAware):
"""
Representation of a disease diagnosed (or excluded) in an investigated individual.
"""
+ @staticmethod
+ def from_raw_parts(
+ term_id: typing.Union[str, hpotk.TermId],
+ name: str,
+ is_observed: bool,
+ onset: typing.Optional[Age] = None,
+ ) -> "Disease":
+ if isinstance(term_id, str):
+ term_id = hpotk.TermId.from_curie(term_id)
+
+ return Disease(
+ term_id=term_id,
+ name=name,
+ is_observed=is_observed,
+ onset=onset,
+ )
+
def __init__(
self,
term_id: hpotk.TermId,
name: str,
is_observed: bool,
+ onset: typing.Optional[Age],
):
self._term_id = hpotk.util.validate_instance(term_id, hpotk.TermId, 'term_id')
self._name = hpotk.util.validate_instance(name, str, 'name')
self._observed = hpotk.util.validate_instance(is_observed, bool, 'is_observed')
+ self._onset = hpotk.util.validate_optional_instance(onset, Age, "onset")
@property
def identifier(self) -> hpotk.TermId:
@@ -132,21 +185,30 @@ def is_present(self) -> bool:
Return `True` if the disease was diagnosed in the individual or `False` if it was excluded.
"""
return self._observed
+
+ @property
+ def onset(self) -> typing.Optional[Age]:
+ """
+ Get the age of onset of the disease or `None` if unknown or otherwise not available.
+ """
+ return self._onset
def __eq__(self, other):
return isinstance(other, Disease) \
and self._term_id == other._term_id \
and self._name == other._name \
- and self._observed == other._observed
+ and self._observed == other._observed \
+ and self._onset == other._onset
def __hash__(self):
- return hash((self._term_id, self._name, self._observed))
+ return hash((self._term_id, self._name, self._observed, self._onset))
def __str__(self):
return f"Disease(" \
f"identifier={self._term_id}, " \
f"name={self._name}, " \
- f"is_present={self._observed})"
+ f"is_present={self._observed}, " \
+ f"onset={self._onset})"
def __repr__(self):
return str(self)
diff --git a/src/gpsea/model/_temporal.py b/src/gpsea/model/_temporal.py
new file mode 100644
index 00000000..2aede84e
--- /dev/null
+++ b/src/gpsea/model/_temporal.py
@@ -0,0 +1,276 @@
+import enum
+import math
+import operator
+import re
+import typing
+
+
+class Timeline(enum.Enum):
+ """
+ `Timeline` represents the stage of temporal development of an organism.
+
+ There are two stages: gestational and postnatal.
+
+ Gestational timeline starts at the last menstrual period and ends at (but does not include) birth.
+ The postnatal timeline starts at birth and ends at death.
+
+ The `Timeline` overloads comparison operators. Gestational timeline is always before postnatal timeline.
+ """
+
+ GESTATIONAL = enum.auto()
+ """
+ Gestational timeline starts at the last menstrual period and ends at birth (excluded).
+ """
+
+ POSTNATAL = enum.auto()
+ """
+ Postnatal timeline starts at birth and ends at death.
+ """
+
+ def __lt__(self, value: object) -> bool:
+ if isinstance(value, Timeline):
+ return self == Timeline.GESTATIONAL and value == Timeline.POSTNATAL
+ else:
+ return NotImplemented
+
+ def __le__(self, value: object) -> bool:
+ if isinstance(value, Timeline):
+ return self < value or self == value
+ else:
+ return NotImplemented
+
+ def __gt__(self, value: object) -> bool:
+ if isinstance(value, Timeline):
+ return self == Timeline.POSTNATAL and value == Timeline.GESTATIONAL
+ else:
+ return NotImplemented
+
+ def __ge__(self, value: object) -> bool:
+ if isinstance(value, Timeline):
+ return self > value or self == value
+ else:
+ return NotImplemented
+
+
+class Age:
+ """
+ Representation of an age of an individual.
+
+ In GPSEA, we model the age at the resolution of a day.
+ The age is either gestational or postnatal. A gestational age is created
+ from the number of weeks and days since the last menstrual period
+ and the postnatal age is created from years, months and days since birth.
+
+ Age overloads the comparison operators and can, thus, be compared or sorted.
+ Gestational age is always before the postnatal age.
+
+ Internally, the age is always stored as the number of days.
+ """
+
+ ISO8601PT = re.compile(
+ r"^P(?P\d+Y)?(?P\d+M)?(?P\d+W)?(?P\d+D)?(T(\d+H)?(\d+M)?(\d+S)?)?$"
+ )
+ DAYS_IN_YEAR = 365.25
+ DAYS_IN_MONTH = DAYS_IN_YEAR / 12
+ DAYS_IN_WEEK = 7
+
+ @staticmethod
+ def gestational(
+ weeks: int,
+ days: int = 0,
+ ) -> "Age":
+ """
+ Create age from the `weeks` and `days` on the gestational timeline.
+
+ :param weeks: a non-negative `int` with the number of completed weeks of gestation.
+ :param days: an `int` in range :math:`[0, 6]` representing the number of completed gestational days.
+ """
+ if not isinstance(weeks, int) or weeks < 0:
+ raise ValueError(f"`weeks` must be non-negative `int` but was {weeks}")
+ if not isinstance(days, int) or 0 > days > 6:
+ raise ValueError(f"`days` must be an `int` between [0,6] was {days}")
+ total = weeks * Age.DAYS_IN_WEEK + days
+ return Age(days=float(total), timeline=Timeline.GESTATIONAL)
+
+ @staticmethod
+ def birth() -> "Age":
+ """
+ Age of an individual at birth.
+ """
+ return BIRTH
+
+ @staticmethod
+ def postnatal_days(days: int) -> "Age":
+ return Age(days=float(days), timeline=Timeline.POSTNATAL)
+
+ @staticmethod
+ def postnatal_years(
+ years: int,
+ ) -> "Age":
+ if not isinstance(years, int) or years < 0:
+ raise ValueError(f"`years` must be non-negative `int` but was {years}")
+ days = years * Age.DAYS_IN_YEAR
+ return Age(days=days, timeline=Timeline.POSTNATAL)
+
+ @staticmethod
+ def postnatal(
+ years: int,
+ months: int,
+ days: int,
+ ) -> "Age":
+ if all(isinstance(val, int) and val >= 0 for val in (years, months, days)):
+ total = 0.
+ total += years * Age.DAYS_IN_YEAR
+ total += months * Age.DAYS_IN_MONTH
+ total += days
+
+ return Age(days=total, timeline=Timeline.POSTNATAL)
+ else:
+ raise ValueError(
+ f"`years`, `months` and `days` must be non-negative `int`s but were {years}, {months}, and {days}"
+ )
+
+ @staticmethod
+ def from_iso8601_period(
+ value: str,
+ ) -> "Age":
+ """
+ Create `Age` from ISO8601 duration.
+
+ A `value` with **weeks** or days is parsed into a gestational age, while a `value` with years, months or days
+ is parsed into a postnatal age. An error is raised if a value for weeks and months (or years) is included
+ at the same time.
+
+
+ Examples
+ --------
+
+ Parse gestational age:
+
+ >>> from gpsea.model import Age
+ >>> gestational = Age.from_iso8601_period("P2W6D")
+ >>> gestational
+ Age(days=20.0, timeline=Timeline.GESTATIONAL)
+
+ Parse postnatal age:
+
+ >>> postnatal = Age.from_iso8601_period("P10Y")
+ >>> postnatal
+ Age(days=3652.5, timeline=Timeline.POSTNATAL)
+
+
+ :param value: a `str` with the duration (e.g. `P22W3D` for a gestational age or `P10Y4M2D` for a postnatal age).
+ """
+ matcher = Age.ISO8601PT.match(value)
+ if matcher:
+ year = matcher.group("year")
+ month = matcher.group("month")
+ week = matcher.group("week")
+ day = matcher.group("day")
+ if all(val is None for val in (year, month, week, day)):
+ raise ValueError(
+ "At least one of year, month, week or day fields must provided"
+ )
+ if week is None:
+ # postnatal
+ if all(val is None for val in (year, month, day)):
+ raise ValueError(
+ f"Year, month or day must be provided for postnatal age: {value}"
+ )
+ years = 0 if year is None else int(year[:-1])
+ months = 0 if month is None else int(month[:-1])
+ days = 0 if day is None else int(day[:-1])
+
+ return Age.postnatal(years=years, months=months, days=days)
+ else:
+ # gestational
+ if any(val is not None for val in (year, month)):
+ raise ValueError(
+ f"Year and month must not be provided for gestational age: {value}"
+ )
+ weeks = 0 if week is None else int(week[:-1])
+ days = 0 if day is None else int(day[:-1])
+
+ return Age.gestational(weeks=weeks, days=days)
+ else:
+ raise ValueError(f"'{value}' did not match ISO8601 pattern")
+
+ def __init__(
+ self,
+ days: float,
+ timeline: Timeline,
+ ):
+ if not isinstance(days, float) or math.isnan(days) or days < 0:
+ raise ValueError(f"`days` must be a non-negative `float` but was {days}")
+ self._days = days
+ if not isinstance(timeline, Timeline):
+ raise ValueError(f"`timeline` must be an instance of `Timeline` but was {timeline}")
+ self._timeline = timeline
+
+ @property
+ def days(self) -> float:
+ return self._days
+
+ @property
+ def timeline(self) -> Timeline:
+ return self._timeline
+
+ @property
+ def is_gestational(self) -> bool:
+ """
+ Return `True` if the age is on gestational timeline.
+ """
+ return self._timeline == Timeline.GESTATIONAL
+
+ @property
+ def is_postnatal(self) -> bool:
+ """
+ Return `True` if the age is on postnatal timeline.
+ """
+ return self._timeline == Timeline.POSTNATAL
+
+ def __lt__(self, value: object) -> bool:
+ return self._compare(operator.lt, value)
+
+ def __le__(self, value: object) -> bool:
+ return self._compare(operator.le, value)
+
+ def __gt__(self, value: object) -> bool:
+ return self._compare(operator.gt, value)
+
+ def __ge__(self, value: object) -> bool:
+ return self._compare(operator.ge, value)
+
+ def _compare(
+ self,
+ op: typing.Callable[[typing.Any, typing.Any], bool],
+ value: object,
+ ) -> bool:
+ if isinstance(value, Age):
+ if op(self._timeline, value._timeline):
+ return True
+ elif self._timeline == value._timeline:
+ return op(self._days, value._days)
+ else:
+ return False
+ else:
+ return NotImplemented
+
+ def __eq__(self, value: object) -> bool:
+ return (
+ isinstance(value, Age)
+ and self._days == value._days
+ and self._timeline == value._timeline
+ )
+
+ def __hash__(self) -> int:
+ return hash((self._days, self._timeline))
+
+ def __repr__(self) -> str:
+ return f"Age(days={self._days}, timeline={self._timeline})"
+
+ def __str__(self) -> str:
+ return repr(self)
+
+
+BIRTH = Age(days=0.0, timeline=Timeline.POSTNATAL)
diff --git a/src/gpsea/model/_test_temporal.py b/src/gpsea/model/_test_temporal.py
new file mode 100644
index 00000000..87bbb8fc
--- /dev/null
+++ b/src/gpsea/model/_test_temporal.py
@@ -0,0 +1,51 @@
+import pytest
+
+from ._temporal import Timeline, Age
+
+
+class TestTimeline:
+
+ @pytest.mark.parametrize(
+ "left, right, expected",
+ [
+ (Timeline.GESTATIONAL, Timeline.GESTATIONAL, False),
+ (Timeline.GESTATIONAL, Timeline.POSTNATAL, True),
+ (Timeline.POSTNATAL, Timeline.GESTATIONAL, False),
+ (Timeline.POSTNATAL, Timeline.POSTNATAL, False),
+ ],
+ )
+ def test_timeline_ordering_lt(
+ self,
+ left: Timeline,
+ right: Timeline,
+ expected: bool,
+ ):
+ assert (left < right) == expected
+ assert (left >= right) != expected
+
+ @pytest.mark.parametrize(
+ "left, right, expected",
+ [
+ (Timeline.GESTATIONAL, Timeline.GESTATIONAL, False),
+ (Timeline.GESTATIONAL, Timeline.POSTNATAL, False),
+ (Timeline.POSTNATAL, Timeline.GESTATIONAL, True),
+ (Timeline.POSTNATAL, Timeline.POSTNATAL, False),
+ ],
+ )
+ def test_timeline_ordering_gt(
+ self,
+ left: Timeline,
+ right: Timeline,
+ expected: bool,
+ ):
+ assert (left > right) == expected
+ assert (left <= right) != expected
+
+
+class TestAge:
+
+ def test_fails_if_days_is_nan(self):
+ with pytest.raises(ValueError) as e:
+ Age(days=float('nan'), timeline=Timeline.POSTNATAL)
+
+ assert e.value.args == ("`days` must be a non-negative `float` but was nan",)
diff --git a/src/gpsea/preprocessing/__init__.py b/src/gpsea/preprocessing/__init__.py
index d8469436..77be3f5f 100644
--- a/src/gpsea/preprocessing/__init__.py
+++ b/src/gpsea/preprocessing/__init__.py
@@ -2,14 +2,12 @@
from ._api import TranscriptCoordinateService, GeneCoordinateService
from ._api import VariantCoordinateFinder, FunctionalAnnotator, ImpreciseSvFunctionalAnnotator, ProteinMetadataService
from ._audit import Auditor, DataSanityIssue, Level, Notepad, NotepadTree
-from ._config import configure_caching_patient_creator, configure_patient_creator
from ._config import load_phenopacket_folder, load_phenopacket_files, load_phenopackets
from ._config import configure_caching_cohort_creator, configure_cohort_creator
from ._config import configure_default_protein_metadata_service, configure_protein_metadata_service
from ._generic import DefaultImpreciseSvFunctionalAnnotator
from ._patient import PatientCreator, CohortCreator
from ._phenopacket import PhenopacketVariantCoordinateFinder, PhenopacketPatientCreator
-from ._phenotype import PhenotypeCreator
from ._protein import ProteinAnnotationCache, ProtCachingMetadataService
from ._uniprot import UniprotProteinMetadataService
from ._variant import VariantAnnotationCache, VarCachingFunctionalAnnotator
@@ -17,7 +15,6 @@
from ._vv import VVHgvsVariantCoordinateFinder, VVMultiCoordinateService
__all__ = [
- 'configure_caching_patient_creator', 'configure_patient_creator',
'configure_caching_cohort_creator', 'configure_cohort_creator',
'configure_default_protein_metadata_service', 'configure_protein_metadata_service',
'VariantCoordinateFinder', 'FunctionalAnnotator', 'ImpreciseSvFunctionalAnnotator', 'ProteinMetadataService',
@@ -26,7 +23,6 @@
'load_phenopacket_folder', 'load_phenopacket_files', 'load_phenopackets',
'PreprocessingValidationResult',
'TranscriptCoordinateService', 'GeneCoordinateService',
- 'PhenotypeCreator',
'ProteinAnnotationCache', 'ProtCachingMetadataService',
'UniprotProteinMetadataService',
'VepFunctionalAnnotator', 'VariantAnnotationCache', 'VarCachingFunctionalAnnotator',
diff --git a/src/gpsea/preprocessing/_config.py b/src/gpsea/preprocessing/_config.py
index 5ae53eac..8ff816b9 100644
--- a/src/gpsea/preprocessing/_config.py
+++ b/src/gpsea/preprocessing/_config.py
@@ -4,6 +4,12 @@
import warnings
import hpotk
+from hpotk.validate import (
+ ValidationRunner,
+ ObsoleteTermIdsValidator,
+ AnnotationPropagationValidator,
+ PhenotypicAbnormalityValidator,
+)
# pyright: reportGeneralTypeIssues=false
from google.protobuf.json_format import Parse
@@ -17,7 +23,7 @@
from ._generic import DefaultImpreciseSvFunctionalAnnotator
from ._patient import CohortCreator
from ._phenopacket import PhenopacketPatientCreator
-from ._phenotype import PhenotypeCreator
+
from ._protein import (
ProteinMetadataService,
ProtCachingMetadataService,
@@ -34,7 +40,7 @@
def configure_caching_cohort_creator(
hpo: hpotk.MinimalOntology,
genome_build: str = "GRCh38.p13",
- validation_runner: typing.Optional[hpotk.validate.ValidationRunner] = None,
+ validation_runner: typing.Optional[ValidationRunner] = None,
cache_dir: typing.Optional[str] = None,
variant_fallback: str = "VEP",
timeout: float = 30.0,
@@ -57,7 +63,7 @@ def configure_caching_cohort_creator(
cache_dir = _configure_cache_dir(cache_dir)
build = _configure_build(genome_build)
- phenotype_creator = _setup_phenotype_creator(hpo, validation_runner)
+ validator = _setup_hpo_validator(hpo, validation_runner)
functional_annotator = _configure_functional_annotator(
cache_dir, variant_fallback, timeout
)
@@ -66,8 +72,9 @@ def configure_caching_cohort_creator(
)
hgvs_annotator = VVHgvsVariantCoordinateFinder(build)
pc = PhenopacketPatientCreator(
+ hpo=hpo,
+ validator=validator,
build=build,
- phenotype_creator=phenotype_creator,
functional_annotator=functional_annotator,
imprecise_sv_functional_annotator=imprecise_sv_functional_annotator,
hgvs_coordinate_finder=hgvs_annotator,
@@ -76,59 +83,10 @@ def configure_caching_cohort_creator(
return CohortCreator(pc)
-def configure_caching_patient_creator(
- hpo: hpotk.MinimalOntology,
- genome_build: str = "GRCh38.p13",
- validation_runner: typing.Optional[hpotk.validate.ValidationRunner] = None,
- cache_dir: typing.Optional[str] = None,
- variant_fallback: str = "VEP",
- timeout: float = 30.0,
-) -> PhenopacketPatientCreator:
- """
- A convenience function for configuring a caching :class:`~gpsea.preprocessing.PhenopacketPatientCreator`.
