ClinVar Miner

Submissions for variant NM_147127.5(EVC2):c.1658A>G (p.Glu553Gly)

gnomAD frequency: 0.00001  dbSNP: rs766349604
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520119 SCV000620882 uncertain significance not provided 2017-09-25 criteria provided, single submitter clinical testing The E553G variant in the EVC2 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The E553G variant is observed in 2/66724 (0.003%) alleles from individuals of non-Finnish background, in the ExAC dataset (Lek et al., 2016). The E553G variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position where amino acids with similar properties to Glutamic acid are tolerated across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret E553G as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV002527637 SCV003467358 uncertain significance Ellis-van Creveld syndrome; Curry-Hall syndrome 2022-06-27 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 553 of the EVC2 protein (p.Glu553Gly). This variant is present in population databases (rs766349604, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with EVC2-related conditions. ClinVar contains an entry for this variant (Variation ID: 452105). 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: "Possibly Damaging"; Align-GVGD: "Class C15"). 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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