{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA377482350", "communityStandardTitle": [ "NM_000314.8(PTEN):c.407G>T (p.Cys136Phe)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=5228", "active": true, "id": "COSM5228" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1787482[alleleid]", "alleleId": 1787482, "preferredName": "NM_000314.8(PTEN):c.407G>T (p.Cys136Phe)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1737618", "RCV": [ "RCV002323108" ], "variationId": 1737618 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.89692923G>T?assembly=hg19", "id": "chr10:g.89692923G>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.87933166G>T?assembly=hg38", "id": "chr10:g.87933166G>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/786204859", "rs": 786204859 } ] }, "genomicAlleles": [ { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 87933166, "referenceAllele": "G", "start": 87933165 } ], "hgvs": [ "NC_000010.11:g.87933166G>T", "CM000672.2:g.87933166G>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000058" }, { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 89692923, "referenceAllele": "G", "start": 89692922 } ], "hgvs": [ "NC_000010.10:g.89692923G>T", "CM000672.1:g.89692923G>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000034" }, { "chromosome": "10", "coordinates": [ { "allele": "T", "end": 89682903, "referenceAllele": "G", "start": 89682902 } ], "hgvs": [ "NC_000010.9:g.89682903G>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000010" }, { "coordinates": [ { "allele": "T", "end": 74728, "referenceAllele": "G", "start": 74727 } ], "hgvs": [ "NG_007466.2:g.74728G>T", "LRG_311:g.74728G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS000591" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 1252, "referenceAllele": "G", "start": 1251 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700029.2:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000514759.2:p.Cys136Phe", "hgvsWellDefined": "ENSP00000514759.2:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS914478" }, { "coordinates": [ { "allele": "T", "end": 1252, "referenceAllele": "G", "start": 1251 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000710265.1:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000518161.1:p.Cys136Phe", "hgvsWellDefined": "ENSP00000518161.1:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS914503" }, { "coordinates": [ { "allele": "T", "end": 548, "referenceAllele": "G", "start": 547 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000472832.3:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000483066.2:p.Cys136Phe", "hgvsWellDefined": "ENSP00000483066.2:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS905199" }, { "coordinates": [ { "allele": "T", "end": 1142, "referenceAllele": "G", "start": 1141 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688158.2:n.1142G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS906571" }, { "coordinates": [ { "allele": "T", "end": 600, "referenceAllele": "G", "start": 599 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688922.2:c.*237G>T" ], "proteinEffect": { "hgvs": "ENSP00000508742.2:n.*237G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS906576" }, { "coordinates": [ { "allele": "T", "end": 1037, "referenceAllele": "G", "start": 1036 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700021.1:c.362G>T" ], "proteinEffect": { "hgvs": "ENSP00000514757.1:p.Cys121Phe", "hgvsWellDefined": "ENSP00000514757.1:p.Cys121Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS910887" }, { "coordinates": [ { "allele": "T", "end": 798, "referenceAllele": "G", "start": 797 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700022.1:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000514758.1:p.Cys136Phe", "hgvsWellDefined": "ENSP00000514758.1:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS910888" }, { "coordinates": [ { "allele": "T", "end": 241, "referenceAllele": "G", "start": 240 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700029.1:c.241G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS910893" }, { "coordinates": [ { "allele": "T", "end": 503, "referenceAllele": "G", "start": 502 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000706954.1:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000516674.1:p.Cys136Phe", "hgvsWellDefined": "ENSP00000516674.1:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS913291" }, { "coordinates": [ { "allele": "T", "end": 1422, "referenceAllele": "G", "start": 1421 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000706955.1:c.*442G>T" ], "proteinEffect": { "hgvs": "ENSP00000516675.1:n.*442G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS913292" }, { "coordinates": [ { "allele": "T", "end": 549, "referenceAllele": "G", "start": 548 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000686459.1:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000508909.1:p.Cys136Phe", "hgvsWellDefined": "ENSP00000508909.1:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS830588" }, { "coordinates": [ { "allele": "T", "end": 1498, "referenceAllele": "G", "start": 1497 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688158.1:c.*518G>T" ], "proteinEffect": { "hgvs": "ENSP00000509254.1:n.