{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA1007663", "communityStandardTitle": [ "NM_001378969.1(KCND3):c.5C>A (p.Ala2Glu)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=1738483", "active": true, "id": "COSM1738483" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=1738484", "active": true, "id": "COSM1738484" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=359196[alleleid]", "alleleId": 359196, "preferredName": "NM_001378969.1(KCND3):c.5C>A (p.Ala2Glu)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/372391", "RCV": [ "RCV000413117", "RCV000618676", "RCV001080205", "RCV000845314" ], "variationId": 372391 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/1-112525344-G-T", "id": "1-112525344-G-T", "variant": "1:112525344 G / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.112525344G>T?assembly=hg19", "id": "chr1:g.112525344G>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.111982722G>T?assembly=hg38", "id": "chr1:g.111982722G>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/201340369", "rs": 201340369 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-112525344-G-T?dataset=gnomad_r2_1", "id": "1-112525344-G-T", "variant": "1:112525344 G / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-111982722-G-T?dataset=gnomad_r3", "id": "1-111982722-G-T", "variant": "1:111982722 G / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-111982722-G-T?dataset=gnomad_r4", "id": "1-111982722-G-T", "variant": "1:111982722 G / T" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 111982722, "referenceAllele": "G", "start": 111982721 } ], "hgvs": [ "NC_000001.11:g.111982722G>T", "CM000663.2:g.111982722G>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 112525344, "referenceAllele": "G", "start": 112525343 } ], "hgvs": [ "NC_000001.10:g.112525344G>T", "CM000663.1:g.112525344G>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 112326867, "referenceAllele": "G", "start": 112326866 } ], "hgvs": [ "NC_000001.9:g.112326867G>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "A", "end": 11434, "referenceAllele": "C", "start": 11433 } ], "hgvs": [ "NG_032011.2:g.11434C>A", "LRG_445:g.11434C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS005092" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 504, "referenceAllele": "C", "start": 503 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "ENST00000703641.1:n.504C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS911842" }, { "coordinates": [ { "allele": "A", "end": 310, "referenceAllele": "C", "start": 309 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "ENST00000703642.1:n.310C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS911843" }, { "coordinates": [ { "allele": "A", "end": 307, "referenceAllele": "C", "start": 306 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "ENST00000703643.1:n.307C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS911844" }, { "coordinates": [ { "allele": "A", "end": 241, "referenceAllele": "C", "start": 240 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "ENST00000302127.5:c.5C>A" ], "proteinEffect": { "hgvs": "ENSP00000306923.4:p.Ala2Glu", "hgvsWellDefined": "ENSP00000306923.4:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS744912", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000302127.5:c.5C>A" }, "RefSeq": { "hgvs": "NM_001378969.1:c.5C>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000306923.4:p.Ala2Glu" }, "RefSeq": { "hgvs": "NP_001365898.1:p.Ala2Glu" } } } }, { "coordinates": [ { "allele": "A", "end": 485, "referenceAllele": "C", "start": 484 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "ENST00000302127.4:c.5C>A" ], "proteinEffect": { "hgvs": "ENSP00000306923.3:p.Ala2Glu", "hgvsWellDefined": "ENSP00000306923.3:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS255122" }, { "coordinates": [ { "allele": "A", "end": 485, "referenceAllele": "C", "start": 484 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "ENST00000315987.6:c.5C>A" ], "proteinEffect": { "hgvs": "ENSP00000319591.2:p.Ala2Glu", "hgvsWellDefined": "ENSP00000319591.2:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS257160" }, { "coordinates": [ { "allele": "A", "end": 75, "referenceAllele": "C", "start": 74 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "ENST00000369697.5:c.5C>A" ], "proteinEffect": { "hgvs": "ENSP00000358711.1:p.Ala2Glu", "hgvsWellDefined": "ENSP00000358711.