{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA019872", "communityStandardTitle": [ "NM_000251.3(MSH2):c.2038C>T (p.Arg680Ter)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=27628", "active": true, "id": "COSM27628" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=45234[alleleid]", "alleleId": 45234, "preferredName": "NM_000251.3(MSH2):c.2038C>T (p.Arg680Ter)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/36572", "RCV": [ "RCV000030248", "RCV000115515", "RCV000202174", "RCV000524372", "RCV000576755", "RCV000677886", "RCV001250040", "RCV004555850" ], "variationId": 36572 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/2-47703538-C-T", "id": "2-47703538-C-T", "variant": "2:47703538 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.47703538C>T?assembly=hg19", 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"http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "ENST00000406134.5:c.2038C>T" ], "proteinEffect": { "hgvs": "ENSP00000384199.1:p.Arg680Ter", "hgvsWellDefined": "ENSP00000384199.1:p.Arg680_Ser921delinsGlnThrGlyValIleValLeuMetAlaGlnIleGlyCysPheValProCysGluSerAlaGluValSerIleValAspCysIleLeuAlaArgValGlyAlaGlyAspSerGlnLeuLysGlyValSerThrPheMetAlaGluMetLeuGluThrAlaSerIleLeuArgSerAlaThrLysAspSerLeuIleIleIleAspGluLeuGlyArgGlyThrSerThrTyrAspGlyPheGlyLeuAlaTrpAlaIleSerGluTyrIleAlaThrLysIleGlyAlaPheCysMetPheAlaThrHisPheHisGluLeuThrAlaLeuAlaAsnGlnIleProThrValAsnAsnLeuHisValThrAlaLeuThrThrGluGluThrLeuThrMetLeuTyrGlnValLysLysGlyValCysAspGlnSerPheGlyIleHisValAlaGluLeuAlaAsnPheProLysHisValIleGluCysAlaLysGlnLysAlaLeuGluLeuGluGluPheGlnTyrIleGlyGluSerGlnGlyTyrAspIleMetGluProAlaAlaLysLysCysTyrLeuGluArgGluAsnLeuArgValThrGluProLysAspGlnCysLeuIleLeuLeuThrTrpLysArgLysLeuArgGlyGlyLysArgSerAlaCysSerArgProGluArgGlnAsnGlnGlySerGlyGluLeuSerTer" }, "referenceSequence": 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"NP_000242.1:p.Arg680_Thr934delinsGlnThrGlyValIleValLeuMetAlaGlnIleGlyCysPheValProCysGluSerAlaGluValSerIleValAspCysIleLeuAlaArgValGlyAlaGlyAspSerGlnLeuLysGlyValSerThrPheMetAlaGluMetLeuGluThrAlaSerIleLeuArgSerAlaThrLysAspSerLeuIleIleIleAspGluLeuGlyArgGlyThrSerThrTyrAspGlyPheGlyLeuAlaTrpAlaIleSerGluTyrIleAlaThrLysIleGlyAlaPheCysMetPheAlaThrHisPheHisGluLeuThrAlaLeuAlaAsnGlnIleProThrValAsnAsnLeuHisValThrAlaLeuThrThrGluGluThrLeuThrMetLeuTyrGlnValLysLysGlyValCysAspGlnSerPheGlyIleHisValAlaGluLeuAlaAsnPheProLysHisValIleGluCysAlaLysGlnLysAlaLeuGluLeuGluGluPheGlnTyrIleGlyGluSerGlnGlyTyrAspIleMetGluProAlaAlaLysLysCysTyrLeuGluArgGluGlnGlyGluLysIleIleGlnGluPheLeuSerLysValLysGlnMetProPheThrGluMetSerGluGluAsnIleThrIleLysLeuLysGlnLeuLysAlaGluValIleAlaLysAsnAsnSerPheValAsnGluIleIleSerArgIleLysValThrThrTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS006313" }, { "@id": "http://reg.genome.network/allele/PA2826465056", "coordinates": [ { "allele": "T", "end": 1979, "referenceAllele": "C", "start": 1978 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "NM_001258281.1:c.1840C>T" ], "proteinEffect": { "hgvs": "NP_001245210.1:p.Arg614Ter", "hgvsWellDefined": "NP_001245210.1:p.Arg614_Thr868delinsGlnThrGlyValIleValLeuMetAlaGlnIleGlyCysPheValProCysGluSerAlaGluValSerIleValAspCysIleLeuAlaArgValGlyAlaGlyAspSerGlnLeuLysGlyValSerThrPheMetAlaGluMetLeuGluThrAlaSerIleLeuArgSerAlaThrLysAspSerLeuIleIleIleAspGluLeuGlyArgGlyThrSerThrTyrAspGlyPheGlyLeuAlaTrpAlaIleSerGluTyrIleAlaThrLysIleGlyAlaPheCysMetPheAlaThrHisPheHisGluLeuThrAlaLeuAlaAsnGlnIleProThrValAsnAsnLeuHisValThrAlaLeuThrThrGluGluThrLeuThrMetLeuTyrGlnValLysLysGlyValCysAspGlnSerPheGlyIleHisValAlaGluLeuAlaAsnPheProLysHisValIleGluCysAlaLysGlnLysAlaLeuGluLeuGluGluPheGlnTyrIleGlyGluSerGlnGlyTyrAspIleMetGluProAlaAlaLysLysCysTyrLeuGluArgGluGlnGlyGluLysIleIleGlnGluPheLeuSerLysValLysGlnMetProPheThrGluMetSerGluGluAsnIleThrIleLysLeuLysGlnLeuLysAlaGluValIleAlaLysAsnAsnSerPheValAsnGluIleIleSerArgIleLysValThrThrTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS019766" }, { "coordinates": [ { "allele": "T", "end": 2110, "referenceAllele": "C", "start": 2109 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "XM_005264332.2:c.2038C>T" ], "proteinEffect": { "hgvs": "XP_005264389.2:p.Arg680Ter", "hgvsWellDefined": "XP_005264389.2:p.Arg680_Gly974delinsGlnThrGlyValIleValLeuMetAlaGlnIleGlyCysPheValProCysGluSerAlaGluValSerIleValAspCysIleLeuAlaArgValGlyAlaGlyAspSerGlnLeuLysGlyValSerThrPheMetAlaGluMetLeuGluThrAlaSerIleLeuArgSerAlaThrLysAspSerLeuIleIleIleAspGluLeuGlyArgGlyThrSerThrTyrAspGlyPheGlyLeuAlaTrpAlaIleSerGluTyrIleAlaThrLysIleGlyAlaPheCysMetPheAlaThrHisPheHisGluLeuThrAlaLeuAlaAsnGlnIleProThrValAsnAsnLeuHisValThrAlaLeuThrThrGluGluThrLeuThrMetLeuTyrGlnValLysLysGlyValCysAspGlnSerPheGlyIleHisValAlaGluLeuAlaAsnPheProLysHisValIleGluCysAlaLysGlnLysAlaLeuGluLeuGluGluPheGlnTyrIleGlyGluSerGlnGlyTyrAspIleMetGluProAlaAlaLysLysCysTyrLeuGluArgGluAsnLeuArgValThrGluProLysAspGlnCysLeuIleLeuLeuThrTrpLysArgLysLeuArgGlyGlyLysArgSerAlaCysSerArgProGluArgGlnAsnGlnGlySerGlyGlyAspPheLysArgLysSerLeuValValCysLysAlaThrAsnProAlaLeuLysTrpIleValProSerProLeuAsnGluPheSerPheIleHisLeuGluLysHisSerLeuValLeuSerMetGluLeuGlnAlaThrSerGlyGlyAlaGlnCysProGlyTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS064175" }, { "coordinates": [ { "allele": "T", "end": 2110, "referenceAllele": "C", "start": 2109 