ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.982C>T (p.Arg328Ter) (rs398124503)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000790671 SCV000226174 pathogenic not provided 2013-09-06 criteria provided, single submitter clinical testing
Counsyl RCV000174804 SCV000485566 likely pathogenic Autosomal recessive polycystic kidney disease 2016-01-06 criteria provided, single submitter clinical testing
Baylor Genetics RCV000174804 SCV001163073 pathogenic Autosomal recessive polycystic kidney disease criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000174804 SCV001362926 pathogenic Autosomal recessive polycystic kidney disease 2019-08-12 criteria provided, single submitter clinical testing Variant summary: PKHD1 c.982C>T (p.Arg328X) 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.1480C>T, p.Arg494X; c.1486C>T, p.Arg496X). The variant allele was found at a frequency of 2.8e-05 in 251214 control chromosomes (gnomAD). The variant, c.982C>T, has been reported in the literature in individuals (in both homozygous and compound heterozygous state) affected with Polycystic Kidney and Hepatic Disease(Bergmann_2003, Denamur_2010). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One submitter has provided clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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