ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.926dup (p.Ser310fs) (rs786204420)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169007 SCV000220147 likely pathogenic Nephropathic cystinosis 2014-03-07 criteria provided, single submitter literature only
Integrated Genetics/Laboratory Corporation of America RCV000780203 SCV000917269 pathogenic Cystinosis 2018-11-29 criteria provided, single submitter clinical testing Variant summary: CTNS c.926dupG (p.Ser310GlnfsX55) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 5.9e-06 in 336774 control chromosomes (gnomAD and publications). c.926dupG has been reported in the literature in multiple homozygote and compound heterozygote individuals affected with Cystinosis (Besouw_2012, Kalatzis_2002, Kiehntopf_2002, Shotelersuk_1998). These data indicate that the variant is very likely to be associated with disease. 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 pathogenic.
Invitae RCV001234762 SCV001407421 pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Nephropathic cystinosis 2019-10-23 criteria provided, single submitter clinical testing This sequence change results in a premature translational stop signal in the CTNS gene (p.Ser310Glnfs*55). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 58 amino acids of the CTNS protein. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with cystinosis (PMID: 9792862, 12204010, 12442267, 27734949). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 1261insG, S310Q in the literature. ClinVar contains an entry for this variant (Variation ID: 188714). For these reasons, this variant has been classified as Pathogenic.
Natera, Inc. RCV000780203 SCV001463153 pathogenic Cystinosis 2020-09-16 no assertion criteria provided clinical testing

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