-
- To create the patient creator, we need hpo-toolkit's representation of HPO. Other options are optional.
-
- :param hpo: a HPO instance.
- :param genome_build: name of the genome build to use, choose from `{'GRCh37.p13', 'GRCh38.p13'}`.
- :param validation_runner: an instance of the validation runner.
- :param cache_dir: path to the folder where we will cache the results fetched from the remote APIs or `None`
- if the cache location should be determined as described in :func:`~gpsea.config.get_cache_dir_path`.
- In any case, the directory will be created if it does not exist (including non-existing parents).
- :param variant_fallback: the fallback variant annotator to use if we cannot find the annotation locally.
- Choose from ``{'VEP'}`` (just one fallback implementation is available at the moment).
- :param timeout: timeout in seconds for the REST APIs
- """
- warnings.warn(
- "`configure_caching_patient_creator` was deprecated. "
- "Use `configure_caching_cohort_creator` instead",
- DeprecationWarning,
- stacklevel=2,
- )
- cache_dir = _configure_cache_dir(cache_dir)
-
- build = _configure_build(genome_build)
- phenotype_creator = _setup_phenotype_creator(hpo, validation_runner)
- functional_annotator = _configure_functional_annotator(
- cache_dir, variant_fallback, timeout
- )
- imprecise_sv_functional_annotator = _configure_imprecise_sv_annotator(
- build, timeout
- )
- hgvs_annotator = VVHgvsVariantCoordinateFinder(build)
- return PhenopacketPatientCreator(
- build=build,
- phenotype_creator=phenotype_creator,
- functional_annotator=functional_annotator,
- imprecise_sv_functional_annotator=imprecise_sv_functional_annotator,
- hgvs_coordinate_finder=hgvs_annotator,
- )
-
-
def configure_cohort_creator(
hpo: hpotk.MinimalOntology,
genome_build: str = "GRCh38.p13",
- validation_runner: typing.Optional[hpotk.validate.ValidationRunner] = None,
+ validation_runner: typing.Optional[ValidationRunner] = None,
variant_fallback: str = "VEP",
timeout: float = 30.0,
) -> CohortCreator[Phenopacket]:
@@ -148,15 +106,18 @@ def configure_cohort_creator(
"""
build = _configure_build(genome_build)
- phenotype_creator = _setup_phenotype_creator(hpo, validation_runner)
+ validator = _setup_hpo_validator(hpo, validation_runner)
functional_annotator = _configure_fallback_functional(variant_fallback, timeout)
imprecise_sv_functional_annotator = _configure_imprecise_sv_annotator(
- build, timeout
+ build,
+ cache_dir=None,
+ timeout=timeout,
)
hgvs_annotator = VVHgvsVariantCoordinateFinder(build)
pc = PhenopacketPatientCreator(
+ hpo=hpo,
+ validator=validator,
build=build,
- phenotype_creator=phenotype_creator,
functional_annotator=functional_annotator,
imprecise_sv_functional_annotator=imprecise_sv_functional_annotator,
hgvs_coordinate_finder=hgvs_annotator,
@@ -165,52 +126,6 @@ def configure_cohort_creator(
return CohortCreator(pc)
-def configure_patient_creator(
- hpo: hpotk.MinimalOntology,
- genome_build: str = "GRCh38.p13",
- validation_runner: typing.Optional[hpotk.validate.ValidationRunner] = None,
- variant_fallback: str = "VEP",
- validation: str = "lenient",
- timeout: float = 30.0,
-) -> PhenopacketPatientCreator: # Rename to something more understandable by user
- """
- A convenience function for configuring a non-caching :class:`~gpsea.preprocessing.PhenopacketPatientCreator`.
-
- To create the patient creator, we need hpo-toolkit's representation of HPO. Other options are optional
-
- :param hpo: a HPO instance.
- :param genome_build: name of the genome build to use, choose from `{'GRCh37.p13', 'GRCh38.p13'}`.
- :param validation_runner: an instance of the validation runner.
- if the data should be cached in `.gpsea_cache` folder in the current working directory.
- In any case, the directory will be created if it does not exist (including non-existing parents).
- :param variant_fallback: the fallback variant annotator to use if we cannot find the annotation locally.
- Choose from ``{'VEP'}`` (just one fallback implementation is available at the moment).
- :param timeout: timeout in seconds for the REST APIs
- """
- warnings.warn(
- "`configure_patient_creator` was deprecated. "
- "Use `configure_cohort_creator` instead",
- DeprecationWarning,
- stacklevel=2,
- )
-
- build = _configure_build(genome_build)
-
- phenotype_creator = _setup_phenotype_creator(hpo, validation_runner)
- functional_annotator = _configure_fallback_functional(variant_fallback, timeout)
- imprecise_sv_functional_annotator = _configure_imprecise_sv_annotator(
- build, timeout
- )
- hgvs_annotator = VVHgvsVariantCoordinateFinder(build)
- return PhenopacketPatientCreator(
- build=build,
- phenotype_creator=phenotype_creator,
- functional_annotator=functional_annotator,
- imprecise_sv_functional_annotator=imprecise_sv_functional_annotator,
- hgvs_coordinate_finder=hgvs_annotator,
- )
-
-
def configure_protein_metadata_service(
cache_dir: typing.Optional[str] = None,
timeout: float = 30.0,
@@ -225,7 +140,11 @@ def configure_protein_metadata_service(
In any case, the directory will be created if it does not exist (including any non-existing parents).
:param timeout: timeout in seconds for the REST APIs.
"""
- warnings.warn('Use `configure_default_protein_metadata_service` instead', DeprecationWarning, stacklevel=2)
+ warnings.warn(
+ "Use `configure_default_protein_metadata_service` instead",
+ DeprecationWarning,
+ stacklevel=2,
+ )
return configure_default_protein_metadata_service(
cache_dir=cache_dir,
timeout=timeout,
@@ -233,9 +152,9 @@ def configure_protein_metadata_service(
def configure_default_protein_metadata_service(
- protein_source: typing.Literal['UNIPROT'] = 'UNIPROT',
+ protein_source: typing.Literal["UNIPROT"] = "UNIPROT",
cache_dir: typing.Optional[str] = None,
- timeout: float = 30.,
+ timeout: float = 30.0,
) -> ProteinMetadataService:
"""
Create default protein metadata service that will cache the protein metadata
@@ -263,16 +182,16 @@ def _configure_protein_service(
) -> ProteinMetadataService:
# (1) ProteinMetadataService
# Setup fallback
- protein_fallback = _configure_fallback_protein_service(
+ fallback_service = _configure_fallback_protein_service(
protein_fallback,
timeout,
)
# Setup protein metadata cache
- prot_cache_dir = os.path.join(cache_dir, 'protein_cache')
+ prot_cache_dir = os.path.join(cache_dir, "protein_cache")
os.makedirs(prot_cache_dir, exist_ok=True)
prot_cache = ProteinAnnotationCache(prot_cache_dir)
# Assemble the final protein metadata service
- protein_metadata_service = ProtCachingMetadataService(prot_cache, protein_fallback)
+ protein_metadata_service = ProtCachingMetadataService(prot_cache, fallback_service)
return protein_metadata_service
@@ -280,19 +199,19 @@ def _configure_fallback_protein_service(
protein_fallback: str,
timeout: float,
) -> ProteinMetadataService:
- if protein_fallback == 'UNIPROT':
+ if protein_fallback == "UNIPROT":
return UniprotProteinMetadataService(timeout)
else:
- raise ValueError(f'Unknown protein fallback annotator type {protein_fallback}')
+ raise ValueError(f"Unknown protein fallback annotator type {protein_fallback}")
def _configure_cache_dir(
cache_dir: typing.Optional[str] = None,
) -> str:
- cache_dir = get_cache_dir_path(cache_dir)
- os.makedirs(cache_dir, exist_ok=True)
+ cache_path = get_cache_dir_path(cache_dir)
+ os.makedirs(cache_path, exist_ok=True)
- return str(cache_dir)
+ return str(cache_path)
def _configure_build(genome_build: str) -> GenomeBuild:
@@ -306,24 +225,21 @@ def _configure_build(genome_build: str) -> GenomeBuild:
)
-def _setup_phenotype_creator(
+def _setup_hpo_validator(
hpo: hpotk.MinimalOntology,
- validator: typing.Optional[hpotk.validate.ValidationRunner],
-) -> PhenotypeCreator:
+ validator: typing.Optional[ValidationRunner],
+) -> ValidationRunner:
if validator is None:
# This will be the default validator
- validator = hpotk.validate.ValidationRunner(
+ return ValidationRunner(
(
- hpotk.validate.ObsoleteTermIdsValidator(hpo),
- hpotk.validate.AnnotationPropagationValidator(hpo),
- hpotk.validate.PhenotypicAbnormalityValidator(hpo),
+ ObsoleteTermIdsValidator(hpo),
+ AnnotationPropagationValidator(hpo),
+ PhenotypicAbnormalityValidator(hpo),
)
)
else:
- validator = hpotk.util.validate_instance(
- validator, hpotk.validate.ValidationRunner, "validator"
- )
- return PhenotypeCreator(hpo, validator)
+ return hpotk.util.validate_instance(validator, ValidationRunner, "validator")
def _configure_functional_annotator(
@@ -358,14 +274,15 @@ def _configure_fallback_functional(
def _configure_imprecise_sv_annotator(
genome_build: GenomeBuild,
- cache_dir: str,
- timeout: float,
+ cache_dir: typing.Optional[str] = None,
+ timeout: float = 30.0,
):
# Setup cache for SVs
- sv_cache_dir = os.path.join(cache_dir, "sv_cache")
- # TODO: implement the cache.
- # os.makedirs(sv_cache_dir, exist_ok=True)
- # var_cache = VariantAnnotationCache(sv_cache_dir)
+ if cache_dir is not None:
+ sv_cache_dir = os.path.join(cache_dir, "sv_cache")
+ # TODO: implement the cache.
+ # os.makedirs(sv_cache_dir, exist_ok=True)
+ # var_cache = VariantAnnotationCache(sv_cache_dir)
return DefaultImpreciseSvFunctionalAnnotator(
gene_coordinate_service=VVMultiCoordinateService(
@@ -412,7 +329,7 @@ def load_phenopacket_files(
) -> typing.Tuple[Cohort, PreprocessingValidationResult]:
"""
Load phenopacket JSON files, validate the data, and assemble into a :class:`~gpsea.model.Cohort`.
-
+
Phenopackets are validated, assembled into a cohort, and the validation results are reported back.
:param pp_files: an iterator with paths to phenopacket JSON files.
@@ -436,7 +353,7 @@ def load_phenopackets(
) -> typing.Tuple[Cohort, PreprocessingValidationResult]:
"""
Validate the phenopackets and assemble into a :class:`~gpsea.model.Cohort`.
-
+
The results of the validation are reported back.
