ClinVar Miner

Submissions for variant NM_031443.4(CCM2):c.160G>A (p.Glu54Lys)

gnomAD frequency: 0.00004  dbSNP: rs759104121
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001363376 SCV001559485 uncertain significance Cerebral cavernous malformation 2 2022-07-05 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with CCM2-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: "Possibly Damaging"; Align-GVGD: "Class C15"). ClinVar contains an entry for this variant (Variation ID: 1054801). This variant is present in population databases (rs759104121, gnomAD 0.009%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 54 of the CCM2 protein (p.Glu54Lys).
Ambry Genetics RCV003246944 SCV003940435 likely benign Inborn genetic diseases 2023-04-24 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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