ClinVar Miner

Submissions for variant NM_000393.5(COL5A2):c.3199C>T (p.Arg1067Cys)

gnomAD frequency: 0.00001  dbSNP: rs539362640
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001141924 SCV001302311 likely benign Ehlers-Danlos syndrome, classic type, 2 2018-01-12 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae RCV001882435 SCV002206524 uncertain significance Ehlers-Danlos syndrome, classic type, 1 2023-02-27 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 898195). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1067 of the COL5A2 protein (p.Arg1067Cys). This variant is present in population databases (rs539362640, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with COL5A2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.
GeneDx RCV003442212 SCV004169633 uncertain significance not provided 2023-05-16 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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