{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA2997134", "communityStandardTitle": [ "NM_080683.3(PTPN13):c.7142C>T (p.Thr2381Ile)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1037525[alleleid]", "alleleId": 1037525, "preferredName": "NM_080683.3(PTPN13):c.7142C>T (p.Thr2381Ile)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1049975", "RCV": [ "RCV001356736" ], "variationId": 1049975 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/4-87730980-C-T", "id": "4-87730980-C-T", "variant": "4:87730980 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr4:g.87730980C>T?assembly=hg19", "id": "chr4:g.87730980C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr4:g.86809827C>T?assembly=hg38", "id": "chr4:g.86809827C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/61730641", "rs": 61730641 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/4-87730980-C-T?dataset=gnomad_r2_1", "id": "4-87730980-C-T", "variant": "4:87730980 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/4-86809827-C-T?dataset=gnomad_r3", "id": "4-86809827-C-T", "variant": "4:86809827 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/4-86809827-C-T?dataset=gnomad_r4", "id": "4-86809827-C-T", "variant": "4:86809827 C / T" } ] }, "genomicAlleles": [ { "chromosome": "4", "coordinates": [ { "allele": "T", "end": 86809827, "referenceAllele": "C", "start": 86809826 } ], "hgvs": [ "NC_000004.12:g.86809827C>T", "CM000666.2:g.86809827C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000052" }, { "chromosome": "4", "coordinates": [ { "allele": "T", "end": 87730980, "referenceAllele": "C", "start": 87730979 } ], "hgvs": [ "NC_000004.11:g.87730980C>T", "CM000666.1:g.87730980C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000028" }, { "chromosome": "4", "coordinates": [ { "allele": "T", "end": 87950004, "referenceAllele": "C", "start": 87950003 } ], "hgvs": [ "NC_000004.10:g.87950004C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000004" }, { "coordinates": [ { "allele": "T", "end": 220513, "referenceAllele": "C", "start": 220512 } ], "hgvs": [ "NG_029704.1:g.220513C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS004592" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 7622, "referenceAllele": "C", "start": 7621 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "ENST00000411767.7:c.7142C>T" ], "proteinEffect": { "hgvs": "ENSP00000407249.2:p.Thr2381Ile", "hgvsWellDefined": "ENSP00000407249.2:p.Thr2381Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS754473", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000411767.7:c.7142C>T" }, "RefSeq": { "hgvs": "NM_080683.3:c.7142C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000407249.2:p.Thr2381Ile" }, "RefSeq": { "hgvs": "NP_542414.1:p.Thr2381Ile" } } } }, { "coordinates": [ { "allele": "T", "end": 6632, "referenceAllele": "C", "start": 6631 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "ENST00000316707.10:c.6569C>T" ], "proteinEffect": { "hgvs": "ENSP00000322675.6:p.Thr2190Ile", "hgvsWellDefined": "ENSP00000322675.6:p.Thr2190Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS257266" }, { "coordinates": [ { "allele": "T", "end": 7205, "referenceAllele": "C", "start": 7204 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "ENST00000411767.6:c.7142C>T" ], "proteinEffect": { "hgvs": "ENSP00000407249.2:p.Thr2381Ile", "hgvsWellDefined": "ENSP00000407249.2:p.Thr2381Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS282300" }, { "coordinates": [ { "allele": "T", "end": 7565, "referenceAllele": "C", "start": 7564 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "ENST00000427191.6:c.7085C>T" ], "proteinEffect": { "hgvs": "ENSP00000408368.2:p.Thr2362Ile", "hgvsWellDefined": "ENSP00000408368.2:p.Thr2362Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS289573" }, { "coordinates": [ { "allele": "T", "end": 7637, "referenceAllele": "C", "start": 7636 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "ENST00000436978.5:c.7157C>T" ], "proteinEffect": { "hgvs": "ENSP00000394794.1:p.Thr2386Ile", "hgvsWellDefined": "ENSP00000394794.1:p.Thr2386Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS294240" }, { "coordinates": [ { "allele": "T", "end": 7162, "referenceAllele": "C", "start": 7161 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "ENST00000511467.1:c.7157C>T" ], "proteinEffect": { "hgvs": "ENSP00000426626.1:p.Thr2386Ile", "hgvsWellDefined": "ENSP00000426626.1:p.Thr2386Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS341727" }, { "@id": "http://reg.genome.network/allele/PA2829657082", "coordinates": [ { "allele": "T", "end": 7565, "referenceAllele": "C", "start": 7564 