ClinVar Miner

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

gnomAD frequency: 0.00001  dbSNP: rs753467164
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae 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 2021-11-05 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 ( At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.