ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.9296C>A (p.Ser3099Ter)

gnomAD frequency: 0.00001  dbSNP: rs757946548
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000498382 SCV000589822 likely pathogenic not provided 2016-04-05 criteria provided, single submitter clinical testing The S3099X variant in the PKHD1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The S3099X variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The S3099X variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.
Baylor Genetics RCV003464070 SCV004204593 likely pathogenic Polycystic kidney disease 4 2024-02-18 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001829415 SCV004531317 pathogenic Autosomal recessive polycystic kidney disease 2023-02-28 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: 432135). This variant has not been reported in the literature in individuals affected with PKHD1-related conditions. This variant is present in population databases (rs757946548, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Ser3099*) 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).
Natera, Inc. RCV001829415 SCV002077955 likely pathogenic Autosomal recessive polycystic kidney disease 2017-03-16 no assertion criteria provided clinical testing

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