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "NM_006264.2:c.7085C>T" ], "proteinEffect": { "hgvs": "NP_006255.1:p.Thr2362Ile", "hgvsWellDefined": "NP_006255.1:p.Thr2362Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS031286" }, { "@id": "http://reg.genome.network/allele/PA2830160368", "coordinates": [ { "allele": "T", "end": 7622, "referenceAllele": "C", "start": 7621 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "NM_080683.2:c.7142C>T" ], "proteinEffect": { "hgvs": "NP_542414.1:p.Thr2381Ile", "hgvsWellDefined": "NP_542414.1:p.Thr2381Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS040245" }, { "@id": "http://reg.genome.network/allele/PA2830160510", "coordinates": [ { "allele": "T", "end": 7049, "referenceAllele": "C", "start": 7048 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "NM_080684.2:c.6569C>T" ], "proteinEffect": { "hgvs": "NP_542415.1:p.Thr2190Ile", "hgvsWellDefined": "NP_542415.1:p.Thr2190Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS040246" }, { "@id": "http://reg.genome.network/allele/PA2499296044", "coordinates": [ { "allele": "T", "end": 7637, "referenceAllele": "C", "start": 7636 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "NM_080685.2:c.7157C>T" ], "proteinEffect": { "hgvs": "NP_542416.1:p.Thr2386Ile", "hgvsWellDefined": "NP_542416.1:p.Thr2386Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS040247" }, { "coordinates": [ { "allele": "T", "end": 7241, "referenceAllele": "C", "start": 7240 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_005263167.1:c.7160C>T" ], "proteinEffect": { "hgvs": "XP_005263224.1:p.Thr2387Ile", "hgvsWellDefined": "XP_005263224.1:p.Thr2387Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS063701" }, { "coordinates": [ { "allele": "A", "end": 1283, "endIntronDirection": "+", "endIntronOffset": 13957, "referenceAllele": "G", "start": 1283, "startIntronDirection": "+", "startIntronOffset": 13956 } ], "gene": "http://reg.genome.network/gene/GN030603", "geneNCBI_id": 345274, "geneSymbol": "SLC10A6", "hgvs": [ "XM_011531923.1:c.1038+13957G>A" ], "proteinEffect": { "hgvs": "XP_011530225.1:n.1038+13957G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS098953" }, { "coordinates": [ { "allele": "T", "end": 7307, "referenceAllele": "C", "start": 7306 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532163.1:c.7226C>T" ], "proteinEffect": { "hgvs": "XP_011530465.1:p.Thr2409Ile", "hgvsWellDefined": "XP_011530465.1:p.Thr2409Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099191" }, { "coordinates": [ { "allele": "T", "end": 7292, "referenceAllele": "C", "start": 7291 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532164.1:c.7211C>T" ], "proteinEffect": { "hgvs": "XP_011530466.1:p.Thr2404Ile", "hgvsWellDefined": "XP_011530466.1:p.Thr2404Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099192" }, { "coordinates": [ { "allele": "T", "end": 7696, "referenceAllele": "C", "start": 7695 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532165.1:c.7208C>T" ], "proteinEffect": { "hgvs": "XP_011530467.1:p.Thr2403Ile", "hgvsWellDefined": "XP_011530467.1:p.Thr2403Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099193" }, { "coordinates": [ { "allele": "T", "end": 7256, "referenceAllele": "C", "start": 7255 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532166.1:c.7175C>T" ], "proteinEffect": { "hgvs": "XP_011530468.1:p.Thr2392Ile", "hgvsWellDefined": "XP_011530468.1:p.Thr2392Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099194" }, { "coordinates": [ { "allele": "T", "end": 7250, "referenceAllele": "C", "start": 7249 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532167.1:c.7169C>T" ], "proteinEffect": { "hgvs": "XP_011530469.1:p.Thr2390Ile", "hgvsWellDefined": "XP_011530469.1:p.Thr2390Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099195" }, { "coordinates": [ { "allele": "T", "end": 7208, "referenceAllele": "C", "start": 7207 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532168.1:c.7127C>T" ], "proteinEffect": { "hgvs": "XP_011530470.1:p.Thr2376Ile", "hgvsWellDefined": "XP_011530470.1:p.Thr2376Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099196" }, { "coordinates": [ { "allele": "T", "end": 7184, "referenceAllele": "C", "start": 7183 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532169.1:c.7103C>T" ], "proteinEffect": { "hgvs": "XP_011530471.1:p.Thr2368Ile", "hgvsWellDefined": "XP_011530471.1:p.Thr2368Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099197" }, { "coordinates": [ { "allele": "T", "end": 6746, "referenceAllele": "C", "start": 6745 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532170.1:c.6665C>T" ], "proteinEffect": { "hgvs": "XP_011530472.1:p.Thr2222Ile", "hgvsWellDefined": "XP_011530472.1:p.Thr2222Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099198" }, { "coordinates": [ { "allele": "T", "end": 6734, "referenceAllele": "C", "start": 6733 