ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.7469A>G (p.Asp2490Gly)

gnomAD frequency: 0.00004  dbSNP: rs746000400
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001246937 SCV001420331 uncertain significance Autosomal recessive polycystic kidney disease 2022-02-04 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 2490 of the PKHD1 protein (p.Asp2490Gly). This variant is present in population databases (rs746000400, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PKHD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 971206). 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 not expected to disrupt PKHD1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV002504362 SCV002816914 uncertain significance Polycystic kidney disease 4 2021-10-13 criteria provided, single submitter clinical testing
Ambry Genetics RCV004034877 SCV005005319 likely benign Inborn genetic diseases 2023-12-22 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Natera, Inc. RCV001246937 SCV002078024 uncertain significance Autosomal recessive polycystic kidney disease 2018-12-17 no assertion criteria provided clinical testing

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