Total submissions: 5
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Counsyl | RCV000169470 | SCV000220909 | likely pathogenic | Nephropathic cystinosis | 2014-11-24 | criteria provided, single submitter | literature only | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV001175037 | SCV001338557 | likely pathogenic | Cystinosis | 2020-04-30 | criteria provided, single submitter | clinical testing | Variant summary: CTNS c.561+1delG is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a cryptic 5 splicing donor site. Four predict the variant creates a 5 donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 250886 control chromosomes (gnomAD). c.561+1delG has been reported in the literature in individuals affected with Cystinosis (Town_1998, Shotelersuk_1998). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic. |
Invitae | RCV002515201 | SCV001591756 | pathogenic | Ocular cystinosis; Juvenile nephropathic cystinosis; Inborn genetic diseases | 2023-02-23 | 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. This sequence change creates a premature translational stop signal (Splice site) 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). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with CTNS-related conditions (PMID: 9537412). This variant is also known as 900/901+1delG, 561+1del. ClinVar contains an entry for this variant (Variation ID: 189067). |
Fulgent Genetics, |
RCV001535992 | SCV001752665 | pathogenic | Ocular cystinosis; Juvenile nephropathic cystinosis; Nephropathic cystinosis | 2021-06-30 | criteria provided, single submitter | clinical testing | |
Baylor Genetics | RCV000169470 | SCV004212952 | pathogenic | Nephropathic cystinosis | 2023-09-05 | criteria provided, single submitter | clinical testing |