{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA408141216", "communityStandardTitle": [ "NM_001386393.1(PANK2):c.118C>T (p.Gln40Ter)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=6377680", "active": true, "id": "COSM6377680" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=2884108[alleleid]", "alleleId": 2884108, "preferredName": "NM_001386393.1(PANK2):c.118C>T (p.Gln40Ter)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/2719723", "RCV": [ "RCV003504088" ], "variationId": 2719723 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr20:g.3870195C>T?assembly=hg19", "id": "chr20:g.3870195C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr20:g.3889548C>T?assembly=hg38", "id": "chr20:g.3889548C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1421161193", "rs": 1421161193 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/20-3889548-C-T?dataset=gnomad_r4", "id": "20-3889548-C-T", "variant": "20:3889548 C / T" } ] }, "genomicAlleles": [ { "chromosome": "20", "coordinates": [ { "allele": "T", "end": 3889548, "referenceAllele": "C", "start": 3889547 } ], "hgvs": [ "NC_000020.11:g.3889548C>T", "CM000682.2:g.3889548C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000068" }, { "chromosome": "20", "coordinates": [ { "allele": "T", "end": 3870195, "referenceAllele": "C", "start": 3870194 } ], "hgvs": [ "NC_000020.10:g.3870195C>T", "CM000682.1:g.3870195C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000044" }, { "chromosome": "20", "coordinates": [ { "allele": "T", "end": 3818195, "referenceAllele": "C", "start": 3818194 } ], "hgvs": [ "NC_000020.9:g.3818195C>T" ], "referenceGenome": 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"http://reg.genome.network/gene/GN015894", "geneNCBI_id": 80025, "geneSymbol": "PANK2", "hgvs": [ "ENST00000610179.6:c.118C>T" ], "proteinEffect": { "hgvs": "ENSP00000477429.2:p.Gln40Ter", "hgvsWellDefined": 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}, "referenceSequence": "http://reg.genome.network/refseq/RS761766" }, { "coordinates": [ { "allele": "T", "end": 162, "referenceAllele": "C", "start": 161 } ], "gene": "http://reg.genome.network/gene/GN015894", "geneNCBI_id": 80025, "geneSymbol": "PANK2", "hgvs": [ "ENST00000643504.2:c.118C>T" ], "proteinEffect": { "hgvs": "ENSP00000495157.2:p.Gln40Ter", "hgvsWellDefined": "ENSP00000495157.2:p.Gln40_Leu154delinsAlaAlaGlyAspProGluGlyArgArgGlnGluProLeuArgArgArgAlaSerSerAlaSerValProAlaValGlyAlaSerAlaGluGlyThrArgArgAspArgLeuGlySerTyrSerGlyProThrSerValSerArgGlnArgValGluSerLeuArgLysLysArgProGlnMetGlySerLeuMetLeuProArgLeuValLeuAsnSerSerTrpSerGlnAlaIlePheProLeuArgProProLysValLeuGlyTyrArgArgGluProLeuCysProThrTrpGlnSerSerThrLysSerPheGlyAsnSerLeuAlaSerTrpLeuTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS767317" }, { "coordinates": [ { "allele": "T", "end": 454, "referenceAllele": "C", "start": 453 } ], "gene": "http://reg.genome.network/gene/GN015894", "geneNCBI_id": 80025, 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"NP_001311121.1:p.Gln150_Phe331delinsAlaAlaGlyAspProGluGlyArgArgGlnGluProLeuArgArgArgAlaSerSerAlaSerValProAlaValGlyAlaSerAlaGluGlyThrArgArgAspArgLeuGlySerTyrSerGlyProThrSerValSerArgGlnArgValGluSerLeuArgLysLysArgProLeuPheProTrpPheGlyLeuAspIleGlyGlyThrLeuValLysLeuValTyrPheGluProLysAspIleThrAlaGluGluGluGluGluGluValGluSerLeuLysSerIleArgLysTyrLeuThrSerAsnValAlaTyrGlySerThrGlyIleArgAspValHisLeuGluLeuLysAspLeuThrLeuCysGlyArgLysGlyAsnLeuHisPheIleArgPheProThrHisAspMetProAlaPheIleGlnMetGlyArgAspLysAsnPheSerSerLeuHisThrValPheCysAlaThrGlyGlyGlyAlaTyrLysPheGluGlnAspPheLeuThrValCysIlePheTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS515804" }, { "coordinates": [ { "allele": "T", "end": 66, "endIntronDirection": "+", "endIntronOffset": 644, "referenceAllele": "C", "start": 66, "startIntronDirection": "+", "startIntronOffset": 643 } ], "gene": "http://reg.genome.network/gene/GN015894", "geneNCBI_id": 80025, "geneSymbol": "PANK2", "hgvs": [ "NM_024960.5:c.