ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.10469G>C (p.Ser3490Thr)

dbSNP: rs149486694
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000794102 SCV000933490 uncertain significance Autosomal recessive polycystic kidney disease 2022-09-06 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 3490 of the PKHD1 protein (p.Ser3490Thr). This variant is present in population databases (rs149486694, 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: 640962). 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.
GeneDx RCV003314646 SCV004014565 uncertain significance not provided 2023-01-17 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Natera, Inc. RCV000794102 SCV001455056 uncertain significance Autosomal recessive polycystic kidney disease 2020-09-16 no assertion criteria provided clinical testing

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