:param phenopackets: path to a folder with phenopacket JSON files. An error is raised if the path does not point to
@@ -455,7 +372,9 @@ def load_phenopackets(
# Turn phenopackets into a cohort using the cohort creator.
# Keep track of the progress by wrapping the list of phenopackets
# with TQDM 😎
- cohort_iter = tqdm(phenopackets, desc="Individuals Processed", file=sys.stdout, unit="individuals")
+ cohort_iter = tqdm(
+ phenopackets, desc="Individuals Processed", file=sys.stdout, unit="individuals"
+ )
notepad = cohort_creator.prepare_notepad("Phenopackets")
cohort = cohort_creator.process(cohort_iter, notepad)
@@ -473,7 +392,7 @@ def _find_phenopacket_files(
fpath_pp_abs = os.path.abspath(pp_dir)
if not os.path.isdir(fpath_pp_abs):
raise ValueError(f"`{fpath_pp_abs}` does not point to a directory")
-
+
for patient_file in os.listdir(pp_dir):
if patient_file.endswith(".json"):
yield os.path.join(pp_dir, patient_file)
diff --git a/src/gpsea/preprocessing/_phenopacket.py b/src/gpsea/preprocessing/_phenopacket.py
index deff10d2..68d38c51 100644
--- a/src/gpsea/preprocessing/_phenopacket.py
+++ b/src/gpsea/preprocessing/_phenopacket.py
@@ -2,9 +2,13 @@
import typing
import hpotk
+from hpotk.util import validate_instance
+from hpotk.validate import ValidationRunner, ValidationLevel
-from phenopackets.schema.v2.phenopackets_pb2 import Phenopacket
import phenopackets.schema.v2.core.individual_pb2 as ppi
+from phenopackets.schema.v2.phenopackets_pb2 import Phenopacket
+from phenopackets.schema.v2.core.base_pb2 import TimeElement as PPTimeElement
+from phenopackets.schema.v2.core.phenotypic_feature_pb2 import PhenotypicFeature as PPPhenotypicFeature
from phenopackets.schema.v2.core.disease_pb2 import Disease as PPDisease
from phenopackets.schema.v2.core.measurement_pb2 import Measurement as PPMeasurement
from phenopackets.schema.v2.core.interpretation_pb2 import GenomicInterpretation
@@ -18,8 +22,12 @@
ImpreciseSvInfo,
VariantInfo,
Variant,
+ Phenotype,
Genotype,
Genotypes,
+ Age,
+ VitalStatus,
+ Status,
)
from gpsea.model.genome import GenomeBuild, GenomicRegion, Strand
from ._api import (
@@ -27,9 +35,8 @@
FunctionalAnnotator,
ImpreciseSvFunctionalAnnotator,
)
-from ._audit import Notepad
+from ._audit import Notepad, Level
from ._patient import PatientCreator
-from ._phenotype import PhenotypeCreator
class PhenopacketGenotypeParser:
@@ -220,41 +227,39 @@ def _looks_like_large_sv(
class PhenopacketPatientCreator(PatientCreator[Phenopacket]):
"""
`PhenopacketPatientCreator` transforms `Phenopacket` into :class:`~gpsea.model.Patient`.
+
+ :param hpo: HPO as :class:`~hpotk.MinimalOntology`.
+ :param validator: validation runner to check HPO terms.
+ :param build: the genome build to use for variants.
+ :param phenotype_creator: a phenotype creator for creating phenotypes.
+ :param functional_annotator: for computing functional annotations.
+ :param imprecise_sv_functional_annotator: for getting info about imprecise variants.
+ :param hgvs_coordinate_finder: for finding chromosomal coordinates for HGVS variant descriptions.
"""
def __init__(
self,
+ hpo: hpotk.MinimalOntology,
+ validator: ValidationRunner,
build: GenomeBuild,
- phenotype_creator: PhenotypeCreator,
functional_annotator: FunctionalAnnotator,
imprecise_sv_functional_annotator: ImpreciseSvFunctionalAnnotator,
hgvs_coordinate_finder: VariantCoordinateFinder[str],
- assume_karyotypic_sex: bool = True,
):
- """
- Create an instance.
-
- :param build: the genome build to use for variants.
- :param phenotype_creator: a phenotype creator for creating phenotypes.
- :param functional_annotator: for computing functional annotations.
- :param imprecise_sv_functional_annotator: for getting info about imprecise variants.
- :param hgvs_coordinate_finder: for finding chromosomal coordinates for HGVS variant descriptions.
- :param assume_karyotypic_sex: `True` if it is OK to assume that `FEMALE` has the `XX` karyotype
- and `MALE` has `XY`.
- """
self._logger = logging.getLogger(__name__)
# Violates DI, but it is specific to this class, so I'll leave it "as is".
self._coord_finder = PhenopacketVariantCoordinateFinder(
build, hgvs_coordinate_finder
)
self._gt_parser = PhenopacketGenotypeParser()
- self._phenotype_creator = hpotk.util.validate_instance(
- phenotype_creator, PhenotypeCreator, "phenotype_creator"
+ self._validator = validate_instance(validator, ValidationRunner, 'validator')
+ self._phenotype_creator = PhenopacketPhenotypicFeatureCreator(
+ hpo=validate_instance(hpo, hpotk.MinimalOntology, 'hpo'),
)
- self._functional_annotator = hpotk.util.validate_instance(
+ self._functional_annotator = validate_instance(
functional_annotator, FunctionalAnnotator, "functional_annotator"
)
- self._imprecise_sv_functional_annotator = hpotk.util.validate_instance(
+ self._imprecise_sv_functional_annotator = validate_instance(
imprecise_sv_functional_annotator,
ImpreciseSvFunctionalAnnotator,
"imprecise_sv_functional_annotator",
@@ -279,7 +284,6 @@ def __init__(
self._so_translocations = {
"1000044", # chromosomal_translocation
}
- self._assume_karyotypic_sex = assume_karyotypic_sex
def process(self, pp: Phenopacket, notepad: Notepad) -> Patient:
"""Creates a Patient from the data in a given Phenopacket
@@ -297,13 +301,15 @@ def process(self, pp: Phenopacket, notepad: Notepad) -> Patient:
# Extract karyotypic sex
indi = notepad.add_subsection("individual")
- sex = self._extract_sex(pp.subject, indi)
+ sex = PhenopacketPatientCreator._extract_sex(pp.subject, indi)
+
+ # Date of death
+ age = PhenopacketPatientCreator._extract_age(pp.subject, indi)
+ vital_status = PhenopacketPatientCreator._extract_vital_status(pp.subject, indi)
# Check phenotypes
pfs = notepad.add_subsection("phenotype-features")
- phenotypes = self._phenotype_creator.process(
- ((pf.type.id, not pf.excluded) for pf in pp.phenotypic_features), pfs
- )
+ phenotypes = self._add_phenotypes(pp.phenotypic_features, pfs)
# Check diseases
dip = notepad.add_subsection("diseases")
@@ -316,14 +322,57 @@ def process(self, pp: Phenopacket, notepad: Notepad) -> Patient:
vs = notepad.add_subsection("variants")
variants = self._add_variants(sample_id, pp, vs)
+ # Complain if we have no genotype or phenotype data to work with
+ if len(variants) == 0:
+ notepad.add_error(
+ f"Individual {pp.id} has no genotype data (variants) to work with",
+ solution="Add variants or remove the individual from the analysis",
+ )
+
+ if all(len(phenotype) == 0 for phenotype in (phenotypes, diseases, measurements)):
+ notepad.add_error(
+ f"Individual {pp.id} has no phenotype data (HPO, a diagnosis, measurement) to work with",
+ solution="Add HPO terms, a diagnosis, or measurements, or remove the individual from the analysis",
+ )
+
return Patient.from_raw_parts(
sample_id,
sex=sex,
+ age=age,
+ vital_status=vital_status,
phenotypes=phenotypes,
measurements=measurements,
variants=variants,
diseases=diseases,
)
+
+ def _add_phenotypes(
+ self,
+ pfs: typing.Iterable[PPPhenotypicFeature],
+ notepad: Notepad,
+ ) -> typing.Sequence[Phenotype]:
+ phenotypes = []
+
+ for i, pf in enumerate(pfs):
+ ith_pf_notepad = notepad.add_subsection(f"#{i}")
+ phenotype = self._phenotype_creator.process(
+ pf=pf,
+ notepad=ith_pf_notepad,
+ )
+ if phenotype is not None:
+ phenotypes.append(phenotype)
+
+ # We check
+ vr = self._validator.validate_all(phenotypes)
+ for result in vr.results:
+ level = PhenopacketPatientCreator._translate_level(result.level)
+ if level is None:
+ # Should not happen. Please let the developers know about this issue!
+ raise ValueError(f'Unknown result validation level {result.level}')
+
+ notepad.add_issue(level, result.message)
+
+ return phenotypes
def _add_diseases(
self, diseases: typing.Sequence[PPDisease], notepad: Notepad
@@ -342,17 +391,49 @@ def _add_diseases(
final_diseases = []
for i, dis in enumerate(diseases):
+ ith_disease_subsection = notepad.add_subsection(f"#{i}")
if not dis.HasField("term"):
- notepad.add_error(f"#{i} has no `term`")
+ ith_disease_subsection.add_error("disease diagnosis has no `term`")
continue
else:
term_id = hpotk.TermId.from_curie(dis.term.id)
-
+
+ if dis.HasField("onset"):
+ onset = PhenopacketPatientCreator._parse_time_element(
+ time_element=dis.onset,
+ notepad=ith_disease_subsection,
+ )
+ else:
+ onset = None
+
# Do not include excluded diseases if we decide to assume excluded if not included
- final_diseases.append(Disease(term_id, dis.term.label, not dis.excluded))
+ final_diseases.append(
+ Disease.from_raw_parts(
+ term_id=term_id,
+ name=dis.term.label,
+ is_observed=not dis.excluded,
+ onset=onset,
+ ),
+ )
return final_diseases
+ @staticmethod
+ def _parse_time_element(
+ time_element: PPTimeElement,
+ notepad: Notepad,
+ ) -> typing.Optional[Age]:
+ case = time_element.WhichOneof("element")
+ if case == "gestational_age":
+ age = time_element.gestational_age
+ return Age.gestational(weeks=age.weeks, days=age.days)
+ elif case == "age":
+ age = time_element.age
+ return Age.from_iso8601_period(value=age.iso8601duration)
+ else:
+ notepad.add_warning(f"`time_element` is in currently unsupported format `{case}`")
+ return None
+
def _add_measurements(
self,
measurements: typing.Sequence[PPMeasurement],
@@ -397,8 +478,8 @@ def _add_measurements(
final_measurements.append(Measurement(test_term_id, test_name, test_result, unit))
return final_measurements
+ @staticmethod
def _extract_sex(
- self,
individual: ppi.Individual,
notepad: Notepad,
) -> typing.Optional[Sex]:
@@ -414,6 +495,50 @@ def _extract_sex(
notepad.add_warning(f'Unknown sex type: {sex}')
return Sex.UNKNOWN_SEX
+ @staticmethod
+ def _extract_age(
+ individual: ppi.Individual,
+ notepad: Notepad,
+ ) -> typing.Optional[Age]:
+ if individual.HasField("time_at_last_encounter"):
+ tale = individual.time_at_last_encounter
+ return PhenopacketPatientCreator._parse_time_element(tale, notepad)
+ return None
+
+ @staticmethod
+ def _extract_vital_status(
+ individual: ppi.Individual,
+ notepad: Notepad,
+ ) -> typing.Optional[VitalStatus]:
+ if individual.HasField("vital_status"):
+ vital_status = individual.vital_status
+
+ if vital_status.status == vital_status.UNKNOWN_STATUS:
+ status = Status.UNKNOWN
+ elif vital_status.status == vital_status.ALIVE:
+ status = Status.ALIVE
+ elif vital_status.status == vital_status.DECEASED:
+ status = Status.DECEASED
+ else:
+ notepad.add_warning(f"Unexpected vital status value {vital_status}")
+ status = Status.UNKNOWN
+
+ if vital_status.HasField("time_of_death"):
+ age_of_death = PhenopacketPatientCreator._parse_time_element(
+ time_element=vital_status.time_of_death,
+ notepad=notepad,
+ )
+ if status == Status.ALIVE and age_of_death is not None:
+ notepad.add_warning("Individual is ALIVE but has age of death")
+ else:
+ age_of_death = None
+ return VitalStatus(
+ status=status,
+ age_of_death=age_of_death,
+ )
+
+ return None
+
def _add_variants(
self,
sample_id: SampleLabels,
@@ -458,8 +583,8 @@ def _add_variants(
)
except ValueError as error:
sub_note.add_warning(
- f"Patient {pp.id} has an error with variant {variant_info.variant_key}",
- f"Try again or remove variant form testing... {error}",
+ f"Individual {pp.id} has an error with variant {variant_info.variant_key}",
+ f"Try again or remove variant from testing... {error}",
)
continue
elif variant_info.has_sv_info():
@@ -471,8 +596,8 @@ def _add_variants(
)
except ValueError as error:
sub_note.add_warning(
- f"Patient {pp.id} has an error with variant {variant_info.variant_key}",
- f"Try again or remove variant form testing... {error}",
+ f"Individual {pp.id} has an error with variant {variant_info.variant_key}",
+ f"Try again or remove variant from testing... {error}",
)
continue
else:
@@ -482,7 +607,7 @@ def _add_variants(
if len(tx_annotations) == 0:
sub_note.add_warning(
- f"Patient {pp.id} has an error with variant {variant_info.variant_key}",
+ f"Individual {pp.id} has an error with variant {variant_info.variant_key}",
"Remove variant from testing... tx_anno == 0",
)
continue
@@ -496,9 +621,6 @@ def _add_variants(
)
)
- if len(variants) == 0:
- notepad.add_error(f"Patient {pp.id} has no variants to work with")
-
return variants
def _extract_variant_info(
@@ -517,7 +639,7 @@ def _extract_variant_info(
except ValueError:
notepad.add_warning(
"Expected a VCF record, a VRS CNV, or an expression with `hgvs.c`"
- f"but had an error retrieving any from patient {sample_id}",
+ f"but had an error retrieving any from individual {sample_id}",
"Remove variant from testing",
)
return None
@@ -601,3 +723,82 @@ def _map_structural_type_to_variant_class(
return None
else:
raise ValueError(f"Unknown structural type {structural_type}")
+
+ @staticmethod
+ def _translate_level(lvl: ValidationLevel) -> typing.Optional[Level]:
+ if lvl == ValidationLevel.WARNING:
+ return Level.WARN
+ elif lvl == ValidationLevel.ERROR:
+ return Level.ERROR
+ else:
+ return None
+
+
+class PhenopacketPhenotypicFeatureCreator:
+ # NOT PART OF THE PUBLIC API
+
+ def __init__(
+ self,
+ hpo: hpotk.MinimalOntology,
+ ):
+ self._hpo = hpo
+
+ def process(
+ self,
+ pf: PPPhenotypicFeature,
+ notepad: Notepad,
+ ) -> typing.Optional[Phenotype]:
+ if not pf.HasField("type"):
+ notepad.add_error("phenotypic feature has no `type`")
+ return None
+
+ # Check the CURIE is well-formed
+ try:
+ term_id = hpotk.TermId.from_curie(curie=pf.type.id)
+ except ValueError as ve:
+ notepad.add_warning(
+ f'{ve.args[0]}',
+ 'Ensure the term ID consists of a prefix (e.g. `HP`) '
+ 'and id (e.g. `0001250`) joined by colon `:` or underscore `_`',
+ )
+ return None
+
+ # Check the term is an HPO concept
+ if term_id.prefix != 'HP':
+ notepad.add_warning(
+ f'{term_id} is not an HPO term',
+ 'Remove non-HPO concepts from the analysis input',
+ )
+ return None
+
+ # Term must be present in HPO
+ term = self._hpo.get_term(term_id)
+ if term is None:
+ notepad.add_warning(
+ f'{term_id} is not in HPO version `{self._hpo.version}`',
+ 'Correct the HPO term or use the latest HPO for the analysis',
+ )
+ return None
+
+ assert term is not None
+ if term.identifier != term_id:
+ # Input includes an obsolete term ID. We emit a warning and update the term ID behind the scenes,
+ # since `term.identifier` always returns the primary term ID.
