ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.11452G>T (p.Val3818Phe)

dbSNP: rs1385935333
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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 RCV000799470 SCV000939134 likely pathogenic Autosomal recessive polycystic kidney disease 2022-12-02 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PKHD1 protein function. ClinVar contains an entry for this variant (Variation ID: 645403). This missense change has been observed in individual(s) with clinical features of polycystic kidney disease (PMID: 30655312; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces valine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 3818 of the PKHD1 protein (p.Val3818Phe).
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV001262018 SCV001439385 uncertain significance Polycystic kidney disease 4 2020-10-14 criteria provided, single submitter research ACMG codes:PM2, PM3
Natera, Inc. RCV000799470 SCV002075482 uncertain significance Autosomal recessive polycystic kidney disease 2021-08-31 no assertion criteria provided clinical testing
Yale Center for Mendelian Genomics, Yale University RCV000799470 SCV002106574 pathogenic Autosomal recessive polycystic kidney disease 2019-01-17 no assertion criteria provided literature only

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