ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.8909_8912del (p.Phe2970fs)

dbSNP: rs1473686155
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001220424 SCV001392412 pathogenic Autosomal recessive polycystic kidney disease 2023-09-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Phe2970Trpfs*68) 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). This variant is present in population databases (no rsID available, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with polycystic kidney disease (PMID: 19914852). ClinVar contains an entry for this variant (Variation ID: 949045). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV002272417 SCV002558309 pathogenic not provided 2022-02-02 criteria provided, single submitter clinical testing Observed with a second variant (phase unknown) in two siblings with nonperinatal presented polycystic kidney disease and congenital hepatic fibrosis in published literature (Gunay-Aygun et al., 2010); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 19914852)
Baylor Genetics RCV003462749 SCV004204603 pathogenic Polycystic kidney disease 4 2023-07-29 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004726991 SCV005339818 pathogenic PKHD1-related disorder 2024-09-27 no assertion criteria provided clinical testing The PKHD1 c.8909_8912delTTGT variant is predicted to result in a frameshift and premature protein termination (p.Phe2970Trpfs*68). This variant was reported with a second PKHD1 variant in an individual with polycystic kidney disease (Gunay-Aygun et al 2010. PubMed ID: 19914852). This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD. Frameshift variants in PKHD1 are expected to be pathogenic. This variant is interpreted as pathogenic.

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