ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.682-1G>T

dbSNP: rs1057516771
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 4
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002535938 SCV000962779 pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases 2024-02-17 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 9 of the CTNS gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CTNS are known to be pathogenic (PMID: 9537412, 27102039). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with cystinosis (PMID: 19863563, 27858370). ClinVar contains an entry for this variant (Variation ID: 664004). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV005092452 SCV002783546 likely pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Nephropathic cystinosis 2021-11-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV003473516 SCV004212947 pathogenic Nephropathic cystinosis 2023-09-24 criteria provided, single submitter clinical testing
GeneDx RCV004702460 SCV005201713 pathogenic not provided 2023-11-08 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 19863563, 27858370)

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.