ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.2155G>A (p.Gly719Ser)

gnomAD frequency: 0.00010  dbSNP: rs369022568
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 5
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001227544 SCV001399905 uncertain significance Nephronophthisis 2022-08-31 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 719 of the NPHP3 protein (p.Gly719Ser). This variant is present in population databases (rs369022568, gnomAD 0.01%). 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: 954988). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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 RCV002484241 SCV002779811 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2022-01-05 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004538477 SCV004112962 uncertain significance NPHP3-related disorder 2023-08-07 criteria provided, single submitter clinical testing The NPHP3 c.2155G>A variant is predicted to result in the amino acid substitution p.Gly719Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.012% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-132415591-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Ambry Genetics RCV004032604 SCV004990279 uncertain significance Inborn genetic diseases 2024-01-29 criteria provided, single submitter clinical testing The c.2155G>A (p.G719S) alteration is located in exon 15 (coding exon 15) of the NPHP3 gene. This alteration results from a G to A substitution at nucleotide position 2155, causing the glycine (G) at amino acid position 719 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Mayo Clinic Laboratories, Mayo Clinic RCV004792823 SCV005410413 uncertain significance not provided 2024-02-27 criteria provided, single submitter clinical testing BP4, PM2

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.