ClinVar Miner

Submissions for variant NM_000493.4(COL10A1):c.772C>T (p.Arg258Ter)

gnomAD frequency: 0.00003  dbSNP: rs765628474
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001156891 SCV001318427 benign Metaphyseal chondrodysplasia, Schmid type 2017-04-28 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Institute of Human Genetics, University of Leipzig Medical Center RCV001156891 SCV001429062 likely pathogenic Metaphyseal chondrodysplasia, Schmid type 2018-09-27 criteria provided, single submitter clinical testing
Mendelics RCV002249740 SCV002518118 uncertain significance not specified 2022-05-04 criteria provided, single submitter clinical testing
Invitae RCV002558368 SCV002966762 uncertain significance not provided 2022-10-09 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 907221). This variant has not been reported in the literature in individuals affected with COL10A1-related conditions. This variant is present in population databases (rs765628474, gnomAD 0.01%). This sequence change creates a premature translational stop signal (p.Arg258*) in the COL10A1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 423 amino acid(s) of the COL10A1 protein.

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