+ notepad.add_warning(
+ f'{term_id} is an obsolete identifier for {term.name}',
+ f'Replace {term_id} with the primary term ID {term.identifier}',
+ )
+
+ if pf.HasField("onset"):
+ onset = PhenopacketPatientCreator._parse_time_element(
+ time_element=pf.onset,
+ notepad=notepad,
+ )
+ else:
+ onset = None
+
+ return Phenotype.from_raw_parts(
+ term_id=term.identifier,
+ is_observed=not pf.excluded,
+ onset=onset,
+ )
diff --git a/src/gpsea/preprocessing/_phenotype.py b/src/gpsea/preprocessing/_phenotype.py
deleted file mode 100644
index c0214540..00000000
--- a/src/gpsea/preprocessing/_phenotype.py
+++ /dev/null
@@ -1,114 +0,0 @@
-import hpotk
-import typing
-import logging
-
-from hpotk.validate import ValidationLevel
-
-from gpsea.model import Phenotype
-
-from ._audit import Auditor, Level, Notepad
-
-
-class PhenotypeCreator(Auditor[typing.Iterable[typing.Tuple[str, bool]], typing.Sequence[Phenotype]]):
- """
- `PhenotypeCreator` validates the input phenotype features and prepares them for the downstream analysis.
-
- The creator expects an iterable with tuples that contain a CURIE and status. The CURIE must correspond
- to a HPO term identifier and status must be a `bool`.
-
- The creator prunes CURIES with simple errors such as malformed CURIE or non-HPO terms and validates the rest
- with HPO toolkit's validator.
- """
-
- def __init__(
- self,
- hpo: hpotk.MinimalOntology,
- validator: hpotk.validate.ValidationRunner,
- ):
- self._logger = logging.getLogger(__name__)
- self._hpo = hpotk.util.validate_instance(hpo, hpotk.MinimalOntology, 'hpo')
- self._validator = hpotk.util.validate_instance(validator, hpotk.validate.ValidationRunner, 'validator')
-
- def process(
- self,
- inputs: typing.Iterable[typing.Tuple[str, bool]],
- notepad: Notepad,
- ) -> typing.Sequence[Phenotype]:
- """
- Map CURIEs and observation states into phenotypes and validate the requirements.
-
- Args:
- inputs (Iterable[Tuple[str, bool]]): 2-element tuples with a CURIE `str` and observation state as `bool`
- (`True` if phenotype was observed).
- notepad: Notepad
- Returns:
- A sequence of phenotypes
- """
- phenotypes = []
-
- for i, (curie, is_observed) in enumerate(inputs):
- # Check the CURIE is well-formed
- try:
- term_id = hpotk.TermId.from_curie(curie)
- except ValueError as ve:
- notepad.add_warning(
- f'#{i} {ve.args[0]}',
- 'Ensure the term ID consists of a prefix (e.g. `HP`) '
- 'and id (e.g. `0001250`) joined by colon `:` or underscore `_`',
- )
- continue
-
- # Check the term is an HPO concept
- if term_id.prefix != 'HP':
- notepad.add_warning(
- f'#{i} {term_id} is not an HPO term',
- 'Remove non-HPO concepts from the analysis input',
- )
- continue
-
- # Term must be present in HPO
- term = self._hpo.get_term(term_id)
- if term is None:
- notepad.add_warning(
- f'#{i} {term_id} is not in HPO version `{self._hpo.version}`',
- 'Correct the HPO term or use the latest HPO for the analysis',
- )
- continue
-
- assert term is not None
- if term.identifier != term_id:
- # Input includes an obsolete term ID. We emit a warning and update the term ID behind the scenes,
- # since `term.identifier` always returns the primary term ID.
- notepad.add_warning(
- f'#{i} {term_id} is an obsolete identifier for {term.name}',
- f'Replace {term_id} with the primary term ID {term.identifier}',
- )
-
- phenotypes.append(Phenotype.from_term(term, is_observed))
-
- # Check we have some phenotype terms to work with.
- if len(phenotypes) == 0:
- notepad.add_warning(
- 'No phenotype terms were left after the validation',
- 'Revise the phenotype terms and try again',
- )
- else:
- vr = self._validator.validate_all(phenotypes)
- for result in vr.results:
- level = PhenotypeCreator._translate_level(result.level)
- if level is None:
- # Should not happen. Please let the developers know about this issue!
- raise ValueError(f'Unknown result validation level {result.level}')
-
- notepad.add_issue(level, result.message)
-
- return phenotypes
-
- @staticmethod
- def _translate_level(lvl: ValidationLevel) -> typing.Optional[Level]:
- if lvl == ValidationLevel.WARNING:
- return Level.WARN
- elif lvl == ValidationLevel.ERROR:
- return Level.ERROR
- else:
- return None
diff --git a/src/gpsea/view/__init__.py b/src/gpsea/view/__init__.py
index 4738197a..8c316af5 100644
--- a/src/gpsea/view/__init__.py
+++ b/src/gpsea/view/__init__.py
@@ -1,6 +1,6 @@
-from ._cohort import CohortViewable
+from ._cohort import CohortViewer
from ._cohort_variant_viewer import CohortVariantViewer
-from ._disease import DiseaseViewable
+from ._disease import DiseaseViewer
from ._phenotype_analysis import summarize_hpo_analysis
from ._protein_viewer import ProteinVariantViewer
from ._protein_visualizable import ProteinVisualizable
@@ -13,9 +13,9 @@
__all__ = [
'GpseaReport',
'CohortVariantViewer',
- 'CohortViewable',
+ 'CohortViewer',
'ProteinVisualizer', 'ProteinVisualizable', 'ProteinVariantViewer',
- 'DiseaseViewable',
+ 'DiseaseViewer',
'MtcStatsViewer',
'summarize_hpo_analysis',
'VariantTranscriptVisualizer',
diff --git a/src/gpsea/view/_cohort.py b/src/gpsea/view/_cohort.py
index 2b36ebea..da154cfd 100644
--- a/src/gpsea/view/_cohort.py
+++ b/src/gpsea/view/_cohort.py
@@ -11,10 +11,10 @@
ToDisplay = namedtuple('ToDisplay', ['hgvs_cdna', 'hgvsp', 'variant_effects'])
-class CohortViewable:
+
+class CohortViewer:
"""
- Class to create a viewable object that is uses a Jinja2 template to create an HTML element
- for display in the Jupyter notebook.
+ `CohortViewer` summarizes the most salient :class:`~gpsea.model.Cohort` aspects into an HTML report.
"""
def __init__(
@@ -41,7 +41,7 @@ def process(
transcript_id: typing.Optional[str] = None,
) -> GpseaReport:
"""
- Create an HTML that should be shown with display(HTML(..)) of the ipython package.
+ Generate the report for a given `cohort`.
Args:
cohort (Cohort): The cohort being analyzed in the current Notebook
@@ -77,7 +77,7 @@ def _prepare_context(
)
variant_counts = list()
- variant_to_display_d = CohortViewable._get_variant_description(cohort, transcript_id)
+ variant_to_display_d = CohortViewer._get_variant_description(cohort, transcript_id)
for variant_key, count in cohort.list_all_variants(top=self._top_variant_count):
# get HGVS or human readable variant
if variant_key in variant_to_display_d:
@@ -90,7 +90,7 @@ def _prepare_context(
hgvs_cdna = ''
protein_name = ''
effects = ''
-
+
variant_counts.append(
{
"variant": variant_key,
@@ -114,22 +114,31 @@ def _prepare_context(
"count": disease_count,
}
)
-
+
n_diseases = len(disease_counts)
var_effects_list = list()
+ var_effects_d = dict()
if transcript_id is not None:
has_transcript = True
data_by_tx = cohort.variant_effect_count_by_tx(tx_id=transcript_id)
- # e.g., data structure -- {'effect}': 'FRAMESHIFT_VARIANT', 'count': 175}, {'effect}': 'STOP_GAINED', 'count': 67},
+ # e.g., data structure
+ # -- {'effect}': 'FRAMESHIFT_VARIANT', 'count': 175},
+ # -- {'effect}': 'STOP_GAINED', 'count': 67},
for tx_id, counter in data_by_tx.items():
if tx_id == transcript_id:
for effect, count in counter.items():
- var_effects_list.append({"effect": effect, "count": count})
+ var_effects_d[effect] = count
+ total = sum(var_effects_d.values())
+ # Sort in descending order based on counts
+ sorted_counts_desc = dict(sorted(var_effects_d.items(), key=lambda item: item[1], reverse=True))
+ for effect, count in sorted_counts_desc.items():
+ percent = f"{round(count / total * 100)}%"
+ var_effects_list.append({"effect": effect, "count": count, "percent": percent})
else:
has_transcript = False
- if transcript_id is None:
transcript_id = "MANE transcript ID"
+
# The following dictionary is used by the Jinja2 HTML template
return {
"n_individuals": len(cohort.all_patients),
@@ -161,21 +170,28 @@ def _get_variant_description(
only_hgvs (bool): do not show the transcript ID part of the HGVS annotation, just the annotation.
