ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.6199C>T (p.Gln2067Ter)

dbSNP: rs1555454604
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV000788767 SCV000928003 pathogenic not provided 2018-10-18 criteria provided, single submitter clinical testing
Cavalleri Lab, Royal College of Surgeons in Ireland RCV001095562 SCV001251193 pathogenic Polycystic kidney disease, adult type 2020-02-05 criteria provided, single submitter research PVS1, PM2, PP4, PP5
GeneDx RCV000788767 SCV002578801 pathogenic not provided 2022-04-20 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 17582161, 30333007, 31740684, 33454723)
Fulgent Genetics, Fulgent Genetics RCV001095562 SCV002810657 pathogenic Polycystic kidney disease, adult type 2022-02-10 criteria provided, single submitter clinical testing
Juno Genomics, Hangzhou Juno Genomics, Inc RCV001095562 SCV005184181 pathogenic Polycystic kidney disease, adult type 2024-07-19 criteria provided, single submitter clinical testing PM2_Supporting+PVS1+PS4_Supporting+PP4
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000501909 SCV000592789 pathogenic Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Gln2067X variant was identified in 1 of 404 proband chromosomes (frequency: 0.002) from individuals or families with ADPKD (Rossetti 2007).The variant was identified in ADPKD Mutation Database (classification definitely pathogenic) and not identified in dbSNP, Clinvitae, ClinVar, GeneInsight COGR, PKD1-LOVD, and PKD1-LOVD 3.0; 1000 Genomes Project, NHLBI GO Exome Sequencing Project (ESP) or the Exome Aggregation Consortium (ExAC) database (Jan 13, 2015). The p.Gln2067X variant leads to a premature stop codon at position 2067, which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the PKD1 gene are an established mechanism of disease in autosomal dominant polycystic kidney disease and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic.

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