ClinVar Miner

Submissions for variant NM_000089.4(COL1A2):c.2260G>T (p.Gly754Cys)

dbSNP: rs72658177
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000596743 SCV000707209 likely pathogenic not provided 2017-04-04 criteria provided, single submitter clinical testing
Invitae RCV002232561 SCV000825762 pathogenic Osteogenesis imperfecta type I; Ehlers-Danlos syndrome, classic type, 1 2023-02-21 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 754 of the COL1A2 protein (p.Gly754Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with osteogenesis imperfecta (PMID: 16879195, 31428121). ClinVar contains an entry for this variant (Variation ID: 501007). 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. Experimental studies have shown that this missense change affects COL1A2 function (PMID: 16879195). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV000596743 SCV004238546 likely pathogenic not provided 2023-07-28 criteria provided, single submitter clinical testing

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