-246+644C>T" ], 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"PANK2", "hgvs": [ "XM_011529364.3:c.448C>T" ], "proteinEffect": { "hgvs": "XP_011527666.1:p.Gln150Ter", "hgvsWellDefined": 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"referenceAllele": "C", "start": 161 } ], "gene": "http://reg.genome.network/gene/GN015894", "geneNCBI_id": 80025, "geneSymbol": "PANK2", "hgvs": [ "NR_136715.2:n.162C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS703943" }, { "@id": "http://reg.genome.network/allele/PA2741878345", "coordinates": [ { "allele": "T", "end": 162, "referenceAllele": "C", "start": 161 } ], "gene": "http://reg.genome.network/gene/GN015894", "geneNCBI_id": 80025, "geneSymbol": "PANK2", "hgvs": [ "NM_001386393.1:c.118C>T" ], "proteinEffect": { "hgvs": "NP_001373322.1:p.Gln40Ter", "hgvsWellDefined": 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}, "referenceSequence": "http://reg.genome.network/refseq/RS724500", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000610179.7:c.118C>T" }, "RefSeq": { "hgvs": "NM_001386393.1:c.118C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000477429.2:p.Gln40Ter" }, "RefSeq": { "hgvs": "NP_001373322.1:p.Gln40Ter" } } } }, { "@id": "http://reg.genome.network/allele/PA2830331584", "coordinates": [ { "allele": "T", "end": 626, "referenceAllele": "C", "start": 625 } ], "gene": "http://reg.genome.network/gene/GN015894", "geneNCBI_id": 80025, "geneSymbol": "PANK2", "hgvs": [ "NM_153638.4:c.448C>T" ], "proteinEffect": { "hgvs": "NP_705902.2:p.Gln150Ter", "hgvsWellDefined": "NP_705902.2:p.Gln150_Pro570delinsAlaAlaGlyAspProGluGlyArgArgGlnGluProLeuArgArgArgAlaSerSerAlaSerValProAlaValGlyAlaSerAlaGluGlyThrArgArgAspArgLeuGlySerTyrSerGlyProThrSerValSerArgGlnArgValGluSerLeuArgLysLysArgProLeuPheProTrpPheGlyLeuAspIleGlyGlyThrLeuValLysLeuValTyrPheGluProLysAspIleThrAlaGluGluGluGluGluGluValGluSerLeuLysSerIleArgLysTyrLeuThrSerAsnValAlaTyrGlySerThrGlyIleArgAspValHisLeuGluLeuLysAspLeuThrLeuCysGlyArgLysGlyAsnLeuHisPheIleArgPheProThrHisAspMetProAlaPheIleGlnMetGlyArgAspLysAsnPheSerSerLeuHisThrValPheCysAlaThrGlyGlyGlyAlaTyrLysPheGluGlnAspPheLeuThrIleGlyAspLeuGlnLeuCysLysLeuAspGluLeuAspCysLeuIleLysGlyIleLeuTyrIleAspSerValGlyPheAsnGlyArgSerGlnCysTyrTyrPheGluAsnProAlaAspSerGluLysCysGlnLysLeuProPheAspLeuLysAsnProTyrProLeuLeuLeuValAsnIleGlySerGlyValSerIleLeuAlaValTyrSerLysAspAsnTyrLysArgValThrGlyThrSerLeuGlyGlyGlyThrPhePheGlyLeuCysCysLeuLeuThrGlyCysThrThrPheGluGluAlaLeuGluMetAlaSerArgGlyAspSerThrLysValAspLysLeuValArgAspIleTyrGlyGlyAspTyrGluArgPheGlyLeuProGlyTrpAlaValAlaSerSerPheGlyAsnMetMetSerLysGluLysArgGluAlaValSerLysGluAspLeuAlaArgAlaThrLeuIleThrIleThrAsnAsnIleGlySerIleAlaArgMetCysAlaLeuAsnGluAsnIleAsnGlnValValPheValGlyAsnPheLeuArgIleAsnThrIleAlaMetArgLeuLeuAlaTyrAlaLeuAspTyrTrpSerLysGlyGlnLeuLysAlaLeuPheSerGluHisGluGlyTyrPheGlyAlaValGlyAlaLeuLeuGluLeuLeuLysIleProTer" }, "referenceSequence": "http://reg.genome.network/refseq/RS729485" } ], "type": "nucleotide" }