{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA377482348", "communityStandardTitle": [ "NM_000314.8(PTEN):c.406T>A (p.Cys136Ser)" ], "externalRecords": { "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.89692922T>A?assembly=hg19", "id": "chr10:g.89692922T>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.87933165T>A?assembly=hg38", "id": "chr10:g.87933165T>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/786201044", "rs": 786201044 } ] }, "genomicAlleles": [ { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 87933165, "referenceAllele": "T", "start": 87933164 } ], "hgvs": [ "NC_000010.11:g.87933165T>A", "CM000672.2:g.87933165T>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000058" }, { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 89692922, "referenceAllele": "T", "start": 89692921 } ], "hgvs": [ "NC_000010.10:g.89692922T>A", "CM000672.1:g.89692922T>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000034" }, { "chromosome": "10", "coordinates": [ { "allele": "A", "end": 89682902, "referenceAllele": "T", "start": 89682901 } ], "hgvs": [ "NC_000010.9:g.89682902T>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000010" }, { "coordinates": [ { "allele": "A", "end": 74727, "referenceAllele": "T", "start": 74726 } ], "hgvs": [ "NG_007466.2:g.74727T>A", "LRG_311:g.74727T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000591" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 1251, "referenceAllele": "T", "start": 1250 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700029.2:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000514759.2:p.Cys136Ser", "hgvsWellDefined": "ENSP00000514759.2:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS914478" }, { "coordinates": [ { "allele": "A", "end": 1251, "referenceAllele": "T", "start": 1250 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000710265.1:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000518161.1:p.Cys136Ser", "hgvsWellDefined": "ENSP00000518161.1:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS914503" }, { "coordinates": [ { "allele": "A", "end": 547, "referenceAllele": "T", "start": 546 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000472832.3:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000483066.2:p.Cys136Ser", "hgvsWellDefined": "ENSP00000483066.2:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS905199" }, { "coordinates": [ { "allele": "A", "end": 1141, "referenceAllele": "T", "start": 1140 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688158.2:n.1141T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS906571" }, { "coordinates": [ { "allele": "A", "end": 599, "referenceAllele": "T", "start": 598 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688922.2:c.*236T>A" ], "proteinEffect": { "hgvs": "ENSP00000508742.2:n.*236T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS906576" }, { "coordinates": [ { "allele": "A", "end": 1036, "referenceAllele": "T", "start": 1035 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700021.1:c.361T>A" ], "proteinEffect": { "hgvs": "ENSP00000514757.1:p.Cys121Ser", "hgvsWellDefined": "ENSP00000514757.1:p.Cys121Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS910887" }, { "coordinates": [ { "allele": "A", "end": 797, "referenceAllele": "T", "start": 796 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700022.1:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000514758.1:p.Cys136Ser", "hgvsWellDefined": "ENSP00000514758.1:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS910888" }, { "coordinates": [ { "allele": "A", "end": 240, "referenceAllele": "T", "start": 239 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700029.1:c.240T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS910893" }, { "coordinates": [ { "allele": "A", "end": 502, "referenceAllele": "T", "start": 501 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000706954.1:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000516674.1:p.Cys136Ser", "hgvsWellDefined": "ENSP00000516674.1:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS913291" }, { "coordinates": [ { "allele": "A", "end": 1421, "referenceAllele": "T", "start": 1420 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000706955.1:c.*441T>A" ], "proteinEffect": { "hgvs": "ENSP00000516675.1:n.*441T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS913292" }, { "coordinates": [ { "allele": "A", "end": 548, "referenceAllele": "T", "start": 547 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000686459.1:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000508909.1:p.Cys136Ser", "hgvsWellDefined": "ENSP00000508909.1:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS830588" }, { "coordinates": [ { "allele": "A", "end": 1497, "referenceAllele": "T", "start": 1496 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688158.1:c.*517T>A" ], "proteinEffect": { "hgvs": "ENSP00000509254.1:n.*517T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS831470" }, { "coordinates": [ { "allele": "A", "end": 898, "referenceAllele": "T", "start": 897 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688308.1:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000508752.1:p.Cys136Ser", "hgvsWellDefined": "ENSP00000508752.1:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS831553" }, { "coordinates": [ { "allele": "A", "end": 327, "referenceAllele": "T", "start": 326 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688922.1:c.327T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS831892" }, { "coordinates": [ { "allele": "A", "end": 1437, "referenceAllele": "T", "start": 1436 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000693560.1:c.925T>A" ], "proteinEffect": { "hgvs": "ENSP00000509861.1:p.Cys309Ser", "hgvsWellDefined": "ENSP00000509861.1:p.Cys309Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS834309" }, { "coordinates": [ { "allele": "A", "end": 1251, "referenceAllele": "T", "start": 1250 