Returns:
- typing.Mapping[str, ToDisplay]: key: variant key, value: namedtuple(display (e.g. HGVS) string of variant, hgvsp protein string of variant)
+ typing.Mapping[str, ToDisplay]:
+ key: variant key,
+ value: namedtuple(display (e.g. HGVS) string of variant, hgvsp protein string of variant)
"""
chrom_to_display = dict()
var_formatter = VariantFormatter(transcript_id)
-
+
for var in cohort.all_variants():
variant_key = var.variant_info.variant_key
display = var_formatter.format_as_string(var)
- tx_annotation = var.get_tx_anno_by_tx_id(transcript_id)
- if tx_annotation is not None:
- hgvsp = tx_annotation.hgvsp
- var_effects = [var_eff.name for var_eff in tx_annotation.variant_effects]
+ if transcript_id is None:
+ tx_annotation = None
else:
+ tx_annotation = var.get_tx_anno_by_tx_id(transcript_id)
+
+ if tx_annotation is None:
hgvsp = None
var_effects = None
+ else:
+ hgvsp = tx_annotation.hgvsp
+ var_effects = [var_eff.name for var_eff in tx_annotation.variant_effects]
+
if only_hgvs:
# do not show the transcript id
fields_dna = display.split(":")
diff --git a/src/gpsea/view/_cohort_variant_viewer.py b/src/gpsea/view/_cohort_variant_viewer.py
index ae960d13..3d741399 100644
--- a/src/gpsea/view/_cohort_variant_viewer.py
+++ b/src/gpsea/view/_cohort_variant_viewer.py
@@ -10,7 +10,7 @@
ToDisplay = namedtuple('ToDisplay', ['hgvs_cdna', 'hgvsp', 'variant_effects'])
-VariantData = namedtuple('VariantData', ['variant_key', 'hgvs_cdna', 'hgvsp', 'variant_effects'])
+VariantData = namedtuple('VariantData', ['variant_key', 'hgvs_cdna', 'hgvsp', 'variant_effects', 'exons'])
class CohortVariantViewer:
@@ -83,6 +83,7 @@ def _prepare_context(
"variant_name": var_data.hgvs_cdna,
"protein_name": var_data.hgvsp,
"variant_effects": ", ".join(var_data.variant_effects),
+ "exons": ", ".join(map(str, var_data.exons)) if var_data.exons is not None else None,
"count": count,
}
)
@@ -129,6 +130,7 @@ def _get_variant_data(
hgvs_cdna=display,
hgvsp="p.?",
variant_effects=[effect],
+ exons=[]
)
else:
variant_key = variant.variant_info.variant_key
@@ -137,9 +139,11 @@ def _get_variant_data(
if tx_annotation is not None:
hgvsp = tx_annotation.hgvsp
var_effects = [var_eff.to_display() for var_eff in tx_annotation.variant_effects]
+ exons=tx_annotation.overlapping_exons
else:
hgvsp = None
var_effects = []
+ exons = []
if only_hgvs:
# do not show the transcript id
fields_dna = display.split(":")
@@ -158,4 +162,5 @@ def _get_variant_data(
hgvs_cdna=display_hgvs_cDNA,
hgvsp=hgvsp,
variant_effects=var_effects,
+ exons=exons
)
diff --git a/src/gpsea/view/_disease.py b/src/gpsea/view/_disease.py
index b5396742..650220d4 100644
--- a/src/gpsea/view/_disease.py
+++ b/src/gpsea/view/_disease.py
@@ -4,10 +4,11 @@
from jinja2 import Environment, PackageLoader
from collections import Counter, defaultdict
+from gpsea.model import Cohort
from ._report import GpseaReport, HtmlGpseaReport
-class DiseaseViewable:
+class DiseaseViewer:
"""
TODO
"""
@@ -21,12 +22,18 @@ def __init__(
environment = Environment(loader=(PackageLoader('gpsea.view', 'templates')))
self._cohort_template = environment.get_template("disease.html")
- def process(self, cohort) -> GpseaReport:
- context = self._prepare_context(cohort)
+ def process(
+ self,
+ cohort: Cohort,
+ ) -> GpseaReport:
+ context = DiseaseViewer._prepare_context(cohort)
html = self._cohort_template.render(context)
return HtmlGpseaReport(html=html)
- def _prepare_context(self, cohort) -> typing.Mapping[str, typing.Any]:
+ @staticmethod
+ def _prepare_context(
+ cohort: Cohort,
+ ) -> typing.Mapping[str, typing.Any]:
diseases = cohort.list_all_diseases()
n_diseases = len(diseases)
disease_counts = list()
diff --git a/src/gpsea/view/templates/all_variants.html b/src/gpsea/view/templates/all_variants.html
index 9640bd1a..0f561426 100644
--- a/src/gpsea/view/templates/all_variants.html
+++ b/src/gpsea/view/templates/all_variants.html
@@ -78,6 +78,7 @@ Variant alleles
Variant key |
Variant (cDNA) |
Variant (protein) |
+ Overlapping Exons |
Effects |
Count |
@@ -86,6 +87,7 @@ Variant alleles
{{ vdata.variant_key }} |
{{ vdata.variant_name }} |
{{ vdata.protein_name }} |
+ {{ vdata.exons }} |
{{ vdata.variant_effects }} |
{{ vdata.count }} |
diff --git a/src/gpsea/view/templates/cohort.html b/src/gpsea/view/templates/cohort.html
index 22108199..c57920e8 100644
--- a/src/gpsea/view/templates/cohort.html
+++ b/src/gpsea/view/templates/cohort.html
@@ -144,11 +144,13 @@ Variant categories for {{ transcript_id }}
| Variant effect |
Annotation Count |
+ Percent |
{% for var_effect in var_effects_list %}
| {{ var_effect.effect }} |
{{ var_effect.count }} |
+ {{ var_effect.percent }} |
{% endfor %}
diff --git a/tests/analysis/conftest.py b/tests/analysis/conftest.py
index 19711790..bde9f2ac 100644
--- a/tests/analysis/conftest.py
+++ b/tests/analysis/conftest.py
@@ -38,8 +38,10 @@ def degenerated_cohort(
Patient.from_raw_parts(
labels=labels_a,
sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(
- Phenotype(
+ Phenotype.from_raw_parts(
term_id=hpotk.TermId.from_curie("HP:0000118"),
is_observed=True,
),
@@ -74,8 +76,10 @@ def degenerated_cohort(
Patient.from_raw_parts(
labels=labels_b,
sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(
- Phenotype(
+ Phenotype.from_raw_parts(
term_id=hpotk.TermId.from_curie("HP:0000118"),
is_observed=True,
),
diff --git a/tests/analysis/pcats/test_hpo_term_analysis.py b/tests/analysis/pcats/test_hpo_term_analysis.py
index 8adc9ff3..cb9a46a1 100644
--- a/tests/analysis/pcats/test_hpo_term_analysis.py
+++ b/tests/analysis/pcats/test_hpo_term_analysis.py
@@ -27,6 +27,7 @@ def phenotype_mtc_filter(
return HpoMtcFilter.default_filter(
hpo=hpo,
term_frequency_threshold=0.2,
+ annotation_frequency_threshold=0.25,
)
@pytest.fixture
diff --git a/tests/analysis/predicate/genotype/conftest.py b/tests/analysis/predicate/genotype/conftest.py
index 74144d7b..69741412 100644
--- a/tests/analysis/predicate/genotype/conftest.py
+++ b/tests/analysis/predicate/genotype/conftest.py
@@ -191,6 +191,8 @@ def patient_w_missense(
return Patient.from_raw_parts(
labels=sample_labels,
sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -206,6 +208,8 @@ def patient_w_frameshift(
return Patient.from_raw_parts(
labels=sample_labels,
sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -330,9 +334,11 @@ def adam(
genesis_missense_mutation: Variant,
genesis_synonymous_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
adam_label,
sex=Sex.MALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -354,9 +360,11 @@ def eve(
genesis_missense_mutation: Variant,
genesis_synonymous_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
eve_label,
sex=Sex.FEMALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -378,9 +386,11 @@ def cain(
genesis_missense_mutation: Variant,
genesis_synonymous_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
cain_label,
sex=Sex.MALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -513,9 +523,11 @@ def walt(
white_missense_mutation: Variant,
white_synonymous_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
walt_label,
sex=Sex.MALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -537,9 +549,11 @@ def skyler(
white_missense_mutation: Variant,
white_synonymous_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
skyler_label,
sex=Sex.FEMALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -561,9 +575,11 @@ def flynn(
white_missense_mutation: Variant,
white_synonymous_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
flynn_label,
sex=Sex.MALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -585,9 +601,11 @@ def holly(
white_missense_mutation: Variant,
white_synonymous_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
holly_label,
sex=Sex.FEMALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -669,9 +687,11 @@ def anakin(
anakin_label: SampleLabels,
skywalker_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
anakin_label,
sex=Sex.MALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -689,9 +709,11 @@ def padme(
padme_label: SampleLabels,
skywalker_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
padme_label,
sex=Sex.FEMALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -709,9 +731,11 @@ def luke(
luke_label: SampleLabels,
skywalker_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
luke_label,
sex=Sex.MALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
@@ -729,9 +753,11 @@ def leia(
leia_label: SampleLabels,
skywalker_mutation: Variant,
) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
leia_label,
sex=Sex.FEMALE,
+ age=None,
+ vital_status=None,
phenotypes=(),
measurements=(),
diseases=(),
diff --git a/tests/analysis/predicate/genotype/test_allele_counter.py b/tests/analysis/predicate/genotype/test_allele_counter.py
index 8cf2c2f2..6b20abcb 100644
--- a/tests/analysis/predicate/genotype/test_allele_counter.py
+++ b/tests/analysis/predicate/genotype/test_allele_counter.py
@@ -177,10 +177,6 @@ def patient(
) -> Patient:
return Patient.from_raw_parts(
labels=sample_labels,
- sex=Sex.UNKNOWN_SEX,
- phenotypes=(),
- measurements=(),
- diseases=(),
variants=(
het_lmna,
hom_alt_lmna,
diff --git a/tests/analysis/predicate/genotype/test_gt_predicates.py b/tests/analysis/predicate/genotype/test_gt_predicates.py
index d799e22d..704d956f 100644
--- a/tests/analysis/predicate/genotype/test_gt_predicates.py
+++ b/tests/analysis/predicate/genotype/test_gt_predicates.py
@@ -280,7 +280,7 @@ def test_biallelic_predicate__invalid_partitions(
biallelic_predicate(
a_predicate=is_missense,
b_predicate=is_synonymous,
- names=("A", "B"),
+ a_label="A", b_label="B",
partitions=partitions
)
@@ -309,11 +309,7 @@ def test_get_question(self):
@staticmethod
def make_patient(label: str, sex: Sex) -> Patient:
- return Patient(
+ return Patient.from_raw_parts(
SampleLabels(label),
sex,
- phenotypes=(),
- measurements=(),
- diseases=(),
- variants=(),
)
diff --git a/tests/analysis/predicate/test_phenotype.py b/tests/analysis/predicate/test_phenotype.py
index 609417a9..78ec8855 100644
--- a/tests/analysis/predicate/test_phenotype.py
+++ b/tests/analysis/predicate/test_phenotype.py
@@ -15,7 +15,7 @@ def test_prepare_hpo_terms_of_interest(
hpo=hpo,
)
- assert len(terms) == 66
+ assert len(terms) == 71
def test_prepare_predicates_for_terms_of_interest(
@@ -27,5 +27,5 @@ def test_prepare_predicates_for_terms_of_interest(
hpo=hpo,
)
- assert len(predicates) == 66
+ assert len(predicates) == 71
assert all(isinstance(p, PhenotypePolyPredicate) for p in predicates)
diff --git a/tests/analysis/pscore/test_counting_scorer.py b/tests/analysis/pscore/test_counting_scorer.py
index 9198a9fa..cf078e9d 100644
--- a/tests/analysis/pscore/test_counting_scorer.py
+++ b/tests/analysis/pscore/test_counting_scorer.py
@@ -54,15 +54,12 @@ def test_a_patient(
labels=SampleLabels("test"),
sex=Sex.UNKNOWN_SEX,
phenotypes=(
- Phenotype(
+ Phenotype.from_raw_parts(
hpotk.TermId.from_curie(curie),
is_observed=True,
)
for curie in curies
),
- measurements=(),
- diseases=(),
- variants=(),
)
actual = counting_scorer.score(patient)
diff --git a/tests/analysis/pscore/test_de_vries_scorer.py b/tests/analysis/pscore/test_de_vries_scorer.py
index 61b9cfee..a96384c7 100644
--- a/tests/analysis/pscore/test_de_vries_scorer.py
+++ b/tests/analysis/pscore/test_de_vries_scorer.py
@@ -67,9 +67,8 @@ def test_a_patient(
expected: int,
devries_scorer: DeVriesPhenotypeScorer,
):
- patient = Patient(
- labels=SampleLabels("test"),
- sex=Sex.UNKNOWN_SEX,
+ patient = Patient.from_raw_parts(
+ labels="test",
phenotypes=(
Phenotype.from_raw_parts(
term_id=curie,
@@ -77,9 +76,6 @@ def test_a_patient(
)
for curie in term_set
),
- measurements=(),
- diseases=(),
- variants=(),
)
actual = devries_scorer.score(patient)
diff --git a/tests/analysis/temporal/test_api.py b/tests/analysis/temporal/test_api.py
new file mode 100644
index 00000000..d2d547db
--- /dev/null
+++ b/tests/analysis/temporal/test_api.py
@@ -0,0 +1,110 @@
+import json
+import os
+
+import hpotk
+import pytest
+
+import pandas as pd
+
+from gpsea.model import Cohort
+from gpsea.io import GpseaJSONDecoder
+from gpsea.analysis.predicate.genotype import (
+ GenotypePolyPredicate,
+ VariantPredicates,
+ monoallelic_predicate,
+)
+from gpsea.analysis.temporal import SurvivalAnalysis, SurvivalAnalysisResult, Survival
+from gpsea.analysis.temporal.endpoint import hpo_onset
+from gpsea.analysis.temporal.stats import LogRankTest
+
+
+@pytest.fixture(scope="module")
+def umod_cohort(
+ fpath_cohort_data_dir: str,
+) -> Cohort:
+ fpath_cohort = os.path.join(fpath_cohort_data_dir, "UMOD.0.1.20.json")
+ with open(fpath_cohort) as fh:
+ return json.load(fh, cls=GpseaJSONDecoder)
+
+
+@pytest.fixture(scope="module")
+def umod_gt_predicate() -> GenotypePolyPredicate:
+ in_exon_3 = VariantPredicates.exon(3, tx_id="NM_003361.4")
+ return monoallelic_predicate(
+ a_predicate=in_exon_3, b_predicate=~in_exon_3,
+ a_label="Exon 3", b_label="Other exon",
+ )
+
+
+class TestSurvivalAnalysis:
+
+ @pytest.fixture(scope="class")
+ def survival_analysis(self) -> SurvivalAnalysis:
+ return SurvivalAnalysis(statistic=LogRankTest())
+
+ def test_compare_genotype_vs_survival(
+ self,
+ survival_analysis: SurvivalAnalysis,
+ hpo: hpotk.MinimalOntology,
+ umod_cohort: Cohort,
+ umod_gt_predicate: GenotypePolyPredicate,
+ ):
+
+ endpoint = hpo_onset(
+ hpo=hpo,
+ term_id="HP:0003774", # Stage 5 chronic kidney disease
+ )
+
+ result = survival_analysis.compare_genotype_vs_survival(
+ cohort=umod_cohort,
+ gt_predicate=umod_gt_predicate,
+ endpoint=endpoint,
+ )
+
+ assert result.pval == pytest.approx(0.062004258)
+
+
+class TestSurvivalAnalysisResult:
+
+ @pytest.fixture(scope="class")
+ def result(
+ self,
+ umod_gt_predicate: GenotypePolyPredicate,
+ ) -> SurvivalAnalysisResult:
+ data = pd.DataFrame(
+ data={
+ "patient_id": ["A", "B", "C"],
+ "genotype": [0, 1, None],
+ "survival": [
+ Survival(value=12.3, is_censored=False),
+ None,
+ Survival(value=45.6, is_censored=True),
+ ],
+ }
+ ).set_index("patient_id")
+ return SurvivalAnalysisResult(
+ gt_predicate=umod_gt_predicate,
+ data=data,
+ pval=0.1234,
+ )
+
+ def test_properties(
+ self,
+ result: SurvivalAnalysisResult,
+ ):
+ assert tuple(result.gt_predicate.get_category_names()) == (
+ "Exon 3",
+ "Other exon",
+ )
+ assert result.data.index.to_list() == ["A", "B", "C"]
+ assert result.pval == pytest.approx(0.1234)
+
+ def test_complete_records(
+ self,
+ result: SurvivalAnalysisResult,
+ ):
+ records = result.complete_records()
+
+ assert records.shape == (1, 2)
+ assert records.loc["A", "genotype"] == 0
+ assert records.loc["A", "survival"] == Survival(value=12.3, is_censored=False)
diff --git a/tests/analysis/temporal/test_base.py b/tests/analysis/temporal/test_base.py
new file mode 100644
index 00000000..e8f01403
--- /dev/null
+++ b/tests/analysis/temporal/test_base.py
@@ -0,0 +1,33 @@
+import pytest
+
+from gpsea.analysis.temporal import Survival
+
+
+class TestSurvival:
+
+ def test_format_survival(self):
+ s = Survival(value=123.4, is_censored=False)
+
+ assert str(s) == "Survival(value=123.4, is_censored=False)"
+
+ @pytest.mark.parametrize(
+ "value",
+ [
+ float("nan"),
+ float("inf"),
+ float("-inf"),
+ ],
+ )
+ def test_survival_value_must_be_finite(
+ self,
+ value: float,
+ ):
+ with pytest.raises(AssertionError) as e:
+ Survival(value=value, is_censored=True)
+
+ assert e.value.args == (f"`value` must be finite and non-NaN, but was {value}",)
+
+ def test_survival_is_hashable(self):
+ s = Survival(value=123, is_censored=True)
+
+ assert hash(s) == -1172739046759774526
diff --git a/tests/analysis/temporal/test_endpoint.py b/tests/analysis/temporal/test_endpoint.py
new file mode 100644
index 00000000..5cfc5f63
--- /dev/null
+++ b/tests/analysis/temporal/test_endpoint.py
@@ -0,0 +1,192 @@
+import hpotk
+import pytest
+
+from gpsea.model import Patient, Age, VitalStatus, Status, Disease, Phenotype
+from gpsea.analysis.temporal.endpoint import death, disease_onset, hpo_onset
+
+
+@pytest.fixture
+def patient_no_data() -> Patient:
+ return Patient.from_raw_parts(
+ labels="?",
+ )
+
+
+@pytest.fixture
+def alive() -> Patient:
+ return Patient.from_raw_parts(
+ labels="A",
+ age=Age.postnatal_days(days=40),
+ vital_status=VitalStatus(status=Status.ALIVE, age_of_death=None),
+ )
+
+
+@pytest.fixture
+def deceased() -> Patient:
+ return Patient.from_raw_parts(
+ labels="D",
+ age=Age.postnatal_days(days=60),
+ vital_status=VitalStatus(
+ status=Status.DECEASED, age_of_death=Age.postnatal_days(60)
+ ),
+ )
+
+
+class TestDeath:
+
+ def test_compute_survival__alive(
+ self,
+ alive: Patient,
+ ):
+ endpoint = death(timeline="postnatal")
+
+ survival = endpoint.compute_survival(alive)
+
+ assert survival is not None
+ assert survival.is_censored
+ assert survival.value == pytest.approx(40.0)
+
+ def test_compute_survival__deceased(
+ self,
+ deceased: Patient,
+ ):
+ endpoint = death(timeline="postnatal")
+
+ survival = endpoint.compute_survival(deceased)
+
+ assert survival is not None
+ assert not survival.is_censored
+ assert survival.value == pytest.approx(60.0)
+
+ def test_compute_survival__unknown(
+ self,
+ patient_no_data: Patient,
+ ):
+ endpoint = death(timeline="postnatal")
+
+ survival = endpoint.compute_survival(patient_no_data)
+
+ assert survival is None
+
+ def test_display_question(self):
+ endpoint = death(timeline="postnatal")
+
+ assert endpoint.display_question() == "Compute time until postnatal death"
+
+
+class TestDiseaseOnset:
+
+ @pytest.fixture(scope="class")
+ def with_disease(self):
+ return Patient.from_raw_parts(
+ labels="X",
+ diseases=(
+ Disease.from_raw_parts(
+ term_id="OMIM:123456",
+ name="NOT REALLY IMPORTANT HERE",
+ is_observed=True,
+ onset=Age.postnatal_days(40),
+ ),
+ ),
+ )
+
+ def test_compute_survival__alive(
+ self,
+ alive: Patient,
+ ):
+ endpoint = disease_onset(disease_id="OMIM:123456")
+
+ survival = endpoint.compute_survival(alive)
+
+ assert survival is not None
+ assert survival.is_censored
+ assert survival.value == pytest.approx(40.0)
+
+ def test_compute_survival__with_target_disease(
+ self,
+ with_disease: Patient,
+ ):
+ endpoint = disease_onset(disease_id="OMIM:123456")
+
+ survival = endpoint.compute_survival(with_disease)
+
+ assert survival is not None
+ assert not survival.is_censored
+ assert survival.value == pytest.approx(40.)