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532171.1:c.6653C>T" ], "proteinEffect": { "hgvs": "XP_011530473.1:p.Thr2218Ile", "hgvsWellDefined": "XP_011530473.1:p.Thr2218Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099199" }, { "coordinates": [ { "allele": "T", "end": 6668, "referenceAllele": "C", "start": 6667 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532172.1:c.6587C>T" ], "proteinEffect": { "hgvs": "XP_011530474.1:p.Thr2196Ile", "hgvsWellDefined": "XP_011530474.1:p.Thr2196Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS099200" }, { "coordinates": [ { "allele": "T", "end": 7696, "referenceAllele": "C", "start": 7695 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_011532165.2:c.7208C>T" ], "proteinEffect": { "hgvs": "XP_011530467.1:p.Thr2403Ile", "hgvsWellDefined": "XP_011530467.1:p.Thr2403Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS550726" }, { "coordinates": [ { "allele": "T", "end": 7681, "referenceAllele": "C", "start": 7680 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_017008511.2:c.7193C>T" ], "proteinEffect": { "hgvs": "XP_016864000.1:p.Thr2398Ile", "hgvsWellDefined": "XP_016864000.1:p.Thr2398Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS563010" }, { "coordinates": [ { "allele": "T", "end": 7639, "referenceAllele": "C", "start": 7638 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_017008512.2:c.7151C>T" ], "proteinEffect": { "hgvs": "XP_016864001.1:p.Thr2384Ile", "hgvsWellDefined": "XP_016864001.1:p.Thr2384Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS563011" }, { "coordinates": [ { "allele": "T", "end": 7624, "referenceAllele": "C", "start": 7623 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_017008513.2:c.7136C>T" ], "proteinEffect": { "hgvs": "XP_016864002.1:p.Thr2379Ile", "hgvsWellDefined": "XP_016864002.1:p.Thr2379Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS563012" }, { "coordinates": [ { "allele": "T", "end": 7588, "referenceAllele": "C", "start": 7587 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_017008514.2:c.7100C>T" ], "proteinEffect": { "hgvs": "XP_016864003.1:p.Thr2367Ile", "hgvsWellDefined": "XP_016864003.1:p.Thr2367Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS563013" }, { "coordinates": [ { "allele": "T", "end": 7135, "referenceAllele": "C", "start": 7134 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_017008515.2:c.6647C>T" ], "proteinEffect": { "hgvs": "XP_016864004.1:p.Thr2216Ile", "hgvsWellDefined": "XP_016864004.1:p.Thr2216Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS563014" }, { "coordinates": [ { "allele": "T", "end": 7123, "referenceAllele": "C", "start": 7122 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "XM_017008516.2:c.6635C>T" ], "proteinEffect": { "hgvs": "XP_016864005.1:p.Thr2212Ile", "hgvsWellDefined": "XP_016864005.1:p.Thr2212Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS563015" }, { "@id": "http://reg.genome.network/allele/PA2830160368", "coordinates": [ { "allele": "T", "end": 7622, "referenceAllele": "C", "start": 7621 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "NM_080683.3:c.7142C>T" ], "proteinEffect": { "hgvs": "NP_542414.1:p.Thr2381Ile", "hgvsWellDefined": "NP_542414.1:p.Thr2381Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS671757", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000411767.7:c.7142C>T" }, "RefSeq": { "hgvs": "NM_080683.3:c.7142C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000407249.2:p.Thr2381Ile" }, "RefSeq": { "hgvs": "NP_542414.1:p.Thr2381Ile" } } } }, { "@id": "http://reg.genome.network/allele/PA2829657082", "coordinates": [ { "allele": "T", "end": 7565, "referenceAllele": "C", "start": 7564 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "NM_006264.3:c.7085C>T" ], "proteinEffect": { "hgvs": "NP_006255.1:p.Thr2362Ile", "hgvsWellDefined": "NP_006255.1:p.Thr2362Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS696654" }, { "@id": "http://reg.genome.network/allele/PA2830160510", "coordinates": [ { "allele": "T", "end": 7049, "referenceAllele": "C", "start": 7048 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "NM_080684.3:c.6569C>T" ], "proteinEffect": { "hgvs": "NP_542415.1:p.Thr2190Ile", "hgvsWellDefined": "NP_542415.1:p.Thr2190Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS699536" }, { "@id": "http://reg.genome.network/allele/PA2499296044", "coordinates": [ { "allele": "T", "end": 7637, "referenceAllele": "C", "start": 7636 } ], "gene": "http://reg.genome.network/gene/GN009646", "geneNCBI_id": 5783, "geneSymbol": "PTPN13", "hgvs": [ "NM_080685.3:c.7157C>T" ], "proteinEffect": { "hgvs": "NP_542416.1:p.Thr2386Ile", "hgvsWellDefined": "NP_542416.1:p.Thr2386Ile" }, "referenceSequence": "http://reg.genome.network/refseq/RS729058" } ], "type": "nucleotide" }