ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.233G>T (p.Gly78Val) (rs202142404)

Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 6
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000726607 SCV000345803 uncertain significance not provided 2016-09-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000283485 SCV000441157 uncertain significance Nephronophthisis 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000343202 SCV000441158 uncertain significance Renal-hepatic-pancreatic dysplasia 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000404760 SCV000441159 uncertain significance Meckel-Gruber syndrome 2016-06-14 criteria provided, single submitter clinical testing
GeneDx RCV000726607 SCV000590321 uncertain significance not provided 2017-06-13 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the NPHP3 gene. The G78V variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G78V variant is observed in 1/8252 (0.01%) alleles from individuals of East Asian background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The G78V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Glycine are tolerated across species. However, in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000283485 SCV000831174 uncertain significance Nephronophthisis 2019-12-05 criteria provided, single submitter clinical testing This sequence change replaces glycine with valine at codon 78 of the NPHP3 protein (p.Gly78Val). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and valine. This variant is present in population databases (rs202142404, ExAC 0.01%). This variant has not been reported in the literature in individuals with NPHP3-related disease. ClinVar contains an entry for this variant (Variation ID: 291105). 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.

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.