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS267649" }, { "@id": "http://reg.genome.network/allele/PA645454868", "coordinates": [ { "allele": "A", "end": 485, "referenceAllele": "C", "start": 484 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "NM_004980.4:c.5C>A", "LRG_445t1:c.5C>A" ], "proteinEffect": { "hgvs": "NP_004971.2:p.Ala2Glu", "hgvsWellDefined": "NP_004971.2:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS030111" }, { "@id": "http://reg.genome.network/allele/PA916062869", "coordinates": [ { "allele": "A", "end": 485, "referenceAllele": "C", "start": 484 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "NM_172198.2:c.5C>A" ], "proteinEffect": { "hgvs": "NP_751948.1:p.Ala2Glu", "hgvsWellDefined": "NP_751948.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS042680" }, { "coordinates": [ { "allele": "A", "end": 149, "referenceAllele": "C", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_005270851.3:c.5C>A" ], "proteinEffect": { "hgvs": "XP_005270908.1:p.Ala2Glu", "hgvsWellDefined": "XP_005270908.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS066686" }, { "coordinates": [ { "allele": "A", "end": 409, "referenceAllele": "C", "start": 408 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_006710629.2:c.5C>A" ], "proteinEffect": { "hgvs": "XP_006710692.1:p.Ala2Glu", "hgvsWellDefined": "XP_006710692.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS068725" }, { "coordinates": [ { "allele": "A", "end": 149, "referenceAllele": "C", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_006710630.2:c.5C>A" ], "proteinEffect": { "hgvs": "XP_006710693.1:p.Ala2Glu", "hgvsWellDefined": "XP_006710693.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS068726" }, { "coordinates": [ { "allele": "A", "end": 149, "referenceAllele": "C", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_006710631.2:c.5C>A" ], "proteinEffect": { "hgvs": "XP_006710694.1:p.Ala2Glu", "hgvsWellDefined": "XP_006710694.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS068727" }, { "coordinates": [ { "allele": "A", "end": 149, "referenceAllele": "C", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_006710632.2:c.5C>A" ], "proteinEffect": { "hgvs": "XP_006710695.1:p.Ala2Glu", "hgvsWellDefined": "XP_006710695.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS068728" }, { "coordinates": [ { "allele": "A", "end": 149, "referenceAllele": "C", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_011541425.1:c.5C>A" ], "proteinEffect": { "hgvs": "XP_011539727.1:p.Ala2Glu", "hgvsWellDefined": "XP_011539727.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS108362" }, { "coordinates": [ { "allele": "A", "end": 149, "referenceAllele": "C", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_011541426.1:c.5C>A" ], "proteinEffect": { "hgvs": "XP_011539728.1:p.Ala2Glu", "hgvsWellDefined": "XP_011539728.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS108363" }, { "coordinates": [ { "allele": "A", "end": 149, "referenceAllele": "C", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_011541427.1:c.5C>A" ], "proteinEffect": { "hgvs": "XP_011539729.1:p.Ala2Glu", "hgvsWellDefined": "XP_011539729.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS108364" }, { "coordinates": [ { "allele": "A", "end": 149, "referenceAllele": "C", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_011541428.1:c.5C>A" ], "proteinEffect": { "hgvs": "XP_011539730.1:p.Ala2Glu", "hgvsWellDefined": "XP_011539730.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS108365" }, { "coordinates": [ { "allele": "A", "end": 150, "referenceAllele": "C", "start": 149 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_005270851.4:c.5C>A" ], "proteinEffect": { "hgvs": "XP_005270908.1:p.Ala2Glu", "hgvsWellDefined": "XP_005270908.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS537012" }, { "coordinates": [ { "allele": "A", "end": 310, "referenceAllele": "C", "start": 309 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_006710629.4:c.5C>A" ], "proteinEffect": { "hgvs": "XP_006710692.1:p.Ala2Glu", "hgvsWellDefined": "XP_006710692.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS537837" }, { "coordinates": [ { "allele": "A", "end": 150, "referenceAllele": "C", "start": 149 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_006710630.3:c.5C>A" ], "proteinEffect": { "hgvs": "XP_006710693.1:p.Ala2Glu", "hgvsWellDefined": "XP_006710693.