{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA344939762", "communityStandardTitle": [ "NM_000081.4(LYST):c.6712C>T (p.Arg2238Ter)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1701661[alleleid]", "alleleId": 1701661, "preferredName": "NM_000081.4(LYST):c.6712C>T (p.Arg2238Ter)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1705577", "RCV": [ "RCV002283891" ], "variationId": 1705577 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235922441G>A?assembly=hg19", "id": "chr1:g.235922441G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235759141G>A?assembly=hg38", "id": "chr1:g.235759141G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/2527805640", "rs": 2527805640 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-235759141-G-A?dataset=gnomad_r4", 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"XP_011542340.1:p.Arg2238_His2842delinsSerHisSerThrIleAlaSerLeuGlyLeuAlaPheProSerGlnAsnGlySerAlaAlaValGlyArgTrpProSerLeuValAspArgAsnThrAspAspTrpGluAsnPheAlaTyrSerLeuGlyTyrGluProAsnTyrAsnArgThrAlaSerAlaHisSerValThrGluAspCysLeuValProIleCysCysGlyLeuTyrGluLeuLeuSerGlyValLeuLeuIleLeuProAspValLeuLeuGluAspValMetAspLysLeuIleGlnAlaAspThrLeuLeuValLeuValAsnHisProSerProAlaIleGlnGlnGlyValIleLysLeuLeuAspAlaTyrPheAlaArgAlaSerLysGluGlnLysAspLysPheLeuLysAsnArgGlyPheSerLeuLeuAlaAsnGlnLeuTyrLeuHisArgGlyThrGlnGluLeuLeuGluCysPheIleGluMetPhePheGlyArgHisIleGlyLeuAspGluGluPheAspLeuGluAspValArgAsnMetGlyLeuPheGlnLysTrpSerValIleProIleLeuGlyLeuIleGluThrSerLeuTyrAspAsnIleLeuLeuHisAsnAlaLeuLeuLeuLeuLeuGlnIleLeuAsnSerCysSerLysValAlaAspMetLeuLeuAspAsnGlyLeuLeuTyrValLeuCysAsnThrValAlaAlaLeuAsnGlyLeuGluLysAsnIleProMetSerGluTyrLysLeuLeuAlaCysAspIleGlnGlnLeuPheIleAlaValThrIleHisAlaCysSerSerSerGlySerGlnTyrPheArgValIleGluAspLeuIleValMetLeuGlyTyrLeuGlnAsnSerLysAsnLysArgThrGlnAsnMetAlaValAlaLeuGlnLeuArgValLeuGlnAlaAlaMetGluPheIleArgThrThrAlaAsnHisAspSerGluAsnLeuThrAspSerLeuGlnSerProSerAlaProHisHisAlaValValGlnLysArgLysSerIleAlaGlySerIleProMetLysGlySerIleIleProHisLeuProArgHisHisPheGlySerTyrGlyGlnLeuProMetProPheSerPheGlyProLeuAsnGlnAspSerSerProGlnPheSerProGlyCysThrThrCysValValProProGlyAlaGlyProArgLysPheProLeuAlaGlnThrGluSerLeuLeuMetLysMetArgSerValAlaAsnAspGluLeuHisValMetMetGlnArgArgMetSerGlnGluAsnProSerGlnAlaThrGluThrGluLeuAlaGlnArgLeuGlnArgLeuThrValLeuAlaValAsnArgIleIleTyrGlnGluPheAsnSerAspIleIleAspIleLeuArgThrProGluAsnValThrGlnSerLysThrSerValPheGlnThrGluIleSerGluGluAsnIleHisHisGluGlnSerSerValPheAsnProPheGlnLysGluIlePheThrTyrLeuValGluGlyPheLysValSerIleGlySerSerLysAlaSerGlySerLysGlnGlnTrpThrLysIleLeuTrpSerCysLysGluThrPheArgMetGlnLeuGlyArgLeuLeuValHisIleLeuSerProAlaHisAlaAlaGlnGluArgLysGlnIlePheGluIleValHisGluProAsnHisGlnGluIleLeuArgAspCysLeuSerProSerLeuGlnAlaHisTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS110951" }, { "coordinates": [ { "allele": "T", "end": 6894, "referenceAllele": "C", "start": 6893 