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000371953.8:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000361021.3:p.Cys136Ser", "hgvsWellDefined": "ENSP00000361021.3:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS750898", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000371953.8:c.406T>A" }, "RefSeq": { "hgvs": "NM_000314.8:c.406T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000361021.3:p.Cys136Ser" }, "RefSeq": { "hgvs": "NP_000305.3:p.Cys136Ser" } } } }, { "coordinates": [ { "allele": "A", "end": 1763, "referenceAllele": "T", "start": 1762 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000371953.7:c.406T>A" ], "proteinEffect": { "hgvs": "ENSP00000361021.3:p.Cys136Ser", "hgvsWellDefined": "ENSP00000361021.3:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS247170" }, { "coordinates": [ { "allele": "A", "end": 232, "referenceAllele": "T", "start": 231 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000498703.1:n.232T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS334650" }, { "coordinates": [ { "allele": "A", "end": 1438, "referenceAllele": "T", "start": 1437 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000610634.1:c.304T>A" ], "proteinEffect": { "hgvs": "ENSP00000477517.1:p.Cys102Ser", "hgvsWellDefined": "ENSP00000477517.1:p.Cys102Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS400508" }, { "@id": "http://reg.genome.network/allele/PA3077023128", "coordinates": [ { "allele": "A", "end": 1437, "referenceAllele": "T", "start": 1436 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.5:c.406T>A" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Cys136Ser", "hgvsWellDefined": "NP_000305.3:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS006376" }, { "@id": "http://reg.genome.network/allele/PA3077023128", "coordinates": [ { "allele": "A", "end": 1437, "referenceAllele": "T", "start": 1436 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.6:c.406T>A" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Cys136Ser", "hgvsWellDefined": "NP_000305.3:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS006377" }, { "coordinates": [ { "allele": "A", "end": 1437, "referenceAllele": "T", "start": 1436 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304717.2:c.925T>A" ], "proteinEffect": { "hgvs": "NP_001291646.2:p.Cys309Ser", "hgvsWellDefined": "NP_001291646.2:p.Cys309Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS025775" }, { "coordinates": [ { "allele": "A", "end": 1392, "referenceAllele": "T", "start": 1391 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304718.1:c.-345T>A" ], "proteinEffect": { "hgvs": "NP_001291647.1:n.-345T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS025776" }, { "coordinates": [ { "allele": "A", "end": 1073, "referenceAllele": "T", "start": 1072 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_006717926.2:c.361T>A" ], "proteinEffect": { "hgvs": "XP_006717989.1:p.Cys121Ser", "hgvsWellDefined": "XP_006717989.1:p.Cys121Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS072385" }, { "coordinates": [ { "allele": "A", "end": 1118, "referenceAllele": "T", "start": 1117 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_011539981.1:c.406T>A" ], "proteinEffect": { "hgvs": "XP_011538283.1:p.Cys136Ser", "hgvsWellDefined": "XP_011538283.1:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS106931" }, { "coordinates": [ { "allele": "A", "end": 4090, "referenceAllele": "T", "start": 4089 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_011539982.1:c.310T>A" ], "proteinEffect": { "hgvs": "XP_011538284.1:p.Cys104Ser", "hgvsWellDefined": "XP_011538284.1:p.Cys104Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS106932" }, { "coordinates": [ { "allele": "A", "end": 1118, "referenceAllele": "T", "start": 1117 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945789.1:n.1118T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS139422" }, { "coordinates": [ { "allele": "A", "end": 1118, "referenceAllele": "T", "start": 1117 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945790.1:n.1118T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS139423" }, { "coordinates": [ { "allele": "A", "end": 1118, "referenceAllele": "T", "start": 1117 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945791.1:n.1118T>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS139424" }, { "@id": "http://reg.genome.network/allele/PA3077023128", "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "T", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.7:c.406T>A" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Cys136Ser", "hgvsWellDefined": "NP_000305.3:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS662397" }, { "coordinates": [ { "allele": "A", "end": 1250, "referenceAllele": "T", "start": 1249 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304717.5:c.925T>A" ], "proteinEffect": { "hgvs": "NP_001291646.4:p.Cys309Ser", "hgvsWellDefined": "NP_001291646.4:p.Cys309Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS664314" }, { "coordinates": [ { "allele": "A", "end": 1205, "referenceAllele": "T", "start": 1204 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304718.2:c.-345T>A" ], "proteinEffect": { "hgvs": "NP_001291647.1:n.-345T>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS664315" }, { "@id": "http://reg.genome.network/allele/PA3077023128", "coordinates": [ { "allele": "A", "end": 1251, "referenceAllele": "T", "start": 1250 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.8:c.406T>A" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Cys136Ser", "hgvsWellDefined": "NP_000305.3:p.Cys136Ser" }, "referenceSequence": "http://reg.genome.network/refseq/RS674788", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000371953.8:c.406T>A" }, "RefSeq": { "hgvs": "NM_000314.8:c.406T>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000361021.3:p.Cys136Ser" }, "RefSeq": { "hgvs": "NP_000305.3:p.Cys136Ser" } } } } ], "type": "nucleotide" }