ClinVar Miner

Submissions for variant NM_004937.3(CTNS):c.771_793del (p.Gly258fs) (rs759623796)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated 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 RCV000820859 SCV000961592 pathogenic Ocular cystinosis; Juvenile nephropathic cystinosis; Nephropathic cystinosis 2018-09-11 criteria provided, single submitter clinical testing 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. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has been observed as homozygous in individuals affected with cystinosis (PMID: 26266097, 10556299). This variant is also known as c.1109_1131del23 in the literature. ClinVar contains an entry for this variant (Variation ID: 496276). Loss-of-function variants in CTNS are known to be pathogenic (PMID: 9537412, 27102039). For these reasons, this variant has been classified as Pathogenic.
Centogene AG - the Rare Disease Company RCV000586519 SCV001424396 pathogenic Cystinosis criteria provided, single submitter clinical testing
Counsyl RCV000984254 SCV001132377 likely pathogenic Nephropathic cystinosis 2014-08-16 no assertion criteria provided clinical testing

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