{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA344929044", "communityStandardTitle": [ "NM_000081.4(LYST):c.10479T>G (p.Phe3493Leu)" ], "externalRecords": { "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235860468A>C?assembly=hg19", "id": "chr1:g.235860468A>C" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.235697168A>C?assembly=hg38", "id": "chr1:g.235697168A>C" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "C", "end": 235697168, "referenceAllele": "A", "start": 235697167 } ], "hgvs": [ "NC_000001.11:g.235697168A>C", "CM000663.2:g.235697168A>C" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "C", "end": 235860468, "referenceAllele": "A", "start": 235860467 } ], "hgvs": [ "NC_000001.10:g.235860468A>C", "CM000663.1:g.235860468A>C" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "C", "end": 233927091, "referenceAllele": "A", "start": 233927090 } ], "hgvs": [ "NC_000001.9:g.233927091A>C" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "G", "end": 191473, "referenceAllele": "T", "start": 191472 } ], "hgvs": [ "NG_007397.1:g.191473T>G", "LRG_143:g.191473T>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS000565" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "G", "end": 1889, "referenceAllele": "T", "start": 1888 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000462376.2:n.1889T>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS905090" }, { "coordinates": [ { "allele": "G", "end": 10806, "referenceAllele": "T", "start": 10805 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697178.1:c.*6174T>G" ], "proteinEffect": { "hgvs": "ENSP00000513163.1:n.*6174T>G" }, "referenceSequence": "http://reg.genome.network/refseq/RS908583" }, { "coordinates": [ { "allele": "G", "end": 3188, "referenceAllele": "T", "start": 3187 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697179.1:n.3188T>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS908584" }, { "coordinates": [ { "allele": "G", "end": 1029, "referenceAllele": "T", "start": 1028 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697235.1:c.1029T>G" ], "proteinEffect": { "hgvs": "ENSP00000513202.1:p.Phe343Leu", "hgvsWellDefined": "ENSP00000513202.1:p.Phe343Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS908623" }, { "coordinates": [ { "allele": "G", "end": 3943, "referenceAllele": "T", "start": 3942 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697236.1:c.3943T>G" ], "proteinEffect": { "hgvs": "ENSP00000513203.1:n.3943T>G" }, "referenceSequence": "http://reg.genome.network/refseq/RS908624" }, { "coordinates": [ { "allele": "G", "end": 1190, "referenceAllele": "T", "start": 1189 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697237.1:c.1190T>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS908625" }, { "coordinates": [ { "allele": "G", "end": 2613, "referenceAllele": "T", "start": 2612 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000697240.1:c.2613T>G" ], "proteinEffect": { "hgvs": "ENSP00000513205.1:p.Phe871Leu", "hgvsWellDefined": "ENSP00000513205.1:p.Phe871Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS908628" }, { "coordinates": [ { "allele": "G", "end": 10640, "referenceAllele": "T", "start": 10639 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.7:c.10479T>G" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Phe3493Leu", "hgvsWellDefined": "ENSP00000374443.2:p.Phe3493Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS752840", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.10479T>G" }, "RefSeq": { "hgvs": "NM_000081.4:c.10479T>G" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Phe3493Leu" }, "RefSeq": { "hgvs": "NP_000072.2:p.Phe3493Leu" } } } }, { "coordinates": [ { "allele": "G", "end": 10654, "referenceAllele": "T", "start": 10653 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389793.6:c.10479T>G" ], "proteinEffect": { "hgvs": "ENSP00000374443.2:p.Phe3493Leu", "hgvsWellDefined": "ENSP00000374443.2:p.Phe3493Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS274290" }, { "coordinates": [ { "allele": "G", "end": 10231, "referenceAllele": "T", "start": 10230 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000389794.7:c.*5903T>G" ], "proteinEffect": { "hgvs": "ENSP00000374444.4:n.