ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.1458C>A (p.Tyr486Ter) (rs786204749)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169599 SCV000221111 likely pathogenic Autosomal recessive polycystic kidney disease 2015-02-03 criteria provided, single submitter literature only
Baylor Genetics RCV000169599 SCV001163067 pathogenic Autosomal recessive polycystic kidney disease criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000169599 SCV001361896 likely pathogenic Autosomal recessive polycystic kidney disease 2019-03-22 criteria provided, single submitter clinical testing Variant summary: PKHD1 c.1458C>A (p.Tyr486X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (c.2341C>T, p.Arg781X; c.5895dupA, p.Leu1966fsX4; c.9319C>T, p.Arg3107X). The variant allele was found at a frequency of 4.1e-06 in 246036 control chromosomes (gnomAD). This variant has been reported in the literature in individuals affected with Polycystic Kidney and Hepatic Disease (Gunay-Aygun_2011, Gunay-Aygun_2010). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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