ClinVar Miner

Submissions for variant NM_000297.4(PKD2):c.965G>A (p.Arg322Gln)

gnomAD frequency: 0.00001  dbSNP: rs145877597
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV000987457 SCV001136752 likely pathogenic Polycystic kidney disease 2 2019-05-28 criteria provided, single submitter clinical testing
3billion RCV000987457 SCV002058428 likely pathogenic Polycystic kidney disease 2 2022-01-03 criteria provided, single submitter clinical testing Same nucleotide change resulting in same amino acid change has been previously reported to be associated with PKD2 related disorder (ClinVar ID: VCV000802079, PMID:15772804, PS1_P). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000448039, PMID:26139440,11968093, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.889, 3CNET: 0.893, PP3_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000004, PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
Fulgent Genetics, Fulgent Genetics RCV000987457 SCV002810413 pathogenic Polycystic kidney disease 2 2022-04-05 criteria provided, single submitter clinical testing
GeneDx RCV003156302 SCV003845573 pathogenic not provided 2022-09-26 criteria provided, single submitter clinical testing Published functional studies suggest this variant impairs PC1 maturation (Gainullin et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25333066, 32332171, 28356211, 15772804, 27835667, 22863349, 23300259, 30333007, 20950398, 16540757, 32588366, 32251715, 31740684, 22383692, 25574838)
PreventionGenetics, part of Exact Sciences RCV003936240 SCV004754987 pathogenic PKD2-related disorder 2024-02-26 criteria provided, single submitter clinical testing The PKD2 c.965G>A variant is predicted to result in the amino acid substitution p.Arg322Gln. This variant has been reported in unrelated patients with autosomal dominant polycystic kidney disease (ADPKD) (Peltola et al. 2005. PubMed ID: 15772804; Trujillano et al. 2014. PubMed ID: 25333066; Robinson et al. 2012. PubMed ID: 22863349). Of note, multiple different substitutions at the same codon have been reported in ADPKD patients (Human Gene Mutation Database). This variant is interpreted as pathogenic.

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