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "XM_011532867.1:c.2038C>T" ], "proteinEffect": { "hgvs": "XP_011531169.1:p.Arg680Ter", "hgvsWellDefined": "XP_011531169.1:p.Arg680_Ala924delinsGlnThrGlyValIleValLeuMetAlaGlnIleGlyCysPheValProCysGluSerAlaGluValSerIleValAspCysIleLeuAlaArgValGlyAlaGlyAspSerGlnLeuLysGlyValSerThrPheMetAlaGluMetLeuGluThrAlaSerIleLeuArgSerAlaThrLysAspSerLeuIleIleIleAspGluLeuGlyArgGlyThrSerThrTyrAspGlyPheGlyLeuAlaTrpAlaIleSerGluTyrIleAlaThrLysIleGlyAlaPheCysMetPheAlaThrHisPheHisGluLeuThrAlaLeuAlaAsnGlnIleProThrValAsnAsnLeuHisValThrAlaLeuThrThrGluGluThrLeuThrMetLeuTyrGlnValLysLysGlyValCysAspGlnSerPheGlyIleHisValAlaGluLeuAlaAsnPheProLysHisValIleGluCysAlaLysGlnLysAlaLeuGluLeuGluGluPheGlnTyrIleGlyGluSerGlnGlyTyrAspIleMetGluProAlaAlaLysLysCysTyrLeuGluArgGluAsnLeuArgValThrGluProLysAspGlnCysLeuIleLeuLeuThrTrpLysArgLysLeuArgGlyGlyLysArgSerAlaCysSerArgProGluArgGlnAsnGlnGlySerAlaThrProSerAlaSerAlaTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS099893" }, { "coordinates": [ { "allele": "T", "end": 2110, "referenceAllele": "C", "start": 2109 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "XR_939685.1:n.2110C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS134381" }, { "coordinates": [ { "allele": "T", "end": 2100, "referenceAllele": "C", "start": 2099 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "XM_005264332.4:c.2038C>T" ], "proteinEffect": { "hgvs": "XP_005264389.2:p.Arg680Ter", "hgvsWellDefined": "XP_005264389.2:p.Arg680_Gly974delinsGlnThrGlyValIleValLeuMetAlaGlnIleGlyCysPheValProCysGluSerAlaGluValSerIleValAspCysIleLeuAlaArgValGlyAlaGlyAspSerGlnLeuLysGlyValSerThrPheMetAlaGluMetLeuGluThrAlaSerIleLeuArgSerAlaThrLysAspSerLeuIleIleIleAspGluLeuGlyArgGlyThrSerThrTyrAspGlyPheGlyLeuAlaTrpAlaIleSerGluTyrIleAlaThrLysIleGlyAlaPheCysMetPheAlaThrHisPheHisGluLeuThrAlaLeuAlaAsnGlnIleProThrValAsnAsnLeuHisValThrAlaLeuThrThrGluGluThrLeuThrMetLeuTyrGlnValLysLysGlyValCysAspGlnSerPheGlyIleHisValAlaGluLeuAlaAsnPheProLysHisValIleGluCysAlaLysGlnLysAlaLeuGluLeuGluGluPheGlnTyrIleGlyGluSerGlnGlyTyrAspIleMetGluProAlaAlaLysLysCysTyrLeuGluArgGluAsnLeuArgValThrGluProLysAspGlnCysLeuIleLeuLeuThrTrpLysArgLysLeuArgGlyGlyLysArgSerAlaCysSerArgProGluArgGlnAsnGlnGlySerGlyGlyAspPheLysArgLysSerLeuValValCysLysAlaThrAsnProAlaLeuLysTrpIleValProSerProLeuAsnGluPheSerPheIleHisLeuGluLysHisSerLeuValLeuSerMetGluLeuGlnAlaThrSerGlyGlyAlaGlnCysProGlyTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS535844" }, { "coordinates": [ { "allele": "T", "end": 2100, "referenceAllele": "C", "start": 2099 