ClinVar Miner

Submissions for variant NM_000090.4(COL3A1):c.1668T>G (p.Ser556Arg)

dbSNP: rs1688319570
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001755054 SCV001995874 uncertain significance not provided 2019-11-08 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Occurs in the triple helical domain at the X position in the canonical Gly-X-Y repeat; although this variant may have an effect on normal protein folding and function, missense substitution at the X position is not a common mechanism of disease (Stenson et al., 2014)
All of Us Research Program, National Institutes of Health RCV004009020 SCV004836324 uncertain significance Ehlers-Danlos syndrome, type 4 2023-12-18 criteria provided, single submitter clinical testing This missense variant replaces serine with arginine at codon 556 of the COL3A1 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with COL3A1-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004770198 SCV005380534 uncertain significance not specified 2024-08-20 criteria provided, single submitter clinical testing Variant summary: COL3A1 c.1668T>G (p.Ser556Arg) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 251084 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1668T>G in individuals affected with COL3A1-related conditions and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1312300). Based on the evidence outlined above, the variant was classified as uncertain significance.

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