*5903T>G" }, "referenceSequence": "http://reg.genome.network/refseq/RS274291" }, { "coordinates": [ { "allele": "G", "end": 5469, "referenceAllele": "T", "start": 5468 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "ENST00000473037.5:n.5469T>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS314875" }, { "@id": "http://reg.genome.network/allele/PA2825050561", "coordinates": [ { "allele": "G", "end": 10661, "referenceAllele": "T", "start": 10660 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.3:c.10479T>G", "LRG_143t1:c.10479T>G" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Phe3493Leu", "hgvsWellDefined": "NP_000072.2:p.Phe3493Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS006145" }, { "@id": "http://reg.genome.network/allele/PA645447876", "coordinates": [ { "allele": "G", "end": 11098, "referenceAllele": "T", "start": 11097 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_001301365.1:c.10479T>G", "LRG_143t2:c.10479T>G" ], "proteinEffect": { "hgvs": "NP_001288294.1:p.Phe3493Leu", "hgvsWellDefined": "NP_001288294.1:p.Phe3493Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS025192" }, { "coordinates": [ { "allele": "G", "end": 10823, "referenceAllele": "T", "start": 10822 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544031.1:c.10641T>G" ], "proteinEffect": { "hgvs": "XP_011542333.1:p.Phe3547Leu", "hgvsWellDefined": "XP_011542333.1:p.Phe3547Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS110944" }, { "coordinates": [ { "allele": "G", "end": 11226, "referenceAllele": "T", "start": 11225 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544032.1:c.10641T>G" ], "proteinEffect": { "hgvs": "XP_011542334.1:p.Phe3547Leu", "hgvsWellDefined": "XP_011542334.1:p.Phe3547Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS110945" }, { "coordinates": [ { "allele": "G", "end": 11024, "referenceAllele": "T", "start": 11023 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.1:c.10641T>G" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Phe3547Leu", "hgvsWellDefined": "XP_011542335.1:p.Phe3547Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS110946" }, { "coordinates": [ { "allele": "G", "end": 10685, "referenceAllele": "T", "start": 10684 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544034.1:c.10503T>G" ], "proteinEffect": { "hgvs": "XP_011542336.1:p.Phe3501Leu", "hgvsWellDefined": "XP_011542336.1:p.Phe3501Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS110947" }, { "coordinates": [ { "allele": "G", "end": 8468, "referenceAllele": "T", "start": 8467 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544036.1:c.8304T>G" ], "proteinEffect": { "hgvs": "XP_011542338.1:p.Phe2768Leu", "hgvsWellDefined": "XP_011542338.1:p.Phe2768Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS110949" }, { "coordinates": [ { "allele": "G", "end": 10973, "referenceAllele": "T", "start": 10972 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544033.2:c.10641T>G" ], "proteinEffect": { "hgvs": "XP_011542335.1:p.Phe3547Leu", "hgvsWellDefined": "XP_011542335.1:p.Phe3547Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS555477" }, { "coordinates": [ { "allele": "G", "end": 8477, "referenceAllele": "T", "start": 8476 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_011544036.2:c.8304T>G" ], "proteinEffect": { "hgvs": "XP_011542338.1:p.Phe2768Leu", "hgvsWellDefined": "XP_011542338.1:p.Phe2768Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS555479" }, { "coordinates": [ { "allele": "G", "end": 10592, "referenceAllele": "T", "start": 10591 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "XM_017000150.1:c.10410T>G" ], "proteinEffect": { "hgvs": "XP_016855639.1:p.Phe3470Leu", "hgvsWellDefined": "XP_016855639.1:p.Phe3470Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS556567" }, { "@id": "http://reg.genome.network/allele/PA2825050561", "coordinates": [ { "allele": "G", "end": 10640, "referenceAllele": "T", "start": 10639 } ], "gene": "http://reg.genome.network/gene/GN001968", "geneNCBI_id": 1130, "geneSymbol": "LYST", "hgvs": [ "NM_000081.4:c.10479T>G" ], "proteinEffect": { "hgvs": "NP_000072.2:p.Phe3493Leu", "hgvsWellDefined": "NP_000072.2:p.Phe3493Leu" }, "referenceSequence": "http://reg.genome.network/refseq/RS674690", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000389793.7:c.10479T>G" }, "RefSeq": { "hgvs": "NM_000081.4:c.10479T>G" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000374443.2:p.Phe3493Leu" }, "RefSeq": { "hgvs": "NP_000072.2:p.Phe3493Leu" } } } } ], "type": "nucleotide" }