ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.5877_5878CA[1] (p.Thr1960fs) (rs771180444)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000177891 SCV000229845 pathogenic not provided 2015-03-17 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000780604 SCV000918014 likely pathogenic Autosomal recessive polycystic kidney disease 2018-11-21 criteria provided, single submitter clinical testing Variant summary: PKHD1 c.5879_5880delCA (p.Thr1960LysfsX9) 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 (e.g. p.Leu1966fsX4, p.Arg3107X, p.Asp3230fsX34). The variant allele was found at a frequency of 7.2e-06 in 276878 control chromosomes (gnomAD). To our knowledge, no occurrence of c.5879_5880delCA in individuals affected with Polycystic Kidney and Hepatic Disease and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Counsyl RCV000780604 SCV001132460 likely pathogenic Autosomal recessive polycystic kidney disease 2014-12-30 no assertion criteria provided clinical testing

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