ClinVar Miner

Submissions for variant NM_000090.3(COL3A1):c.515A>C (p.Tyr172Ser) (rs771654029)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000245198 SCV000319502 uncertain significance Cardiovascular phenotype 2015-03-25 criteria provided, single submitter clinical testing Rarity in general population databases (dbsnp, esp, 1000 genomes);Insufficient or conflicting evidence
Illumina Clinical Services Laboratory,Illumina RCV000389469 SCV000425501 benign Ehlers-Danlos syndrome, type 4 2018-01-13 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.
Invitae RCV000389469 SCV000831640 uncertain significance Ehlers-Danlos syndrome, type 4 2019-08-01 criteria provided, single submitter clinical testing This sequence change replaces tyrosine with serine at codon 172 of the COL3A1 protein (p.Tyr172Ser). The tyrosine residue is moderately conserved and there is a large physicochemical difference between tyrosine and serine. This variant is present in population databases (rs771654029, ExAC 0.07%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has not been reported in the literature in individuals with COL3A1-related disease. ClinVar contains an entry for this variant (Variation ID: 263946). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Unknown"; Align-GVGD: "Class C0"). 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.
Color RCV001186234 SCV001352602 likely benign Familial thoracic aortic aneurysm and aortic dissection 2019-11-26 criteria provided, single submitter clinical testing

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