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.1:c.6712C>T" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Arg2238Ter", "hgvsWellDefined": "XP_011542341.1:p.Arg2238_Ala2555delinsSerHisSerThrIleAlaSerLeuGlyLeuAlaPheProSerGlnAsnGlySerAlaAlaValGlyArgTrpProSerLeuValAspArgAsnThrAspAspTrpGluAsnPheAlaTyrSerLeuGlyTyrGluProAsnTyrAsnArgThrAlaSerAlaHisSerValThrGluAspCysLeuValProIleCysCysGlyLeuTyrGluLeuLeuSerGlyValLeuLeuIleLeuProAspValLeuLeuGluAspValMetAspLysLeuIleGlnAlaAspThrLeuLeuValLeuValAsnHisProSerProAlaIleGlnGlnGlyValIleLysLeuLeuAspAlaTyrPheAlaArgAlaSerLysGluGlnLysAspLysPheLeuLysAsnArgGlyPheSerLeuLeuAlaAsnGlnLeuTyrLeuHisArgGlyThrGlnGluLeuLeuGluCysPheIleGluMetPhePheGlyArgHisIleGlyLeuAspGluGluPheAspLeuGluAspValArgAsnMetGlyLeuPheGlnLysTrpSerValIleProIleLeuGlyLeuIleGluThrSerLeuTyrAspAsnIleLeuLeuHisAsnAlaLeuLeuLeuLeuLeuGlnIleLeuAsnSerCysSerLysValAlaAspMetLeuLeuAspAsnGlyLeuLeuTyrValLeuCysAsnThrValAlaAlaLeuAsnGlyLeuGluLysAsnIleProMetSerGluTyrLysLeuLeuAlaCysAspIleGlnGlnLeuPheIleAlaValThrIleHisAlaCysSerSerSerGlySerGlnTyrPheArgValIleGluAspLeuIleValMetLeuGlyTyrLeuGlnAsnSerLysAsnLysArgThrGlnIleSerSerValPheArgTyrGlyCysCysThrThrAlaTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS110952" }, { "coordinates": [ { "allele": "T", "end": 7044, "referenceAllele": "C", "start": 7043 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.2:c.6712C>T" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Arg2238Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS555477" }, { "coordinates": [ { "allele": "T", "end": 6894, "referenceAllele": "C", "start": 6893 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544035.2:c.6712C>T" ], "proteinEffect": { "hgvs": "XP_011542337.1:p.Arg2238Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS555478" }, { "coordinates": [ { "allele": "T", "end": 4548, "referenceAllele": "C", "start": 4547 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544036.2:c.4375C>T" ], "proteinEffect": { "hgvs": "XP_011542338.1:p.Arg1459Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS555479" }, { "coordinates": [ { "allele": "T", "end": 6894, "referenceAllele": "C", "start": 6893 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544037.2:c.6712C>T" ], "proteinEffect": { "hgvs": "XP_011542339.1:p.Arg2238Ter", "hgvsWellDefined": "XP_011542339.1:p.Arg2238_His2876delinsSerHisSerThrIleAlaSerLeuGlyLeuAlaPheProSerGlnAsnGlySerAlaAlaValGlyArgTrpProSerLeuValAspArgAsnThrAspAspTrpGluAsnPheAlaTyrSerLeuGlyTyrGluProAsnTyrAsnArgThrAlaSerAlaHisSerValThrGluAspCysLeuValProIleCysCysGlyLeuTyrGluLeuLeuSerGlyValLeuLeuIleLeuProAspValLeuLeuGluAspValMetAspLysLeuIleGlnAlaAspThrLeuLeuValLeuValAsnHisProSerProAlaIleGlnGlnGlyValIleLysLeuLeuAspAlaTyrPheAlaArgAlaSerLysGluGlnLysAspLysPheLeuLysAsnArgGlyPheSerLeuLeuAlaAsnGlnLeuTyrLeuHisArgGlyThrGlnGluLeuLeuGluCysPheIleGluMetPhePheGlyArgHisIleGlyLeuAspGluGluPheAspLeuGluAspValArgAsnMetGlyLeuPheGlnLysTrpSerValIleProIleLeuGlyLeuIleGluThrSerLeuTyrAspAsnIleLeuLeuHisAsnAlaLeuLeuLeuLeuLeuGlnIleLeuAsnSerCysSerLysValAlaAspMetLeuLeuAspAsnGlyLeuLeuTyrValLeuCysAsnThrValAlaAlaLeuAsnGlyLeuGluLysAsnIleProMetSerGluTyrLysLeuLeuAlaCysAspIleGlnGlnLeuPheIleAlaValThrIleHisAlaCysSerSerSerGlySerGlnTyrPheArgValIleGluAspLeuIleValMetLeuGlyTyrLeuGlnAsnSerLysAsnLysArgThrGlnAsnMetAlaValAlaLeuGlnLeuArgValLeuGlnAlaAlaMetGluPheIleArgThrThrAlaAsnHisAspSerGluAsnLeuThrAspSerLeuGlnSerProSerAlaProHisHisAlaValValGlnLysArgLysSerIleAlaGlySerIleProMetLysGlySerIleIleProHisLeuProArgHisHisPheGlySerTyrGlyGlnLeuProMetProPheSerPheGlyProLeuAsnGlnAspSerSerProGlnPheSerProGlyCysThrThrCysValValProProGlyAlaGlyProArgLysPheProLeuAlaGlnThrGluSerLeuLeuMetLysMetArgSerValAlaAsnAspGluLeuHisValMetMetGlnArgArgMetSerGlnGluAsnProSerGlnAlaThrGluThrGluLeuAlaGlnArgLeuGlnArgLeuThrValLeuAlaValAsnArgIleIleTyrGlnGluPheAsnSerAspIleIleAspIleLeuArgThrProGluAsnValThrGlnSerLysThrSerValPheGlnThrGluIleSerGluGluAsnIleHisHisGluGlnSerSerValPheAsnProPheGlnLysGluIlePheThrTyrLeuValGluGlyPheLysValSerIleGlySerSerLysAlaSerGlySerLysGlnGlnTrpThrLysIleLeuTrpSerCysLysGluThrPheArgMetGlnLeuGlyArgLeuLeuValHisIleLeuSerProAlaHisAlaAlaGlnGluArgLysGlnIlePheGluIleValHisGluProAsnHisGlnGluIleLeuArgAspCysLeuSerProSerLeuGlnArgGluIleCysIleAspTyrSerThrAlaProTyrArgLeuLeuTyrSerSerLysLysGluGlnThrThrGlyThrSerThrIleMetAspGluSerGlnLysHisTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS555480" }, { "coordinates": [ { "allele": "T", "end": 6894, "referenceAllele": "C", "start": 6893 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544039.2:c.6712C>T" ], "proteinEffect": { "hgvs": "XP_011542341.1:p.Arg2238Ter", "hgvsWellDefined": "XP_011542341.1:p.Arg2238_Ala2555delinsSerHisSerThrIleAlaSerLeuGlyLeuAlaPheProSerGlnAsnGlySerAlaAlaValGlyArgTrpProSerLeuValAspArgAsnThrAspAspTrpGluAsnPheAlaTyrSerLeuGlyTyrGluProAsnTyrAsnArgThrAlaSerAlaHisSerValThrGluAspCysLeuValProIleCysCysGlyLeuTyrGluLeuLeuSerGlyValLeuLeuIleLeuProAspValLeuLeuGluAspValMetAspLysLeuIleGlnAlaAspThrLeuLeuValLeuValAsnHisProSerProAlaIleGlnGlnGlyValIleLysLeuLeuAspAlaTyrPheAlaArgAlaSerLysGluGlnLysAspLysPheLeuLysAsnArgGlyPheSerLeuLeuAlaAsnGlnLeuTyrLeuHisArgGlyThrGlnGluLeuLeuGluCysPheIleGluMetPhePheGlyArgHisIleGlyLeuAspGluGluPheAspLeuGluAspValArgAsnMetGlyLeuPheGlnLysTrpSerValIleProIleLeuGlyLeuIleGluThrSerLeuTyrAspAsnIleLeuLeuHisAsnAlaLeuLeuLeuLeuLeuGlnIleLeuAsnSerCysSerLysValAlaAspMetLeuLeuAspAsnGlyLeuLeuTyrValLeuCysAsnThrValAlaAlaLeuAsnGlyLeuGluLysAsnIleProMetSerGluTyrLysLeuLeuAlaCysAspIleGlnGlnLeuPheIleAlaValThrIleHisAlaCysSerSerSerGlySerGlnTyrPheArgValIleGluAspLeuIleValMetLeuGlyTyrLeuGlnAsnSerLysAsnLysArgThrGlnIleSerSerValPheArgTyrGlyCysCysThrThrAlaTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS555481" }, { "coordinates": [ { "allele": "T", "end": 6894, "referenceAllele": "C", "start": 6893 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_017000150.1:c.6712C>T" ], "proteinEffect": { "hgvs": "XP_016855639.1:p.Arg2238Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS556567" }, { "coordinates": [ { "allele": "T", "end": 6894, "referenceAllele": "C", "start": 6893 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736946.2:n.6894C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS587794" }, { "coordinates": [ { "allele": "T", "end": 6894, "referenceAllele": "C", "start": 6893 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736947.1:n.6894C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS587795" }, { "coordinates": [ { "allele": "T", "end": 6894, "referenceAllele": "C", "start": 6893 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XR_001736948.1:n.6894C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS587796" }, { "coordinates": [ { "allele": "T", "end": 6873, "referenceAllele": "C", "start": 6872 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.4:c.6712C>T" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Arg2238Ter" }, "referenceSequence": "http://reg.genome.network/refseq/RS674690", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.6712C>T" }, "RefSeq": { "hgvs": "NM_000081.4:c.6712C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Arg2238Ter" }, "RefSeq": { "hgvs": "NP_000072.2:p.Arg2238Ter" } } } } ], "type": "nucleotide" }