+
+ def test_compute_survival__off_target_disease(
+ self,
+ with_disease: Patient,
+ ):
+ endpoint = disease_onset(disease_id="OMIM:100000")
+
+ survival = endpoint.compute_survival(with_disease)
+
+ assert survival is None
+
+ def test_display_question(self):
+ endpoint = disease_onset(disease_id="OMIM:100000")
+
+ assert endpoint.display_question() == "Compute time until postnatal diagnosis of OMIM:100000"
+
+
+class TestPhenotypeOnset:
+
+ @pytest.fixture
+ def phenotyped(self) -> Patient:
+ return Patient.from_raw_parts(
+ labels="P",
+ age=Age.postnatal_years(30),
+ vital_status=VitalStatus(status=Status.ALIVE, age_of_death=None),
+ phenotypes=(
+ Phenotype.from_raw_parts(
+ "HP:0007359", # Focal-onset seizure
+ is_observed=True,
+ onset=Age.postnatal_days(20),
+ ),
+ Phenotype.from_raw_parts(
+ "HP:0020219", # Motor seizure
+ is_observed=True,
+ onset=Age.postnatal_days(25),
+ ),
+ Phenotype.from_raw_parts(
+ "HP:0011153", # Focal motor seizure
+ is_observed=False,
+ onset=Age.postnatal_days(25),
+ )
+ )
+ )
+
+ def test_compute_survival__alive(
+ self,
+ hpo: hpotk.MinimalOntology,
+ alive: Patient,
+ ):
+ endpoint = hpo_onset(hpo, term_id="HP:0001250") # Seizure
+
+ survival = endpoint.compute_survival(alive)
+
+ assert survival is not None
+ assert survival.is_censored
+ assert survival.value == pytest.approx(40.)
+
+ def test_compute_survival__phenotyped(
+ self,
+ hpo: hpotk.MinimalOntology,
+ phenotyped: Patient,
+ ):
+ endpoint = hpo_onset(hpo, term_id="HP:0001250") # Seizure
+
+ survival = endpoint.compute_survival(phenotyped)
+
+ assert survival is not None
+ assert not survival.is_censored
+ assert survival.value == pytest.approx(20.) # Focal-onset seizure has the earliest onset
+
+ def test_display_question(
+ self,
+ hpo: hpotk.MinimalOntology,
+ ):
+ endpoint = hpo_onset(hpo, term_id="HP:0001250") # Seizure
+
+ assert endpoint.display_question() == "Compute time until postnatal onset of Seizure"
diff --git a/tests/analysis/temporal/test_statistics.py b/tests/analysis/temporal/test_statistics.py
new file mode 100644
index 00000000..f13c2fef
--- /dev/null
+++ b/tests/analysis/temporal/test_statistics.py
@@ -0,0 +1,30 @@
+import pytest
+
+from gpsea.analysis.temporal import Survival
+from gpsea.analysis.temporal.stats import LogRankTest
+
+
+class TestLogRankTest:
+
+ def test_compute_pval(self):
+ statistic = LogRankTest()
+
+ values = (
+ (
+ Survival(1.0, is_censored=True),
+ Survival(10.0, is_censored=True),
+ Survival(10.0, is_censored=False),
+ Survival(13.0, is_censored=False),
+ Survival(16.0, is_censored=True),
+ ),
+ (
+ Survival(1.0, is_censored=False),
+ Survival(4.0, is_censored=True),
+ Survival(4.2, is_censored=False),
+ Survival(6.0, is_censored=False),
+ Survival(3.0, is_censored=True),
+ ),
+ )
+ pval = statistic.compute_pval(values)
+
+ assert pval == pytest.approx(0.013383101)
diff --git a/tests/analysis/test_mtc_filter.py b/tests/analysis/test_mtc_filter.py
index f70d7350..2599eedc 100644
--- a/tests/analysis/test_mtc_filter.py
+++ b/tests/analysis/test_mtc_filter.py
@@ -12,6 +12,20 @@
from gpsea.model import Cohort
+@pytest.fixture(scope='module')
+def patient_counts(
+ suox_cohort: Cohort,
+ suox_gt_predicate: GenotypePolyPredicate,
+ suox_pheno_predicates: typing.Sequence[PhenotypePolyPredicate[hpotk.TermId]],
+) -> typing.Sequence[pd.DataFrame]:
+ _, counts = apply_predicates_on_patients(
+ patients=suox_cohort.all_patients,
+ gt_predicate=suox_gt_predicate,
+ pheno_predicates=suox_pheno_predicates,
+ )
+ return counts
+
+
class TestHpoMtcFilter:
@pytest.fixture
@@ -25,20 +39,6 @@ def mtc_filter(
annotation_frequency_threshold=.1,
)
- @pytest.fixture(scope='class')
- def patient_counts(
- self,
- suox_cohort: Cohort,
- suox_gt_predicate: GenotypePolyPredicate,
- suox_pheno_predicates: typing.Sequence[PhenotypePolyPredicate[hpotk.TermId]],
- ) -> typing.Sequence[pd.DataFrame]:
- _, counts = apply_predicates_on_patients(
- patients=suox_cohort.all_patients,
- gt_predicate=suox_gt_predicate,
- pheno_predicates=suox_pheno_predicates,
- )
- return counts
-
@pytest.fixture(scope='class')
def gt_predicate(
self,
@@ -180,46 +180,6 @@ def test_filter_terms_to_test(
None, None,
]
- def test_specified_term_mtc_filter(
- self,
- suox_gt_predicate: GenotypePolyPredicate,
- suox_pheno_predicates: typing.Sequence[PhenotypePolyPredicate[hpotk.TermId]],
- patient_counts: typing.Sequence[pd.DataFrame],
- suox_cohort: Cohort,
- ):
- """
- The point of this test is to check that if we filter to test only one term ("HP:0032350"), then this
- is the only term that should survive the filter. We start with a total of five terms (n_usable==5),
- but after our filter, only one survives, and we have four cases in which the
- reason for filtering out is 'Non-specified term'
- """
- specified_filter = SpecifiedTermsMtcFilter(
- terms_to_test=(hpotk.TermId.from_curie("HP:0032350"),),
- )
-
- mtc_report = specified_filter.filter(
- gt_predicate=suox_gt_predicate,
- ph_predicates=suox_pheno_predicates,
- counts=patient_counts,
- cohort_size=len(suox_cohort),
- )
- assert isinstance(mtc_report, typing.Sequence)
- assert len(mtc_report) == 5
-
- is_passed = [r.is_passed() for r in mtc_report]
- assert is_passed == [
- False, False, True, False, False,
- ]
-
- reasons = [r.reason for r in mtc_report]
- assert reasons == [
- 'Non-specified term',
- 'Non-specified term',
- None,
- 'Non-specified term',
- 'Non-specified term',
- ]
-
def test_min_observed_HPO_threshold(
self,
suox_pheno_predicates: typing.Sequence[PhenotypePolyPredicate[hpotk.TermId]],
@@ -290,3 +250,66 @@ def test_min_observed_HPO_threshold(
ph_predicate=hypertonia_predicate,
)
assert max_f == pytest.approx(0.5714, abs=EPSILON)
+
+
+class TestSpecifyTermsMtcFilter:
+
+ def test_specified_term_mtc_filter(
+ self,
+ suox_gt_predicate: GenotypePolyPredicate,
+ suox_pheno_predicates: typing.Sequence[PhenotypePolyPredicate[hpotk.TermId]],
+ patient_counts: typing.Sequence[pd.DataFrame],
+ suox_cohort: Cohort,
+ ):
+ """
+ The point of this test is to check that if we filter to test only one term ("HP:0032350"), then this
+ is the only term that should survive the filter. We start with a total of five terms (n_usable==5),
+ but after our filter, only one survives, and we have four cases in which the
+ reason for filtering out is 'Non-specified term'
+ """
+ specified_filter = SpecifiedTermsMtcFilter(
+ terms_to_test=(
+ hpotk.TermId.from_curie("HP:0032350"),
+ ),
+ )
+
+ mtc_report = specified_filter.filter(
+ gt_predicate=suox_gt_predicate,
+ ph_predicates=suox_pheno_predicates,
+ counts=patient_counts,
+ cohort_size=len(suox_cohort),
+ )
+ assert isinstance(mtc_report, typing.Sequence)
+ assert len(mtc_report) == 5
+
+ is_passed = [r.is_passed() for r in mtc_report]
+ assert is_passed == [
+ False, False, True, False, False,
+ ]
+
+ reasons = [r.reason for r in mtc_report]
+ assert reasons == [
+ 'Non-specified term',
+ 'Non-specified term',
+ None,
+ 'Non-specified term',
+ 'Non-specified term',
+ ]
+
+ @pytest.mark.parametrize(
+ "val, msg",
+ [
+ ("NotACurie", "The CURIE NotACurie has no colon `:` or underscore `_`"),
+ (0, "0 is neither `str` nor `hpotk.TermId`"),
+ ]
+ )
+ def test_explodes_if_invalid_terms_provided(
+ self,
+ val: typing.Any,
+ msg: str
+ ):
+ with pytest.raises(ValueError) as e:
+ SpecifiedTermsMtcFilter(
+ terms_to_test=(val,),
+ )
+ assert e.value.args == (msg,)
diff --git a/tests/conftest.py b/tests/conftest.py
index 699ba283..0ddf7393 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -49,11 +49,24 @@ def fpath_project_dir(fpath_test_dir: str) -> str:
@pytest.fixture(scope='session')
def fpath_test_dir() -> str:
"""
- Path to `tests` folder
+ Path to `tests` folder.
"""
return os.path.dirname(os.path.abspath(__file__))
+@pytest.fixture(scope='session')
+def fpath_docs_dir(fpath_project_dir: str) -> str:
+ """
+ Path to `docs` folder.
