ClinVar Miner

Submissions for variant NM_000089.4(COL1A2):c.2845G>A (p.Gly949Ser)

dbSNP: rs72659312
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000755949 SCV000883632 pathogenic not provided 2017-11-14 criteria provided, single submitter clinical testing
Invitae RCV002233746 SCV001579527 pathogenic Osteogenesis imperfecta type I; Ehlers-Danlos syndrome, classic type, 1 2023-11-04 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 949 of the COL1A2 protein (p.Gly949Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with autosomal dominant osteogenesis imperfecta (PMID: 8081394, 17078022, 18996919, 34306033). In at least one individual the variant was observed to be de novo. This variant is also known as Gly859Ser. ClinVar contains an entry for this variant (Variation ID: 618026). 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 with a positive predictive value of 95%. 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.
GeneDx RCV000755949 SCV002574413 pathogenic not provided 2022-09-15 criteria provided, single submitter clinical testing Occurs in the triple helical domain and replaces the glycine in the canonical Gly-X-Y repeat; missense substitution of a canonical glycine residue is expected to disrupt normal protein folding and function, and this is an established mechanism of disease (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 33879512, 17078022, 18996919, 32335875, 34306033, 8081394, 28528406)
CeGaT Center for Human Genetics Tuebingen RCV000755949 SCV004032749 pathogenic not provided 2024-01-01 criteria provided, single submitter clinical testing COL1A2: PS2, PM1, PM2, PS4:Moderate, PP3

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