ClinVar Miner

Submissions for variant NM_000090.4(COL3A1):c.3928G>A (p.Val1310Ile)

gnomAD frequency: 0.00001  dbSNP: rs1688692242
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001758352 SCV001996894 uncertain significance not provided 2019-11-08 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Not located in the triple helical region, where the majority of pathogenic missense variants occur (Stenson et al., 2014)
PreventionGenetics, part of Exact Sciences RCV004536291 SCV004114096 uncertain significance COL3A1-related disorder 2022-10-14 criteria provided, single submitter clinical testing The COL3A1 c.3928G>A variant is predicted to result in the amino acid substitution p.Val1310Ile. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Labcorp Genetics (formerly Invitae), Labcorp RCV003633595 SCV004508661 uncertain significance Ehlers-Danlos syndrome, type 4 2024-01-30 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 1310 of the COL3A1 protein (p.Val1310Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with COL3A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1310228). 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 not expected to disrupt COL3A1 protein function with a negative predictive value of 95%. 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.

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