+ """
+ return os.path.join(fpath_project_dir, "docs")
+
+
+@pytest.fixture(scope='session')
+def fpath_cohort_data_dir(fpath_docs_dir: str) -> str:
+ return os.path.join(fpath_docs_dir, "cohort-data")
+
+
@pytest.fixture(scope='session')
def fpath_test_data_dir(fpath_test_dir: str) -> str:
return os.path.join(fpath_test_dir, 'test_data')
@@ -338,6 +351,8 @@ def toy_cohort(
Patient.from_raw_parts(
SampleLabels('HetSingleVar'),
sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(
test_phenotypes['arachnodactyly_T'],
test_phenotypes['spasticity_F'],
@@ -350,6 +365,8 @@ def toy_cohort(
Patient.from_raw_parts(
SampleLabels('HetDoubleVar1'),
sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(
test_phenotypes['arachnodactyly_T'], test_phenotypes['seizure_T'], test_phenotypes['spasticity_T'],
),
@@ -359,7 +376,9 @@ def toy_cohort(
),
Patient.from_raw_parts(
SampleLabels('HetDoubleVar2'),
- sex=Sex.UNKNOWN_SEX,
+ sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(
test_phenotypes['arachnodactyly_F'], test_phenotypes['spasticity_T'], test_phenotypes['seizure_T'],
),
@@ -370,6 +389,8 @@ def toy_cohort(
Patient.from_raw_parts(
SampleLabels('HomoVar'),
sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(
test_phenotypes['arachnodactyly_T'], test_phenotypes['spasticity_T'], test_phenotypes['seizure_T'],
),
@@ -380,6 +401,8 @@ def toy_cohort(
Patient.from_raw_parts(
SampleLabels('LargeCNV'),
sex=Sex.UNKNOWN_SEX,
+ age=None,
+ vital_status=None,
phenotypes=(
test_phenotypes['arachnodactyly_T'], test_phenotypes['spasticity_T'], test_phenotypes['seizure_F'],
),
@@ -395,17 +418,17 @@ def toy_cohort(
@pytest.fixture(scope='session')
def test_phenotypes() -> typing.Mapping[str, Phenotype]:
return {
- 'arachnodactyly_T': Phenotype(hpotk.TermId.from_curie('HP:0001166'), True),
- 'seizure_T': Phenotype(hpotk.TermId.from_curie('HP:0001250'), True),
- 'focal_clonic_seizure_T': Phenotype(
+ 'arachnodactyly_T': Phenotype.from_raw_parts(hpotk.TermId.from_curie('HP:0001166'), True),
+ 'seizure_T': Phenotype.from_raw_parts(hpotk.TermId.from_curie('HP:0001250'), True),
+ 'focal_clonic_seizure_T': Phenotype.from_raw_parts(
hpotk.TermId.from_curie('HP:0002266'), True,
),
- 'spasticity_T': Phenotype(hpotk.TermId.from_curie('HP:0001257'), True),
+ 'spasticity_T': Phenotype.from_raw_parts(hpotk.TermId.from_curie('HP:0001257'), True),
- 'arachnodactyly_F': Phenotype(hpotk.TermId.from_curie('HP:0001166'), False),
- 'seizure_F': Phenotype(hpotk.TermId.from_curie('HP:0001250'), False),
- 'spasticity_F': Phenotype(hpotk.TermId.from_curie('HP:0001257'), False),
- 'focal_clonic_seizure_F': Phenotype(
+ 'arachnodactyly_F': Phenotype.from_raw_parts(hpotk.TermId.from_curie('HP:0001166'), False),
+ 'seizure_F': Phenotype.from_raw_parts(hpotk.TermId.from_curie('HP:0001250'), False),
+ 'spasticity_F': Phenotype.from_raw_parts(hpotk.TermId.from_curie('HP:0001257'), False),
+ 'focal_clonic_seizure_F': Phenotype.from_raw_parts(
hpotk.TermId.from_curie('HP:0002266'), False,
),
}
@@ -414,8 +437,8 @@ def test_phenotypes() -> typing.Mapping[str, Phenotype]:
@pytest.fixture(scope='session')
def test_diseases() -> typing.Mapping[str, Disease]:
return {
- 'KBG_T': Disease(hpotk.TermId.from_curie("OMIM:148050"), "KBG syndrome", True),
- 'KBG_F': Disease(hpotk.TermId.from_curie("OMIM:148050"), "KBG syndrome", False),
+ 'KBG_T': Disease.from_raw_parts(hpotk.TermId.from_curie("OMIM:148050"), "KBG syndrome", True),
+ 'KBG_F': Disease.from_raw_parts(hpotk.TermId.from_curie("OMIM:148050"), "KBG syndrome", False),
}
diff --git a/tests/model/test_temporal.py b/tests/model/test_temporal.py
new file mode 100644
index 00000000..78e228bf
--- /dev/null
+++ b/tests/model/test_temporal.py
@@ -0,0 +1,87 @@
+import pytest
+
+from gpsea.model import Age
+
+
+class TestAge:
+
+ @pytest.mark.parametrize(
+ "weeks, days, expected",
+ [
+ (0, 6, 6.0),
+ (4, 2, 30.0),
+ (20, 0, 140.0),
+ ],
+ )
+ def test_gestational(self, weeks: int, days: int, expected: int):
+ age = Age.gestational(weeks, days=days)
+ assert age.days == expected
+ assert age.is_gestational
+
+ @pytest.mark.parametrize(
+ "years, expected",
+ [
+ (0, 0.),
+ (1, 365.25),
+ (10, 3652.5),
+ ],
+ )
+ def test_postnatal_years(
+ self,
+ years: int,
+ expected: float,
+ ):
+ age = Age.postnatal_years(years=years)
+ assert age.days == pytest.approx(expected)
+
+ @pytest.mark.parametrize(
+ "days, expected",
+ [
+ (0, 0.),
+ (1, 1.),
+ (10, 10.),
+ ],
+ )
+ def test_postnatal_days(
+ self,
+ days: int,
+ expected: float,
+ ):
+ age = Age.postnatal_days(days=days)
+ assert age.days == pytest.approx(expected)
+
+ @pytest.mark.parametrize(
+ "value, is_postnatal, days",
+ [
+ ("P1D", True, 1.),
+ ("P1Y", True, 365.25),
+ ("P0W6D", False, 6.),
+ ("P4W2D", False, 30.),
+ ]
+ )
+ def test_from_iso8601_period(
+ self,
+ value: str,
+ is_postnatal: bool,
+ days: float,
+ ):
+ age = Age.from_iso8601_period(value)
+ assert age.is_postnatal == is_postnatal
+ assert age.days == pytest.approx(days)
+
+ @pytest.mark.parametrize(
+ "value, error",
+ [
+ ("P", "At least one of year, month, week or day fields must provided"),
+ ("P4M1W1D", "Year and month must not be provided for gestational age: P4M1W1D"),
+ ("Whatever", "'Whatever' did not match ISO8601 pattern"),
+ ]
+ )
+ def test_from_iso8601_period__errors(
+ self,
+ value: str,
+ error: str,
+ ):
+ with pytest.raises(ValueError) as e:
+ Age.from_iso8601_period(value)
+ assert e.value.args == (error,)
diff --git a/tests/preprocessing/test_patient_and_cohort_creator.py b/tests/preprocessing/test_patient_and_cohort_creator.py
index 901030e0..0ac8fbdc 100644
--- a/tests/preprocessing/test_patient_and_cohort_creator.py
+++ b/tests/preprocessing/test_patient_and_cohort_creator.py
@@ -5,7 +5,7 @@
import pytest
from gpsea.model.genome import GenomeBuild
-from gpsea.preprocessing import PhenotypeCreator, FunctionalAnnotator, ImpreciseSvFunctionalAnnotator, VariantCoordinateFinder
+from gpsea.preprocessing import FunctionalAnnotator, ImpreciseSvFunctionalAnnotator, VariantCoordinateFinder
from gpsea.preprocessing import VepFunctionalAnnotator, VarCachingFunctionalAnnotator, VVHgvsVariantCoordinateFinder, DefaultImpreciseSvFunctionalAnnotator
from gpsea.preprocessing import PhenopacketPatientCreator
from gpsea.preprocessing import VVMultiCoordinateService
@@ -14,17 +14,6 @@
class TestPhenopacketCohortCreator:
- @pytest.fixture
- def phenotype_creator(
- self,
- hpo: hpotk.MinimalOntology,
- validation_runner: hpotk.validate.ValidationRunner,
- ) -> PhenotypeCreator:
- return PhenotypeCreator(
- hpo=hpo,
- validator=validation_runner,
- )
-
@pytest.fixture
def functional_annotator(
self,
@@ -64,15 +53,17 @@ def variant_coordinate_finder(
@pytest.fixture
def patient_creator(
self,
+ hpo: hpotk.MinimalOntology,
+ validation_runner: hpotk.validate.ValidationRunner,
genome_build: GenomeBuild,
- phenotype_creator: PhenotypeCreator,
functional_annotator: FunctionalAnnotator,
imprecise_sv_functional_annotator: ImpreciseSvFunctionalAnnotator,
variant_coordinate_finder: VariantCoordinateFinder,
) -> PhenopacketPatientCreator:
return PhenopacketPatientCreator(
+ hpo=hpo,
+ validator=validation_runner,
build=genome_build,
- phenotype_creator=phenotype_creator,
functional_annotator=functional_annotator,
imprecise_sv_functional_annotator=imprecise_sv_functional_annotator,
hgvs_coordinate_finder=variant_coordinate_finder,
diff --git a/tests/preprocessing/test_phenopacket.py b/tests/preprocessing/test_phenopacket.py
index b1e597a1..f4630186 100644
--- a/tests/preprocessing/test_phenopacket.py
+++ b/tests/preprocessing/test_phenopacket.py
@@ -21,7 +21,8 @@
ImpreciseSvFunctionalAnnotator,
DefaultImpreciseSvFunctionalAnnotator,
)
-from gpsea.preprocessing import PhenopacketPatientCreator, PhenotypeCreator
+from gpsea.preprocessing import Level
+from gpsea.preprocessing import PhenopacketPatientCreator
from gpsea.preprocessing import VVMultiCoordinateService
@@ -135,17 +136,6 @@ def read_genomic_interpretation_json(fpath: str) -> GenomicInterpretation:
class TestPhenopacketPatientCreator:
- @pytest.fixture
- def phenotype_creator(
- self,
- hpo: hpotk.MinimalOntology,
- validation_runner: hpotk.validate.ValidationRunner,
- ) -> PhenotypeCreator:
- return PhenotypeCreator(
- hpo=hpo,
- validator=validation_runner,
- )
-
@pytest.fixture
def functional_annotator(
self,
@@ -185,15 +175,17 @@ def variant_coordinate_finder(
@pytest.fixture
def patient_creator(
self,
+ hpo: hpotk.MinimalOntology,
+ validation_runner: hpotk.validate.ValidationRunner,
genome_build: GenomeBuild,
- phenotype_creator: PhenotypeCreator,
functional_annotator: FunctionalAnnotator,
imprecise_sv_functional_annotator: ImpreciseSvFunctionalAnnotator,
variant_coordinate_finder: VariantCoordinateFinder,
) -> PhenopacketPatientCreator:
return PhenopacketPatientCreator(
+ hpo=hpo,
+ validator=validation_runner,
build=genome_build,
- phenotype_creator=phenotype_creator,
functional_annotator=functional_annotator,
imprecise_sv_functional_annotator=imprecise_sv_functional_annotator,
hgvs_coordinate_finder=variant_coordinate_finder,
@@ -227,6 +219,15 @@ def test_phenopacket_patient_creator(
patient.labels.label_summary() == "individual 1[PMID_30968594_individual_1]"
)
assert patient.sex.is_male()
+ assert patient.age is not None
+ assert patient.age.days == pytest.approx(334.8125)
+ assert patient.age.is_postnatal
+
+ assert patient.vital_status is not None
+ assert patient.vital_status.is_deceased
+ assert patient.vital_status.age_of_death is not None
+ assert patient.vital_status.age_of_death.days == pytest.approx(365.25)
+ assert patient.vital_status.age_of_death.is_postnatal
# 6 Phenotype features
assert len(patient.phenotypes) == 6
@@ -271,4 +272,64 @@ def test_phenopacket_patient_creator(
values = tuple(m.test_result for m in patient.measurements)
assert values == (800.0, 127.0, 180.2, 116.6, 52.93, 23.71)
- # TODO: test disease and variants/interpretations
+ # a disease
+ assert len(patient.diseases) == 1
+
+ disease = patient.diseases[0]
+ assert disease.identifier.value == "OMIM:201910"
+ assert disease.is_present is True
+
+ assert disease.onset is not None
+ assert disease.onset.is_postnatal is True
+ assert disease.onset.days == pytest.approx(20.)
+
+ def test_individual_with_no_genotype(
+ self,
+ phenopacket: Phenopacket,
+ patient_creator: PhenopacketPatientCreator,
+ ):
+ """
+ Check if we get an error if no genotype info is available.
+ """
+ pp = Phenopacket()
+ pp.CopyFrom(phenopacket)
+ del pp.interpretations[:] # clear variants
+
+ notepad = patient_creator.prepare_notepad("no-gt")
+
+ _ = patient_creator.process(pp=pp, notepad=notepad)
+
+ errors = tuple(notepad.errors())
+
+ assert len(errors) == 1
+ error = errors[0]
+ assert error.level == Level.ERROR
+ assert error.message == "Individual PMID_30968594_individual_1 has no genotype data (variants) to work with"
+ assert error.solution == "Add variants or remove the individual from the analysis"
+
+ def test_individual_with_no_phenotype(
+ self,
+ phenopacket: Phenopacket,
+ patient_creator: PhenopacketPatientCreator,
+ ):
+ """
+ Check if we get an error if no phenotype info is available.
