{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA636456", "communityStandardTitle": [ "NM_022089.4(ATP13A2):c.3529G>A (p.Gly1177Ser)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=1336341", "active": true, "id": "COSM1336341" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=4787170", "active": true, "id": "COSM4787170" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=578778[alleleid]", "alleleId": 578778, "preferredName": "NM_022089.4(ATP13A2):c.3529G>A (p.Gly1177Ser)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/587913", "RCV": [ "RCV000878446", "RCV002279497", "RCV002312397", "RCV004547892" ], "variationId": 587913 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/1-17312730-C-T", "id": "1-17312730-C-T", "variant": "1:17312730 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.17312730C>T?assembly=hg19", "id": "chr1:g.17312730C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.16986235C>T?assembly=hg38", "id": "chr1:g.16986235C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/547860186", "rs": 547860186 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-17312730-C-T?dataset=gnomad_r2_1", "id": "1-17312730-C-T", "variant": "1:17312730 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-16986235-C-T?dataset=gnomad_r3", "id": "1-16986235-C-T", "variant": "1:16986235 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-16986235-C-T?dataset=gnomad_r4", "id": "1-16986235-C-T", "variant": "1:16986235 C / T" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 16986235, "referenceAllele": "C", "start": 16986234 } ], "hgvs": [ "NC_000001.11:g.16986235C>T", "CM000663.2:g.16986235C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 17312730, "referenceAllele": "C", "start": 17312729 } ], "hgvs": [ "NC_000001.10:g.17312730C>T", "CM000663.1:g.17312730C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 17185317, "referenceAllele": "C", "start": 17185316 } ], "hgvs": [ "NC_000001.9:g.17185317C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "A", "end": 30694, "referenceAllele": "G", "start": 30693 } ], "hgvs": [ "NG_009054.1:g.30694G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001396" }, { "coordinates": [ { "allele": "A", "end": 352, "referenceAllele": "G", "start": 351 } ], "hgvs": [ "NG_029688.1:g.352G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS004578" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 3719, "referenceAllele": "G", "start": 3718 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "ENST00000326735.13:c.3529G>A" ], "proteinEffect": { "hgvs": "ENSP00000327214.8:p.Gly1177Ser", "hgvsWellDefined": "ENSP00000327214.8:p.Gly1177Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS746785", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000326735.13:c.3529G>A" }, "RefSeq": { "hgvs": "NM_022089.4:c.3529G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000327214.8:p.Gly1177Ser" }, "RefSeq": { "hgvs": "NP_071372.1:p.Gly1177Ser" } } } }, { "coordinates": [ { "allele": "A", "end": 3563, "referenceAllele": "G", "start": 3562 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "ENST00000326735.12:c.3529G>A" ], "proteinEffect": { "hgvs": "ENSP00000327214.8:p.Gly1177Ser", "hgvsWellDefined": "ENSP00000327214.8:p.Gly1177Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS258661" }, { "coordinates": [ { "allele": "A", "end": 3404, "referenceAllele": "G", "start": 3403 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "ENST00000341676.9:c.3227G>A" ], "proteinEffect": { "hgvs": "ENSP00000341115.5:p.Arg1076Gln", "hgvsWellDefined": "ENSP00000341115.5:p.Arg1076Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS261383" }, { "coordinates": [ { "allele": "A", "end": 3704, "referenceAllele": "G", "start": 3703 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "ENST00000452699.5:c.3514G>A" ], "proteinEffect": { "hgvs": "ENSP00000413307.1:p.Gly1172Ser", "hgvsWellDefined": "ENSP00000413307.1:p.Gly1172Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS301738" }, { "coordinates": [ { "allele": "A", "end": 1575, "referenceAllele": "G", "start": 1574 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "ENST00000466561.1:n.1575G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS309903" }, { "coordinates": [ { "allele": "A", "end": 947, "referenceAllele": "G", "start": 