ClinVar Genomic variation as it relates to human health

This sequence change replaces glycine, which is neutral and non-polar, with tryptophan, which is neutral and slightly polar, at codon 2575 of the COL7A1 protein (p.Gly2575Trp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with COL7A1-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt COL7A1 protein function with a positive predictive value of 95%. This variant disrupts the triple helix domain of COL7A1. Glycine residues within the Gly-Xaa-Yaa repeats of the triple helix domain are required for the structure and stability of fibrillar collagens (PMID: 7695699, 8218237, 19344236), and variants at these glycine residues in COL7A1 are more frequently observed in individuals with disease than in the general population (PMID: 22058051). However, the clinical significance of this observation remains uncertain since only a limited number of affected individuals have been described to date. This variant disrupts the p.Gly2575 amino acid residue in COL7A1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8592061, 16971478, 18450758). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

Variant summary: COL7A1 c.7723G>T (p.Gly2575Trp) results in a non-conservative amino acid change within the triple-helical region of the encoded protein sequence and disrupts a glycine residue at position 1 of a Gly-X-Y repeat. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 191218 control chromosomes (gnomAD). To our knowledge, no occurrence of c.7723G>T in individuals affected with Dystrophic Epidermolysis Bullosa and no experimental evidence demonstrating its impact on protein function have been reported. However, a variant resulting in a different amino acid change at the same position, p.Gly2575Arg, has been classified as pathogenic, suggesting this Gly residue is important for normal protein function. ClinVar contains an entry for this variant (Variation ID: 2802793). Based on the evidence outlined above, the variant was classified as likely pathogenic.