ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.563C>T (p.Thr188Met)

gnomAD frequency: 0.00015  dbSNP: rs200711763
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000729081 SCV000856718 uncertain significance not provided 2018-05-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001036261 SCV001199614 uncertain significance Nephronophthisis 2024-11-04 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 188 of the NPHP4 protein (p.Thr188Met). This variant is present in population databases (rs200711763, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. ClinVar contains an entry for this variant (Variation ID: 593910). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt NPHP4 protein function with a positive predictive value of 80%. 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000729081 SCV002541087 uncertain significance not provided 2021-06-22 criteria provided, single submitter clinical testing

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