rs66612022
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM2PP2PP3_StrongPP5_Very_Strong
The NM_000089.4(COL1A2):c.982G>A(p.Gly328Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_000089.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL1A2 | NM_000089.4 | c.982G>A | p.Gly328Ser | missense_variant | Exon 19 of 52 | ENST00000297268.11 | NP_000080.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 37
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Osteogenesis imperfecta Pathogenic:1
Osteogenesis Imperfecta, indeterminate type -
Ehlers-Danlos syndrome, cardiac valvular type Pathogenic:1
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 32659730) - PS3_supporting. The c.982G>A;p.(Gly328Ser) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 456848; PMID: 22589248; 16705691; 9272740; 27519266; 26307460) - PS4. This variant is not present in population databases (rs66612022, gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. Pathogenic missense variant in this residue have been reported (Clinvar ID: 618025; 372735) - PM5. The variant co-segregated with disease in multiple affected family members (PMID: 26307460) - PP1. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic. -
Osteogenesis imperfecta with normal sclerae, dominant form Pathogenic:1
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM1,PM2,PM5,PP3. -
not provided Pathogenic:1
Observed frequently in unrelated patients with osteogenesis imperfecta from different ethnic backgrounds in published literature (Lee et al., 2006; Marini et al., 2007; Bardai et al., 2016; Ho Duy et al., 2016) and not observed in controls; 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); Not observed in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 22589248, 15024745, 27509835, 9594376, 31414283, 9272740, 32123938, 31853946, 32659730, 16705691, 26307460, 21667357, 24668929, 17875077, 27519266, 29907962, 7860070, 31447884, 17078022, 29453417, 32770541) -
Osteogenesis imperfecta type I;C0268335:Ehlers-Danlos syndrome, classic type, 1 Pathogenic:1
This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 328 of the COL1A2 protein (p.Gly328Ser). 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: 7860070, 9272740, 16705691, 17078022, 22589248). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 456848). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt COL1A2 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects COL1A2 function (PMID: 7860070, 9272740, 9594376). For these reasons, this variant has been classified as Pathogenic. -
Postmenopausal osteoporosis;C0268358:Osteogenesis imperfecta, perinatal lethal;C0268362:Osteogenesis imperfecta type III;C0268363:Osteogenesis imperfecta with normal sclerae, dominant form;C4303789:Ehlers-Danlos syndrome, cardiac valvular type;CN293783:Ehlers-Danlos syndrome, arthrochalasia type, 2 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at