ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.116G>T (p.Arg39Leu)

gnomAD frequency: 0.00001  dbSNP: rs753467164
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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 RCV001295101 SCV001484012 uncertain significance Nephronophthisis 2022-03-03 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 39 of the NPHP3 protein (p.Arg39Leu). This variant is present in population databases (rs753467164, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 999142). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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 RCV002499540 SCV002793276 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2024-04-04 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004531075 SCV004114253 uncertain significance NPHP3-related disorder 2023-03-14 criteria provided, single submitter clinical testing The NPHP3 c.116G>T variant is predicted to result in the amino acid substitution p.Arg39Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.021% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-132441084-C-A). 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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