ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.4039G>A (p.Val1347Met)

gnomAD frequency: 0.00003  dbSNP: rs201087689
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002104043 SCV002393050 likely benign Autosomal recessive polycystic kidney disease 2024-01-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002282689 SCV002571034 uncertain significance not specified 2022-07-12 criteria provided, single submitter clinical testing Variant summary: PKHD1 c.4039G>A (p.Val1347Met) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 251314 control chromosomes (gnomAD, Sharp_2005). This frequency is not significantly higher than expected for a pathogenic variant in PKHD1 causing Polycystic Kidney And Hepatic Disease (0.00012 vs 0.0071), allowing no conclusion about variant significance. c.4039G>A has been reported in the literature in individuals affected with Polycystic Kidney Disease (Sharp_2005). This report does not provide unequivocal conclusions about association of the variant with Polycystic Kidney And Hepatic Disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One ClinVar submitter has assessed the variant since 2014: the variant was classified as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.
GeneDx RCV003443007 SCV004167830 uncertain significance not provided 2023-04-03 criteria provided, single submitter clinical testing Reported in a patient with polycystic kidney disease in published literature (Sharp et al., 2005); limited case-level information provided; In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 15805161)

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