*518G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS831470" }, { "coordinates": [ { "allele": "T", "end": 899, "referenceAllele": "G", "start": 898 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688308.1:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000508752.1:p.Cys136Phe", "hgvsWellDefined": "ENSP00000508752.1:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS831553" }, { "coordinates": [ { "allele": "T", "end": 328, "referenceAllele": "G", "start": 327 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688922.1:c.328G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS831892" }, { "coordinates": [ { "allele": "T", "end": 1438, "referenceAllele": "G", "start": 1437 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000693560.1:c.926G>T" ], "proteinEffect": { "hgvs": "ENSP00000509861.1:p.Cys309Phe", "hgvsWellDefined": "ENSP00000509861.1:p.Cys309Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS834309" }, { "coordinates": [ { "allele": "T", "end": 1252, "referenceAllele": "G", "start": 1251 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000371953.8:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000361021.3:p.Cys136Phe", "hgvsWellDefined": "ENSP00000361021.3:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS750898", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000371953.8:c.407G>T" }, "RefSeq": { "hgvs": "NM_000314.8:c.407G>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000361021.3:p.Cys136Phe" }, "RefSeq": { "hgvs": "NP_000305.3:p.Cys136Phe" } } } }, { "coordinates": [ { "allele": "T", "end": 1764, "referenceAllele": "G", "start": 1763 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000371953.7:c.407G>T" ], "proteinEffect": { "hgvs": "ENSP00000361021.3:p.Cys136Phe", "hgvsWellDefined": "ENSP00000361021.3:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS247170" }, { "coordinates": [ { "allele": "T", "end": 233, "referenceAllele": "G", "start": 232 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000498703.1:n.233G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS334650" }, { "coordinates": [ { "allele": "T", "end": 1439, "referenceAllele": "G", "start": 1438 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000610634.1:c.305G>T" ], "proteinEffect": { "hgvs": "ENSP00000477517.1:p.Cys102Phe", "hgvsWellDefined": "ENSP00000477517.1:p.Cys102Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS400508" }, { "@id": "http://reg.genome.network/allele/PA2825117922", "coordinates": [ { "allele": "T", "end": 1438, "referenceAllele": "G", "start": 1437 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.5:c.407G>T" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Cys136Phe", "hgvsWellDefined": "NP_000305.3:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS006376" }, { "@id": "http://reg.genome.network/allele/PA2825117922", "coordinates": [ { "allele": "T", "end": 1438, "referenceAllele": "G", "start": 1437 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.6:c.407G>T" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Cys136Phe", "hgvsWellDefined": "NP_000305.3:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS006377" }, { "coordinates": [ { "allele": "T", "end": 1438, "referenceAllele": "G", "start": 1437 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304717.2:c.926G>T" ], "proteinEffect": { "hgvs": "NP_001291646.2:p.Cys309Phe", "hgvsWellDefined": "NP_001291646.2:p.Cys309Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS025775" }, { "coordinates": [ { "allele": "T", "end": 1393, "referenceAllele": "G", "start": 1392 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304718.1:c.-344G>T" ], "proteinEffect": { "hgvs": "NP_001291647.1:n.-344G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS025776" }, { "coordinates": [ { "allele": "T", "end": 1074, "referenceAllele": "G", "start": 1073 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_006717926.2:c.362G>T" ], "proteinEffect": { "hgvs": "XP_006717989.1:p.Cys121Phe", "hgvsWellDefined": "XP_006717989.1:p.Cys121Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS072385" }, { "coordinates": [ { "allele": "T", "end": 1119, "referenceAllele": "G", "start": 1118 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_011539981.1:c.407G>T" ], "proteinEffect": { "hgvs": "XP_011538283.1:p.Cys136Phe", "hgvsWellDefined": "XP_011538283.1:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS106931" }, { "coordinates": [ { "allele": "T", "end": 4091, "referenceAllele": "G", "start": 4090 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_011539982.1:c.311G>T" ], "proteinEffect": { "hgvs": "XP_011538284.1:p.Cys104Phe", "hgvsWellDefined": "XP_011538284.1:p.Cys104Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS106932" }, { "coordinates": [ { "allele": "T", "end": 1119, "referenceAllele": "G", "start": 1118 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945789.1:n.1119G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS139422" }, { "coordinates": [ { "allele": "T", "end": 1119, "referenceAllele": "G", "start": 1118 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945790.1:n.1119G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS139423" }, { "coordinates": [ { "allele": "T", "end": 1119, "referenceAllele": "G", "start": 1118 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945791.1:n.1119G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS139424" }, { "@id": "http://reg.genome.network/allele/PA2825117922", "coordinates": [ { "allele": "T", "end": 1251, "referenceAllele": "G", "start": 1250 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.7:c.407G>T" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Cys136Phe", "hgvsWellDefined": "NP_000305.3:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS662397" }, { "@id": "http://reg.genome.network/allele/PA2580193417", "coordinates": [ { "allele": "T", "end": 1251, "referenceAllele": "G", "start": 1250 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304717.5:c.926G>T" ], "proteinEffect": { "hgvs": "NP_001291646.4:p.Cys309Phe", "hgvsWellDefined": "NP_001291646.4:p.Cys309Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS664314" }, { "coordinates": [ { "allele": "T", "end": 1206, "referenceAllele": "G", "start": 1205 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304718.2:c.-344G>T" ], "proteinEffect": { "hgvs": "NP_001291647.1:n.-344G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS664315" }, { "@id": "http://reg.genome.network/allele/PA2825117922", "coordinates": [ { "allele": "T", "end": 1252, "referenceAllele": "G", "start": 1251 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.8:c.407G>T" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Cys136Phe", "hgvsWellDefined": "NP_000305.3:p.Cys136Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS674788", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000371953.8:c.407G>T" }, "RefSeq": { "hgvs": "NM_000314.8:c.407G>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000361021.3:p.Cys136Phe" }, "RefSeq": { "hgvs": "NP_000305.3:p.Cys136Phe" } } } } ], "type": "nucleotide" }