ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.810C>A (p.Ser270Arg)

dbSNP: rs754448530
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000666991 SCV000791375 uncertain significance Autosomal recessive polycystic kidney disease 2017-05-10 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002499157 SCV002812240 uncertain significance Polycystic kidney disease 4 2022-05-16 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000666991 SCV003265567 pathogenic Autosomal recessive polycystic kidney disease 2024-01-29 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 270 of the PKHD1 protein (p.Ser270Arg). This variant is present in population databases (rs754448530, gnomAD 0.003%). This missense change has been observed in individual(s) with autosomal recessive polycystic kidney disease and/or PKHD1-related conditions (PMID: 27225849; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 551838). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PKHD1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

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