ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.1920T>G (p.Asp640Glu)

gnomAD frequency: 0.00001  dbSNP: rs869312915
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 2
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000210561 SCV000262839 likely pathogenic Inborn genetic diseases 2013-12-09 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002517434 SCV003525453 pathogenic Nephronophthisis 2022-03-11 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt NPHP3 protein function. ClinVar contains an entry for this variant (Variation ID: 224989). This missense change has been observed in individual(s) with clinical features of nephronophthisis (PMID: 25356970). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 640 of the NPHP3 protein (p.Asp640Glu).

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.