ClinVar Miner

Submissions for variant NM_001159773.2(CANT1):c.643G>A (p.Glu215Lys)

dbSNP: rs773215035
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000996613 SCV001151427 likely pathogenic not provided 2019-01-01 criteria provided, single submitter clinical testing
3billion RCV001260984 SCV002011903 pathogenic Desbuquois dysplasia 1 2021-10-02 criteria provided, single submitter clinical testing Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogeic with strong evidence (ClinVar ID: VCV000808323.7, PMID: 31988067, PS1) and CANT1 enzyme activity study showed defective neuclotidase acitivity (PMID: 31988067, PS3). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000004, PM2). Missense changes are a common disease-causing mechanism (PP2). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.907, 3Cnet: 0.742, PP3). Patient's phenotype is considered compatible with Desbuquois dysplasia 1 (3billion dataset, PP4). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline
OMIM RCV001260984 SCV001438358 pathogenic Desbuquois dysplasia 1 2020-10-19 no assertion criteria provided literature only

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