946 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "ENST00000502418.1:c.947G>A" ], "proteinEffect": { "hgvs": "ENSP00000423065.1:p.Arg316Gln", "hgvsWellDefined": "ENSP00000423065.1:p.Arg316Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS334988" }, { "@id": "http://reg.genome.network/allele/PA2825836056", "coordinates": [ { "allele": "A", "end": 3748, "referenceAllele": "G", "start": 3747 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "NM_001141973.2:c.3514G>A" ], "proteinEffect": { "hgvs": "NP_001135445.1:p.Gly1172Ser", "hgvsWellDefined": "NP_001135445.1:p.Gly1172Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS012784" }, { "@id": "http://reg.genome.network/allele/PA2825837436", "coordinates": [ { "allele": "A", "end": 3461, "referenceAllele": "G", "start": 3460 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "NM_001141974.2:c.3227G>A" ], "proteinEffect": { "hgvs": "NP_001135446.1:p.Arg1076Gln", "hgvsWellDefined": "NP_001135446.1:p.Arg1076Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS012785" }, { "@id": "http://reg.genome.network/allele/PA891850239", "coordinates": [ { "allele": "A", "end": 3763, "referenceAllele": "G", "start": 3762 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "NM_022089.3:c.3529G>A" ], "proteinEffect": { "hgvs": "NP_071372.1:p.Gly1177Ser", "hgvsWellDefined": "NP_071372.1:p.Gly1177Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS037187" }, { "coordinates": [ { "allele": "A", "end": 3593, "referenceAllele": "G", "start": 3592 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_005245809.1:c.3359G>A" ], "proteinEffect": { "hgvs": "XP_005245866.1:p.Arg1120Gln", "hgvsWellDefined": "XP_005245866.1:p.Arg1120Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057382" }, { "coordinates": [ { "allele": "A", "end": 3590, "referenceAllele": "G", "start": 3589 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_005245810.1:c.3356G>A" ], "proteinEffect": { "hgvs": "XP_005245867.1:p.Arg1119Gln", "hgvsWellDefined": "XP_005245867.1:p.Arg1119Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057383" }, { "coordinates": [ { "allele": "A", "end": 3578, "referenceAllele": "G", "start": 3577 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_005245811.1:c.3344G>A" ], "proteinEffect": { "hgvs": "XP_005245868.1:p.Arg1115Gln", "hgvsWellDefined": "XP_005245868.1:p.Arg1115Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057384" }, { "coordinates": [ { "allele": "A", "end": 3566, "referenceAllele": "G", "start": 3565 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_005245812.1:c.3332G>A" ], "proteinEffect": { "hgvs": "XP_005245869.1:p.Arg1111Gln", "hgvsWellDefined": "XP_005245869.1:p.Arg1111Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057385" }, { "coordinates": [ { "allele": "A", "end": 3533, "referenceAllele": "G", "start": 3532 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_005245813.1:c.3299G>A" ], "proteinEffect": { "hgvs": "XP_005245870.1:p.Arg1100Gln", "hgvsWellDefined": "XP_005245870.1:p.Arg1100Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057386" }, { "coordinates": [ { "allele": "A", "end": 3476, "referenceAllele": "G", "start": 3475 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_005245815.1:c.3242G>A" ], "proteinEffect": { "hgvs": "XP_005245872.1:p.Arg1081Gln", "hgvsWellDefined": "XP_005245872.1:p.Arg1081Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS057387" }, { "coordinates": [ { "allele": "A", "end": 3575, "referenceAllele": "G", "start": 3574 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_006710512.1:c.3341G>A" ], "proteinEffect": { "hgvs": "XP_006710575.1:p.Arg1114Gln", "hgvsWellDefined": "XP_006710575.1:p.Arg1114Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS068650" }, { "coordinates": [ { "allele": "A", "end": 3551, "referenceAllele": "G", "start": 3550 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_006710513.1:c.3317G>A" ], "proteinEffect": { "hgvs": "XP_006710576.1:p.Arg1106Gln", "hgvsWellDefined": "XP_006710576.1:p.Arg1106Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS068651" }, { "coordinates": [ { "allele": "A", "end": 3578, "referenceAllele": "G", "start": 3577 