ClinVar Genomic variation as it relates to human health

The G225A pathogenic variant in the COL3A1 gene has previously been reported in one individual with vascular Ehlers Danlos syndrome (EDS type IV) (Pepin et al., 2014). In addition, different missense variants affecting the same residue (G225V, G225D) have also been reported in association with vascular EDS (Pepin et al., 2014; Drera et al., 2011). The G225A variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Although the G225A variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties, it occurs at a position that is conserved across species. In addition, in silico analysis predicts this variant is probably damaging to the protein structure/function. Furthermore, the G225A variant affects a Glycine residue in a Gly-X-Y motif in the triple helical region of the COL3A1 gene, where the majority of pathogenic missense variants occur (Stenson et al., 2014; Symoens et al., 2012).

This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 225 of the COL3A1 protein (p.Gly225Ala). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of vascular Ehlers-Danlos syndrome (PMID: 24922459, 31126764; externalcommunication). ClinVar contains an entry for this variant (Variation ID: 101469). 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 COL3A1 protein function. This variant disrupts the triple helix domain of COL3A1. 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). In COL3A1, variants that affect these glycine residues are significantly enriched in individuals with disease (PMID: 24922459, 25758994) compared to the general population (ExAC). This variant disrupts the p.Gly225 amino acid residue in COL3A1. Other variant(s) that disrupt this residue have been observed in individuals with COL3A1-related conditions (PMID: 22019127), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.

The p.Gly225Ala variant in COL3A1 has been reported in at least 1 individual with clinical features of Ehlers-Danlos syndrome type IV (EDS IV, vascular) (Pepin 2014) and was absent from large population studies. Computational prediction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. Variants in COL3A1 affecting conserved glycine (Gly) residues of the G-X-Y repeat region in the triple helical collagen domain, where this variant is located, are strongly associated with EDS IV (Pepin 2000, Pepin 2014, Frank 2015). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant EDS IV. ACMG/AMP Criteria applied: PM1, PS4_Supporting, PM2, PP3.

The p.G225A variant (also known as c.674G>C), located in coding exon 8 of the COL3A1 gene, results from a G to C substitution at nucleotide position 674. The glycine at codon 225 is replaced by alanine, an amino acid with similar properties. The majority (approximately two-thirds) of COL3A1 mutations identified to date have involved the substitution of another amino acid for glycine within the triple-helical domain (Pepin MG et al. Genet Med. 2014;16(12):881-8; Frank M et al. Eur J Hum Genet. 2015;23(12):1657-64). This particular glycine substitution has been reported in two vascular Ehlers-Danlos syndrome (vEDS) cohorts (Pepin MG, Genet. Med. 2014 Dec; 16(12):881-8; Shalhub S et al. J. Vasc. Surg., 2019 Nov;70:1543-1554). Internal structural analysis indicates that this alteration disrupts the characteristic G-X-Y motif in the COL3A1 protein and inserts a bulky side chain into a sterically-constrained region (Bella J et al. Science. 1994;266:75-81; Hohenester E et al. Proc. Natl. Acad. Sci. U.S.A. 2008;105:18273-7; Ambry internal data). Two alterations in the same codon, p.G225D and p.G225S, have also been associated with vEDS (Drera B et al. J. Dermatol. Sci., 2011 Dec;64:237-40; Legrand A et al. Genet. Med., 2019 07;21:1568-1575). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

The COL3A1 c.674G>C variant is predicted to result in the amino acid substitution p.Gly225Ala. This variant, also referred to as p.Gly58Ala using the legacy nomenclature, has been reported in an individual with Ehlers-Danlos syndrome IV (vascular type) (Table S1, Pepin et al. 2014. PubMed ID: 24922459). Alternate nucleotide changes affecting the same amino acid (p.Gly225Ser; p.Gly225Asp; and p.Gly225Val) have also been reported in individuals with COL3A1-associated disease (Table S2, Legrand et al. 2019. PubMed ID: 30474650; Drera et al. 2011. PubMed ID: 22019127; p.Gly225Val was reported as G58V in Pepin et al. 2000. PubMed ID: 10706896). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as likely pathogenic.