ClinVar Miner

Submissions for variant NM_000089.4(COL1A2):c.2387G>C (p.Gly796Ala)

dbSNP: rs72658189
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000519428 SCV000617385 pathogenic not provided 2019-09-12 criteria provided, single submitter clinical testing Identified in an individual with osteogenesis imperfecta type IV in published literature (Marini et al., 2007); Found within the triple helical region and replaces the Gly position in the canonical Gly-X-Y repeat of COL1A2; Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 17078022, 30715774)
Invitae RCV002231208 SCV001589939 pathogenic Osteogenesis imperfecta type I; Ehlers-Danlos syndrome, classic type, 1 2022-07-06 criteria provided, single submitter clinical testing This missense change has been observed in individuals with osteogenesis imperfecta (PMID: 17078022, 30715774). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the triple helix domain of COL1A2. 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 COL1A2, variants affecting these glycine residues are significantly enriched in individuals with disease (PMID: 9016532, 17078022) compared to the general population (ExAC). 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 COL1A2 protein function. ClinVar contains an entry for this variant (Variation ID: 449351). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 796 of the COL1A2 protein (p.Gly796Ala).

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