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS537838" }, { "coordinates": [ { "allele": "A", "end": 150, "referenceAllele": "C", "start": 149 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_006710631.3:c.5C>A" ], "proteinEffect": { "hgvs": "XP_006710694.1:p.Ala2Glu", "hgvsWellDefined": "XP_006710694.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS537839" }, { "coordinates": [ { "allele": "A", "end": 150, "referenceAllele": "C", "start": 149 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_006710632.3:c.5C>A" ], "proteinEffect": { "hgvs": "XP_006710695.1:p.Ala2Glu", "hgvsWellDefined": "XP_006710695.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS537840" }, { "coordinates": [ { "allele": "A", "end": 150, "referenceAllele": "C", "start": 149 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_011541425.3:c.5C>A" ], "proteinEffect": { "hgvs": "XP_011539727.1:p.Ala2Glu", "hgvsWellDefined": "XP_011539727.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS554423" }, { "coordinates": [ { "allele": "A", "end": 150, "referenceAllele": "C", "start": 149 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_011541426.2:c.5C>A" ], "proteinEffect": { "hgvs": "XP_011539728.1:p.Ala2Glu", "hgvsWellDefined": "XP_011539728.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS554424" }, { "coordinates": [ { "allele": "A", "end": 150, "referenceAllele": "C", "start": 149 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_011541427.3:c.5C>A" ], "proteinEffect": { "hgvs": "XP_011539729.1:p.Ala2Glu", "hgvsWellDefined": "XP_011539729.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS554425" }, { "coordinates": [ { "allele": "A", "end": 150, "referenceAllele": "C", "start": 149 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_011541428.2:c.5C>A" ], "proteinEffect": { "hgvs": "XP_011539730.1:p.Ala2Glu", "hgvsWellDefined": "XP_011539730.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS554426" }, { "coordinates": [ { "allele": "A", "end": 402, "referenceAllele": "C", "start": 401 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_017001244.2:c.5C>A" ], "proteinEffect": { "hgvs": "XP_016856733.1:p.Ala2Glu", "hgvsWellDefined": "XP_016856733.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS557451" }, { "coordinates": [ { "allele": "A", "end": 310, "referenceAllele": "C", "start": 309 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "XM_017001245.2:c.5C>A" ], "proteinEffect": { "hgvs": "XP_016856734.1:p.Ala2Glu", "hgvsWellDefined": "XP_016856734.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS557452" }, { "@id": "http://reg.genome.network/allele/PA2828800889", "coordinates": [ { "allele": "A", "end": 241, "referenceAllele": "C", "start": 240 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "NM_001378969.1:c.5C>A" ], "proteinEffect": { "hgvs": "NP_001365898.1:p.Ala2Glu", "hgvsWellDefined": "NP_001365898.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS721868", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000302127.5:c.5C>A" }, "RefSeq": { "hgvs": "NM_001378969.1:c.5C>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000306923.4:p.Ala2Glu" }, "RefSeq": { "hgvs": "NP_001365898.1:p.Ala2Glu" } } } }, { "@id": "http://reg.genome.network/allele/PA2828801295", "coordinates": [ { "allele": "A", "end": 241, "referenceAllele": "C", "start": 240 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "NM_001378970.1:c.5C>A" ], "proteinEffect": { "hgvs": "NP_001365899.1:p.Ala2Glu", "hgvsWellDefined": "NP_001365899.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS721869" }, { "@id": "http://reg.genome.network/allele/PA645454868", "coordinates": [ { "allele": "A", "end": 504, "referenceAllele": "C", "start": 503 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "NM_004980.5:c.5C>A" ], "proteinEffect": { "hgvs": "NP_004971.2:p.Ala2Glu", "hgvsWellDefined": "NP_004971.2:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS727569" }, { "@id": "http://reg.genome.network/allele/PA916062869", "coordinates": [ { "allele": "A", "end": 504, "referenceAllele": "C", "start": 503 } ], "gene": "http://reg.genome.network/gene/GN006239", "geneNCBI_id": 3752, "geneSymbol": "KCND3", "hgvs": [ "NM_172198.3:c.5C>A" ], "proteinEffect": { "hgvs": "NP_751948.1:p.Ala2Glu", "hgvsWellDefined": "NP_751948.1:p.Ala2Glu" }, "referenceSequence": "http://reg.genome.network/refseq/RS729539" } ], "type": "nucleotide" }