ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.9547C>T (p.Arg3183Ter)

dbSNP: rs1485297878
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000681685 SCV002562630 pathogenic not provided 2023-05-30 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: 22508176, 31740684, 35177841, 30586318, 35783601)
Eurofins-Biomnis RCV003236587 SCV003935072 pathogenic Polycystic kidney disease, adult type 2022-10-07 criteria provided, single submitter clinical testing
Gharavi Laboratory, Columbia University RCV000681685 SCV000809132 pathogenic not provided 2018-09-16 no assertion criteria provided research
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292451 SCV001480973 pathogenic Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Arg3183X variant was identified in 2 of 1400 proband chromosomes (frequency: 0.001) from individuals or families with ADPKD (Audrezet 2012). The variant was also identified in ADPKD Mutation Database (definitely pathogenic). The variant was not identified in dbSNP, ClinVar, Clinvitae, GeneInsight-COGR, LOVD 3.0, PKD1-LOVD, databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The c.9547C>T variant leads to a premature stop codon at position 3183, 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 ADPKD 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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