Total submissions: 8
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000586519 | SCV000698526 | pathogenic | Cystinosis | 2017-07-05 | criteria provided, single submitter | clinical testing | Variant summary: The variant results in the deletion of a 23 nucleotides leading to a termination codon at position 288 of CTNS. The variant was present at a low frequency in the large and broad cohorts of the ExAC project (3/121,076 chromosomes) while it was observed in multiple CTNS patients in the literature. Considering all evidence, the variant was classified as pathogenic. |
Invitae | RCV002530936 | SCV000961592 | pathogenic | Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases | 2023-08-05 | criteria provided, single submitter | clinical testing | For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 496276). This variant is also known as c.1109_1131del23. This premature translational stop signal has been observed in individuals with cystinosis (PMID: 10556299, 26266097). This variant is present in population databases (rs759623796, gnomAD 0.02%). This sequence change creates a premature translational stop signal (p.Gly258Serfs*30) in the CTNS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CTNS are known to be pathogenic (PMID: 9537412, 27102039). |
Centogene AG - |
RCV000586519 | SCV001424396 | pathogenic | Cystinosis | criteria provided, single submitter | clinical testing | ||
Johns Hopkins Genomics, |
RCV000984254 | SCV001573147 | pathogenic | Nephropathic cystinosis | 2021-04-26 | criteria provided, single submitter | clinical testing | This 23 bp deletion in CTNS has been previously reported in individuals with nephropathic cystinosis. This CTNS variant (rs759623796) is rare (<0.1%) in a large population dataset (gnomAD: 7/251296 total alleles; 0.003%; no homozygotes) and there is an entry in ClinVar. This frameshift variant results in a premature stop codon in exon 11 likely leading to nonsense-mediated decay and lack of protein production. We consider this variant to be pathogenic. |
Revvity Omics, |
RCV003139887 | SCV003819373 | pathogenic | not provided | 2021-12-02 | criteria provided, single submitter | clinical testing | |
Baylor Genetics | RCV000984254 | SCV004215218 | pathogenic | Nephropathic cystinosis | 2022-12-25 | criteria provided, single submitter | clinical testing | |
Counsyl | RCV000984254 | SCV001132377 | likely pathogenic | Nephropathic cystinosis | 2014-08-16 | no assertion criteria provided | clinical testing | |
Natera, |
RCV000586519 | SCV002093236 | pathogenic | Cystinosis | 2021-01-26 | no assertion criteria provided | clinical testing |