ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.9464A>G (p.Tyr3155Cys)

gnomAD frequency: 0.00001  dbSNP: rs957419550
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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 RCV002033050 SCV002115117 likely pathogenic Autosomal recessive polycystic kidney disease 2023-06-05 criteria provided, single submitter clinical testing This variant is present in population databases (no rsID available, gnomAD 0.005%). This missense change has been observed in individuals with clinical features of polycystic kidney disease (PMID: 15698423, 31395954, 33226606). ClinVar contains an entry for this variant (Variation ID: 1347236). 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. 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. This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 3155 of the PKHD1 protein (p.Tyr3155Cys).
GeneDx RCV003154203 SCV003842476 likely pathogenic not provided 2023-02-21 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31395954, 15698423, 30275481, 33226606)
Baylor Genetics RCV003470946 SCV004204684 pathogenic Polycystic kidney disease 4 2024-01-11 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV003470946 SCV005669558 likely pathogenic Polycystic kidney disease 4 2024-04-02 criteria provided, single submitter clinical testing

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