ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.10856del (p.Lys3619fs)

dbSNP: rs1554183235
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667303 SCV000791734 pathogenic Autosomal recessive polycystic kidney disease 2017-07-20 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000667303 SCV001587250 pathogenic Autosomal recessive polycystic kidney disease 2021-10-14 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 552098). This premature translational stop signal has been observed in individual(s) with polycystic kidney disease (PMID: 12846734, 19021639). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Lys3619Serfs*7) in the PKHD1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PKHD1 are known to be pathogenic (PMID: 19940839).
Baylor Genetics RCV003459584 SCV004204599 pathogenic Polycystic kidney disease 4 2023-07-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000667303 SCV004804166 pathogenic Autosomal recessive polycystic kidney disease 2024-01-04 criteria provided, single submitter clinical testing Variant summary: PKHD1 c.10856delA (p.Lys3619SerfsX7) 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. The variant was absent in 250964 control chromosomes (gnomAD). c.10856delA has been reported in the literature in individuals affected with Polycystic Kidney And Hepatic Disease (example: Rossetti_2003). The following publication has been ascertained in the context of this evaluation (PMID: 12846734). Four submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Natera, Inc. RCV000667303 SCV002075499 pathogenic Autosomal recessive polycystic kidney disease 2021-03-25 no assertion criteria provided clinical testing

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