ClinVar Miner

Submissions for variant NM_004370.6(COL12A1):c.8059A>T (p.Ile2687Phe)

gnomAD frequency: 0.00001  dbSNP: rs1391973492
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520496 SCV000618939 uncertain significance not provided 2017-07-03 criteria provided, single submitter clinical testing The I2687F variant in the COL12A1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The I2687F variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The I2687F variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Isoleucine are tolerated across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret I2687F as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV000526132 SCV000656198 uncertain significance Ullrich congenital muscular dystrophy 2; Bethlem myopathy 2 2022-08-09 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with COL12A1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 450364). This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces isoleucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 2687 of the COL12A1 protein (p.Ile2687Phe).

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