ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.6296_6297del (p.Val2099fs)

dbSNP: rs910497248
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586446 SCV000699871 likely pathogenic Autosomal recessive polycystic kidney disease 2017-02-23 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.6296_6297delTG (p.Val2099Alafs) variant results in a premature termination codon, predicted to cause a truncated or absent PKHD1 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., c.9319C>T [p.Arg3107X] and c.9689delA [p.Asp3230fs). One in silico tool predicts a damaging outcome for this variant. This variant is absent in the large control population database ExAC (0/121238 control chromosomes). One publication has implicated this variant, in trans with another truncating variant, as disease causative (Denamur_Kidney Int_2010). Taken together, this variant is classified as likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000586446 SCV002245873 pathogenic Autosomal recessive polycystic kidney disease 2021-07-31 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: 496523). This variant is also known as p.V2099AdelfsX2106.. This premature translational stop signal has been observed in individual(s) with autosomal recessive polycystic kidney disease (PMID: 19940839). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Val2099Alafs*8) 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 RCV003465326 SCV004204677 pathogenic Polycystic kidney disease 4 2023-04-24 criteria provided, single submitter clinical testing

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