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "XM_011532867.2:c.2038C>T" ], "proteinEffect": { "hgvs": "XP_011531169.1:p.Arg680Ter", "hgvsWellDefined": "XP_011531169.1:p.Arg680_Ala924delinsGlnThrGlyValIleValLeuMetAlaGlnIleGlyCysPheValProCysGluSerAlaGluValSerIleValAspCysIleLeuAlaArgValGlyAlaGlyAspSerGlnLeuLysGlyValSerThrPheMetAlaGluMetLeuGluThrAlaSerIleLeuArgSerAlaThrLysAspSerLeuIleIleIleAspGluLeuGlyArgGlyThrSerThrTyrAspGlyPheGlyLeuAlaTrpAlaIleSerGluTyrIleAlaThrLysIleGlyAlaPheCysMetPheAlaThrHisPheHisGluLeuThrAlaLeuAlaAsnGlnIleProThrValAsnAsnLeuHisValThrAlaLeuThrThrGluGluThrLeuThrMetLeuTyrGlnValLysLysGlyValCysAspGlnSerPheGlyIleHisValAlaGluLeuAlaAsnPheProLysHisValIleGluCysAlaLysGlnLysAlaLeuGluLeuGluGluPheGlnTyrIleGlyGluSerGlnGlyTyrAspIleMetGluProAlaAlaLysLysCysTyrLeuGluArgGluAsnLeuArgValThrGluProLysAspGlnCysLeuIleLeuLeuThrTrpLysArgLysLeuArgGlyGlyLysArgSerAlaCysSerArgProGluArgGlnAsnGlnGlySerAlaThrProSerAlaSerAlaTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS551004" }, { "coordinates": [ { "allele": "T", "end": 2100, "referenceAllele": "C", "start": 2099 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "XR_001738747.2:n.2100C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS589206" }, { "coordinates": [ { "allele": "T", "end": 2100, "referenceAllele": "C", "start": 2099 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "XR_939685.2:n.2100C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS612357" }, { "@id": "http://reg.genome.network/allele/PA248541", "coordinates": [ { "allele": "T", "end": 2074, "referenceAllele": "C", "start": 2073 } ], "gene": "http://reg.genome.network/gene/GN007325", "geneNCBI_id": 4436, "geneSymbol": "MSH2", "hgvs": [ "NM_000251.3:c.2038C>T" ], "proteinEffect": { "hgvs": "NP_000242.1:p.Arg680Ter", "hgvsWellDefined": "NP_000242.1:p.Arg680_Thr934delinsGlnThrGlyValIleValLeuMetAlaGlnIleGlyCysPheValProCysGluSerAlaGluValSerIleValAspCysIleLeuAlaArgValGlyAlaGlyAspSerGlnLeuLysGlyValSerThrPheMetAlaGluMetLeuGluThrAlaSerIleLeuArgSerAlaThrLysAspSerLeuIleIleIleAspGluLeuGlyArgGlyThrSerThrTyrAspGlyPheGlyLeuAlaTrpAlaIleSerGluTyrIleAlaThrLysIleGlyAlaPheCysMetPheAlaThrHisPheHisGluLeuThrAlaLeuAlaAsnGlnIleProThrValAsnAsnLeuHisValThrAlaLeuThrThrGluGluThrLeuThrMetLeuTyrGlnValLysLysGlyValCysAspGlnSerPheGlyIleHisValAlaGluLeuAlaAsnPheProLysHisValIleGluCysAlaLysGlnLysAlaLeuGluLeuGluGluPheGlnTyrIleGlyGluSerGlnGlyTyrAspIleMetGluProAlaAlaLysLysCysTyrLeuGluArgGluGlnGlyGluLysIleIleGlnGluPheLeuSerLysValLysGlnMetProPheThrGluMetSerGluGluAsnIleThrIleLysLeuLysGlnLeuLysAlaGluValIleAlaLysAsnAsnSerPheValAsnGluIleIleSerArgIleLysValThrThrTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS674763", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000233146.7:c.2038C>T" }, "RefSeq": { "hgvs": "NM_000251.3:c.2038C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000233146.2:p.Arg680Ter" }, "RefSeq": { "hgvs": "NP_000242.1:p.Arg680Ter" } } } } ], "type": "nucleotide" }