+ """
+ pp = Phenopacket()
+ pp.CopyFrom(phenopacket)
+ # clear phenotype
+ del pp.phenotypic_features[:]
+ del pp.diseases[:]
+ del pp.measurements[:]
+
+ notepad = patient_creator.prepare_notepad("no-gt")
+
+ _ = patient_creator.process(pp=pp, notepad=notepad)
+
+ errors = tuple(notepad.errors())
+
+ assert len(errors) == 1
+ error = errors[0]
+ assert error.level == Level.ERROR
+ assert error.message == "Individual PMID_30968594_individual_1 has no phenotype data (HPO, a diagnosis, measurement) to work with"
+ assert error.solution == "Add HPO terms, a diagnosis, or measurements, or remove the individual from the analysis"
diff --git a/tests/preprocessing/test_phenotype_creator.py b/tests/preprocessing/test_phenotype_creator.py
deleted file mode 100644
index f3c8adc8..00000000
--- a/tests/preprocessing/test_phenotype_creator.py
+++ /dev/null
@@ -1,73 +0,0 @@
-import hpotk
-import pytest
-
-from gpsea.preprocessing import PhenotypeCreator, Level
-
-
-class TestPhenotypeCreator:
-
- @pytest.fixture
- def phenotype_creator(
- self, hpo: hpotk.MinimalOntology,
- validation_runner: hpotk.validate.ValidationRunner,
- ) -> PhenotypeCreator:
- return PhenotypeCreator(hpo, validation_runner)
-
- @pytest.mark.parametrize(
- 'curie, message, solution',
- [
- (
- 'WalterWhite',
- '#0 The CURIE WalterWhite has no colon `:` or underscore `_`',
- 'Ensure the term ID consists of a prefix (e.g. `HP`) and id (e.g. `0001250`) '
- 'joined by colon `:` or underscore `_`',
- ),
- (
- 'NCIT_C12345',
- '#0 NCIT:C12345 is not an HPO term',
- 'Remove non-HPO concepts from the analysis input',
- ),
- (
- 'HP:999999',
- '#0 HP:999999 is not in HPO version `2024-04-26`',
- 'Correct the HPO term or use the latest HPO for the analysis',
- ),
- ]
- )
- def test_input_curies(
- self,
- phenotype_creator: PhenotypeCreator,
- curie: str, message: str, solution: str,
- ):
- inputs = ((curie, True),)
-
- notepad = phenotype_creator.prepare_notepad('top-level')
- phenotypes = phenotype_creator.process(inputs, notepad)
-
- assert len(phenotypes) == 0
-
- issues = list(notepad.issues)
- assert len(issues) == 2
-
- first = issues[0]
- assert first.message == message
- assert first.solution == solution
-
- def test_annotation_propagation(self, phenotype_creator: PhenotypeCreator):
- inputs = (
- ('HP:0001250', False), # Seizure
- ('HP:0002266', True), # Focal clonic seizure
- )
-
- notepad = phenotype_creator.prepare_notepad('top-level')
- phenotypes = phenotype_creator.process(inputs, notepad)
-
- assert len(phenotypes) == 2
-
- issues = list(notepad.issues)
- assert len(issues) == 1
-
- first = issues[0]
- assert first.level == Level.ERROR
- assert first.message == 'Terms should not contain both present Focal clonic seizure [HP:0002266] and its present or excluded ancestor Seizure [HP:0001250]'
- assert first.solution is None
diff --git a/tests/test_data/SUOX.json b/tests/test_data/SUOX.json
index ebaed2c9..a5b884bb 100644
--- a/tests/test_data/SUOX.json
+++ b/tests/test_data/SUOX.json
@@ -6,10 +6,13 @@
"meta_label": "PMID_36303223_individual_10_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -17,7 +20,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -144,10 +148,13 @@
"meta_label": "PMID_36303223_individual_11_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -155,7 +162,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -397,10 +405,13 @@
"meta_label": "PMID_36303223_individual_12_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -408,7 +419,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -535,10 +547,13 @@
"meta_label": "PMID_36303223_individual_13_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -546,7 +561,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -673,50 +689,63 @@
"meta_label": "PMID_36303223_individual_14_PMID_11825068"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0034332",
- "is_present": true
+ "is_present": true,
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},
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
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},
{
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- "is_present": true
+ "is_present": true,
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},
{
"term_id": "HP:0000252",
- "is_present": true
+ "is_present": true,
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},
{
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- "is_present": true
+ "is_present": true,
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{
"term_id": "HP:0032350",
- "is_present": true
+ "is_present": true,
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{
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- "is_present": true
+ "is_present": true,
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},
{
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+ "is_present": false,
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{
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+ "is_present": false,
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{
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- "is_present": false
+ "is_present": false,
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{
"term_id": "HP:0012610",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -724,7 +753,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 152.1875,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -851,34 +884,43 @@
"meta_label": "PMID_36303223_individual_15_PMID_12001203"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
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},
{
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+ "is_present": true,
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{
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{
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+ "is_present": false,
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{
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+ "is_present": false,
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{
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+ "is_present": false,
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{
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- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -886,7 +928,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 0.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -1013,42 +1059,53 @@
"meta_label": "PMID_36303223_individual_16_PMID_12368985"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
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{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
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{
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+ "is_present": true,
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{
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{
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{
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+ "is_present": true,
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{
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+ "is_present": true,
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{
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{
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+ "is_present": false,
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{
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- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -1056,7 +1113,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 24.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -1298,50 +1359,63 @@
"meta_label": "PMID_36303223_individual_17_PMID_15952210"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
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{
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+ "is_present": true,
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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+ "is_present": false,
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}
],
"measurements": [],
@@ -1349,7 +1423,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 3.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -1476,54 +1554,68 @@
"meta_label": "PMID_36303223_individual_18_PMID_23414711"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
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{
"term_id": "HP:0012758",
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+ "is_present": true,
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{
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{
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{
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{
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{
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{
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{
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{
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{
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+ "is_present": false,
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}
],
"measurements": [],
@@ -1531,7 +1623,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 365.25,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -1658,62 +1754,78 @@
"meta_label": "PMID_36303223_individual_19_PMID_23452914"
},
"sex": "FEMALE",
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+ "vital_status": null,
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{
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{
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{
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{
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+ "is_present": false,
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}
],
"measurements": [],
@@ -1721,7 +1833,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 365.25,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -1848,46 +1964,58 @@
"meta_label": "PMID_36303223_individual_1_PMID_9050047"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
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{
"term_id": "HP:0012758",
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{
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{
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{
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{
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{
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{
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{
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}
],
"measurements": [],
@@ -1895,7 +2023,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 0.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -2022,30 +2154,38 @@
"meta_label": "PMID_36303223_individual_20_PMID_24938149"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
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{
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{
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{
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+ "is_present": false,
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}
],
"measurements": [],
@@ -2053,7 +2193,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 0.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -2295,46 +2439,58 @@
"meta_label": "PMID_36303223_individual_21_PMID_27289259"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
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{
"term_id": "HP:0012758",
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{
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{
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{
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{
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{
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{
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+ "is_present": false,
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}
],
"measurements": [],
@@ -2342,7 +2498,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 15.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -2469,46 +2629,58 @@
"meta_label": "PMID_36303223_individual_22_PMID_27289259"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0012758",
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{
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{
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{
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{
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{
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{
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{
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{
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{
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}
],
"measurements": [],
@@ -2516,7 +2688,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 39.4375,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -2643,42 +2819,53 @@
"meta_label": "PMID_36303223_individual_23_PMID_28725568"
},
"sex": "MALE",
+ "age": null,
+ "vital_status": null,
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{
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{
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{
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{
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{
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],
"measurements": [],
@@ -2686,7 +2873,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -2928,42 +3119,53 @@
"meta_label": "PMID_36303223_individual_24_PMID_28629418"
},
"sex": "FEMALE",
+ "age": null,
+ "vital_status": null,
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{
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{
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{
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{
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{
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{
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"measurements": [],
@@ -2971,7 +3173,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -3098,42 +3304,53 @@
"meta_label": "PMID_36303223_individual_25_PMID_31870341"
},
"sex": "MALE",
+ "age": null,
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@@ -3141,7 +3358,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -3383,42 +3604,53 @@
"meta_label": "PMID_36303223_individual_26_PMID_31870341"
},
"sex": "MALE",
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+ "vital_status": null,
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@@ -3426,7 +3658,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -3668,42 +3904,53 @@
"meta_label": "PMID_36303223_individual_27_PMID_31870341"
},
"sex": "FEMALE",
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+ "vital_status": null,
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@@ -3711,7 +3958,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -3953,46 +4204,58 @@
"meta_label": "PMID_36303223_individual_28_PMID_33335014"
},
"sex": "FEMALE",
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@@ -4000,7 +4263,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -4127,50 +4394,63 @@
"meta_label": "PMID_36303223_individual_29_PMID_33335014"
},
"sex": "MALE",
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@@ -4178,7 +4458,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -4305,46 +4589,58 @@
"meta_label": "PMID_36303223_individual_2_PMID_9600976"
},
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@@ -4352,7 +4648,11 @@
{
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"name": "Sulfite oxidase deficiency",
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+ "timeline": "POSTNATAL"
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],
"variants": [
@@ -4479,62 +4779,78 @@
"meta_label": "PMID_36303223_individual_30_PMID_31806255"
},
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@@ -4542,7 +4858,11 @@
{
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+ "timeline": "POSTNATAL"
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],
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@@ -4669,62 +4989,78 @@
"meta_label": "PMID_36303223_individual_31_PMID_31806255"
},
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@@ -4732,7 +5068,11 @@
{
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"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -4859,46 +5199,58 @@
"meta_label": "PMID_36303223_individual_32_PMID_34025712"
},
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@@ -4906,7 +5258,11 @@
{
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"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -5148,30 +5504,38 @@
"meta_label": "PMID_36303223_individual_33_PMID_33405344"
},
"sex": "FEMALE",
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@@ -5179,7 +5543,11 @@
{
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+ "timeline": "POSTNATAL"
+ }
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],
"variants": [
@@ -5421,30 +5789,38 @@
"meta_label": "PMID_36303223_individual_34_PMID_33405344"
},
"sex": "MALE",
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@@ -5452,7 +5828,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
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+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -5694,58 +6074,73 @@
"meta_label": "PMID_36303223_individual_35_PMID_36303223"
},
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@@ -5753,7 +6148,8 @@
{
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"variants": [
@@ -5995,50 +6391,63 @@
"meta_label": "PMID_36303223_individual_3_PMID_10519592"
},
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- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0000252",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0010934",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0011814",
- "is_present": false
+ "is_present": false,
+ "onset": null
},
{
"term_id": "HP:0012610",
- "is_present": false
+ "is_present": false,
+ "onset": null
}
],
"measurements": [],
@@ -6046,7 +6455,11 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": {
+ "days": 0.0,
+ "timeline": "POSTNATAL"
+ }
}
],
"variants": [
@@ -6288,10 +6701,13 @@
"meta_label": "PMID_36303223_individual_4_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -6299,7 +6715,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6426,10 +6843,13 @@
"meta_label": "PMID_36303223_individual_5_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -6437,7 +6857,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6679,10 +7100,13 @@
"meta_label": "PMID_36303223_individual_6_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -6690,7 +7114,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6817,10 +7242,13 @@
"meta_label": "PMID_36303223_individual_7_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -6828,7 +7256,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -6955,10 +7384,13 @@
"meta_label": "PMID_36303223_individual_8_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -6966,7 +7398,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
@@ -7093,10 +7526,13 @@
"meta_label": "PMID_36303223_individual_9_PMID_12112661"
},
"sex": "UNKNOWN_SEX",
+ "age": null,
+ "vital_status": null,
"phenotypes": [
{
"term_id": "HP:0001250",
- "is_present": true
+ "is_present": true,
+ "onset": null
}
],
"measurements": [],
@@ -7104,7 +7540,8 @@
{
"term_id": "OMIM:272300",
"name": "Sulfite oxidase deficiency",
- "is_observed": true
+ "is_observed": true,
+ "onset": null
}
],
"variants": [
diff --git a/tests/test_data/phenopackets/PMID_30968594_individual_1.json b/tests/test_data/phenopackets/PMID_30968594_individual_1.json
index e83686e7..81b5f510 100644
--- a/tests/test_data/phenopackets/PMID_30968594_individual_1.json
+++ b/tests/test_data/phenopackets/PMID_30968594_individual_1.json
@@ -2,7 +2,20 @@
"id": "PMID_30968594_individual_1",
"subject": {
"id": "individual 1",
- "sex": "MALE"
+ "sex": "MALE",
+ "time_at_last_encounter": {
+ "age": {
+ "iso8601duration": "P11M"
+ }
+ },
+ "vital_status": {
+ "status": "DECEASED",
+ "time_of_death": {
+ "age": {
+ "iso8601duration": "P1Y"
+ }
+ }
+ }
},
"phenotypicFeatures": [
{
@@ -21,6 +34,11 @@
"type": {
"id": "HP:0003154",
"label": "Increased circulating ACTH level"
+ },
+ "onset": {
+ "age": {
+ "iso8601duration": "P20D"
+ }
}
},
{
diff --git a/tests/test_generate_doc_cohorts.py b/tests/test_generate_doc_cohorts.py
index 7dca58e8..6be71454 100644
--- a/tests/test_generate_doc_cohorts.py
+++ b/tests/test_generate_doc_cohorts.py
@@ -47,7 +47,14 @@ def load_cohort(
with phenopacket_registry.open_phenopacket_store(
TestGenerateCohortsForDocumentation.PHENOPACKET_STORE_VERSION,
) as ps:
- phenopackets = tuple(ps.iter_cohort_phenopackets(cohort_name))
+ # Sort the phenopackets by ID to get deterministic behavior
+ # for testing.
+ phenopackets = tuple(
+ sorted(
+ ps.iter_cohort_phenopackets(cohort_name),
+ key=lambda pp: pp.id + pp.subject.id
+ )
+ )
cohort, qc = load_phenopackets(
phenopackets=iter(phenopackets),
@@ -80,6 +87,7 @@ def dump_cohort(
"CYP21A2",
"RERE",
"TBX5",
+ "UMOD",
]
)
def test_generate_cohorts(
diff --git a/tests/test_io.py b/tests/test_io.py
index 7d45cabd..c380e96e 100644
--- a/tests/test_io.py
+++ b/tests/test_io.py
@@ -31,7 +31,14 @@ def test_regenerate_cohort(
registry = configure_phenopacket_registry(store_dir=tmp_path)
with registry.open_phenopacket_store('0.1.18') as ps:
- phenopackets = tuple(ps.iter_cohort_phenopackets('SUOX'))
+ # Sort the phenopackets by ID to get deterministic behavior
+ # for testing.
+ phenopackets = tuple(
+ sorted(
+ ps.iter_cohort_phenopackets('SUOX'),
+ key=lambda pp: pp.id + pp.subject.id
+ )
+ )
cohort_creator = configure_caching_cohort_creator(hpo, timeout=30.)
cohort, validation = load_phenopackets(
diff --git a/tests/view/test_view.py b/tests/view/test_view.py
index 21e3fdb3..05792b48 100644
--- a/tests/view/test_view.py
+++ b/tests/view/test_view.py
@@ -4,28 +4,28 @@
import pytest
from gpsea.model import Cohort
-from gpsea.view import CohortViewable
+from gpsea.view import CohortViewer
-class TestCohortViewable:
+class TestCohortViewer:
@pytest.fixture
- def cohort_viewable(
+ def cohort_viewer(
self,
hpo: hpotk.MinimalOntology,
- ) -> CohortViewable:
- return CohortViewable(
+ ) -> CohortViewer:
+ return CohortViewer(
hpo=hpo,
)
def test_process(
self,
- cohort_viewable: CohortViewable,
+ cohort_viewer: CohortViewer,
toy_cohort: Cohort,
):
toy_transcript_id = "NM_123.1"
- report = cohort_viewable.process(
+ report = cohort_viewer.process(
cohort=toy_cohort, transcript_id=toy_transcript_id
)