ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.470G>A (p.Gly157Asp)

gnomAD frequency: 0.00001  dbSNP: rs1278235097
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000794343 SCV000933743 pathogenic Autosomal recessive polycystic kidney disease 2023-01-10 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as 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) performed at Invitae indicates that this missense variant is expected to disrupt PKHD1 protein function. ClinVar contains an entry for this variant (Variation ID: 641166). This missense change has been observed in individual(s) with clinical features of polycystic kidney disease (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 not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 157 of the PKHD1 protein (p.Gly157Asp).
Natera, Inc. RCV000794343 SCV001453289 uncertain significance Autosomal recessive polycystic kidney disease 2020-09-16 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004748968 SCV005363892 uncertain significance PKHD1-related disorder 2024-05-21 no assertion criteria provided clinical testing The PKHD1 c.470G>A variant is predicted to result in the amino acid substitution p.Gly157Asp. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. In ClinVar, this variant has conflicting interpretations of uncertain significance and pathogenic. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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