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_011541128.1:c.3344G>A" ], "proteinEffect": { "hgvs": "XP_011539430.1:p.Arg1115Gln", "hgvsWellDefined": "XP_011539430.1:p.Arg1115Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS108071" }, { "coordinates": [ { "allele": "A", "end": 3386, "referenceAllele": "G", "start": 3385 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_011541129.1:c.3152G>A" ], "proteinEffect": { "hgvs": "XP_011539431.1:p.Arg1051Gln", "hgvsWellDefined": "XP_011539431.1:p.Arg1051Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS108072" }, { "coordinates": [ { "allele": "A", "end": 3748, "referenceAllele": "G", "start": 3747 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_017000844.1:c.3514G>A" ], "proteinEffect": { "hgvs": "XP_016856333.1:p.Gly1172Ser", "hgvsWellDefined": "XP_016856333.1:p.Gly1172Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS557124" }, { "coordinates": [ { "allele": "A", "end": 3745, "referenceAllele": "G", "start": 3744 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_017000845.1:c.3511G>A" ], "proteinEffect": { "hgvs": "XP_016856334.1:p.Gly1171Ser", "hgvsWellDefined": "XP_016856334.1:p.Gly1171Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS557125" }, { "coordinates": [ { "allele": "A", "end": 3721, "referenceAllele": "G", "start": 3720 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_017000846.1:c.3487G>A" ], "proteinEffect": { "hgvs": "XP_016856335.1:p.Gly1163Ser", "hgvsWellDefined": "XP_016856335.1:p.Gly1163Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS557126" }, { "coordinates": [ { "allele": "A", "end": 3718, "referenceAllele": "G", "start": 3717 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_017000847.1:c.3484G>A" ], "proteinEffect": { "hgvs": "XP_016856336.1:p.Gly1162Ser", "hgvsWellDefined": "XP_016856336.1:p.Gly1162Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS557127" }, { "coordinates": [ { "allele": "A", "end": 3646, "referenceAllele": "G", "start": 3645 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_017000848.1:c.3412G>A" ], "proteinEffect": { "hgvs": "XP_016856337.1:p.Gly1138Ser", "hgvsWellDefined": "XP_016856337.1:p.Gly1138Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS557128" }, { "coordinates": [ { "allele": "A", "end": 3631, "referenceAllele": "G", "start": 3630 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_017000849.1:c.3397G>A" ], "proteinEffect": { "hgvs": "XP_016856338.1:p.Gly1133Ser", "hgvsWellDefined": "XP_016856338.1:p.Gly1133Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS557129" }, { "coordinates": [ { "allele": "A", "end": 3556, "referenceAllele": "G", "start": 3555 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "XM_017000850.1:c.3322G>A" ], "proteinEffect": { "hgvs": "XP_016856339.1:p.Gly1108Ser", "hgvsWellDefined": "XP_016856339.1:p.Gly1108Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS557130" }, { "@id": "http://reg.genome.network/allele/PA891850239", "coordinates": [ { "allele": "A", "end": 3719, "referenceAllele": "G", "start": 3718 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "NM_022089.4:c.3529G>A" ], "proteinEffect": { "hgvs": "NP_071372.1:p.Gly1177Ser", "hgvsWellDefined": "NP_071372.1:p.Gly1177Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS670368", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000326735.13:c.3529G>A" }, "RefSeq": { "hgvs": "NM_022089.4:c.3529G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000327214.8:p.Gly1177Ser" }, "RefSeq": { "hgvs": "NP_071372.1:p.Gly1177Ser" } } } }, { "@id": "http://reg.genome.network/allele/PA2825836056", "coordinates": [ { "allele": "A", "end": 3704, "referenceAllele": "G", "start": 3703 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "NM_001141973.3:c.3514G>A" ], "proteinEffect": { "hgvs": "NP_001135445.1:p.Gly1172Ser", "hgvsWellDefined": "NP_001135445.1:p.Gly1172Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS677479" }, { "@id": "http://reg.genome.network/allele/PA2825837436", "coordinates": [ { "allele": "A", "end": 3417, "referenceAllele": "G", "start": 3416 } ], "gene": "http://reg.genome.network/gene/GN030213", "geneNCBI_id": 23400, "geneSymbol": "ATP13A2", "hgvs": [ "NM_001141974.3:c.3227G>A" ], "proteinEffect": { "hgvs": "NP_001135446.1:p.Arg1076Gln", "hgvsWellDefined": "NP_001135446.1:p.Arg1076Gln" }, "referenceSequence": "http://reg.genome.network/refseq/RS677480" } ], "type": "nucleotide" }