ClinVar Miner

Submissions for variant NM_001159773.2(CANT1):c.643G>T (p.Glu215Ter)

gnomAD frequency: 0.00001  dbSNP: rs773215035
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000778522 SCV000914801 uncertain significance Desbuquois dysplasia 1 2018-12-12 criteria provided, single submitter clinical testing The CANT1 c.643G>T (p.Glu215Ter) variant is a stop-gained variant that is predicted to result in a premature termination of the protein. A literature search was performed for the gene, cDNA, and amino acid change. No publications were found based on this search. The p.Glu215Ter variant is not found in the 1000 Genomes Project, the Exome Sequencing Project, Exome Aggregation Consortium, or the Genome Aggregation Database. This variant is located in the last exon and may escape nonsense-mediated decay. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of stop-gained variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for Desbuquois dysplasia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Labcorp Genetics (formerly Invitae), Labcorp RCV003768428 SCV004632645 pathogenic not provided 2023-03-29 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 631792). This premature translational stop signal has been observed in individual(s) with CANT1-related conditions (PMID: 31587486). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu215*) in the CANT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CANT1 are known to be pathogenic (PMID: 19853239, 21037275, 22539336).

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