ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.406del (p.Thr136fs)

dbSNP: rs1379989124
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
Eurofins Ntd Llc (ga) RCV000734775 SCV000862944 pathogenic not provided 2018-08-17 criteria provided, single submitter clinical testing
Blueprint Genetics RCV000734775 SCV000927974 likely pathogenic not provided 2018-10-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001228010 SCV001400391 pathogenic Nephronophthisis 2024-07-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Thr136Argfs*13) in the NPHP3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHP3 are known to be pathogenic (PMID: 18371931, 23559409). This variant is present in population databases (no rsID available, gnomAD 0.004%). This premature translational stop signal has been observed in individual(s) with nephronophthisis (PMID: 23188109). ClinVar contains an entry for this variant (Variation ID: 598394). For these reasons, this variant has been classified as Pathogenic.
PreventionGenetics, part of Exact Sciences RCV004527767 SCV004107842 pathogenic NPHP3-related disorder 2022-12-19 criteria provided, single submitter clinical testing The NPHP3 c.406delA variant is predicted to result in a frameshift and premature protein termination (p.Thr136Argfs*13). This variant was reported in the homozygous state in an individual with infantile nephronophthisis (Halbritter et al 2012. PubMed ID: 23188109). This variant is reported in 0.0041% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-132438661-GT-G). Frameshift variants in NPHP3 are expected to be pathogenic. This variant is interpreted as pathogenic.
GeneDx RCV000734775 SCV005441467 pathogenic not provided 2024-06-23 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31589614, 36090483, 23559409, 18371931, 23188109)

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.