ClinVar Miner

Submissions for variant NM_019066.5(MAGEL2):c.2818C>T (p.Pro940Ser)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002600000 SCV003502193 uncertain significance not provided 2022-08-07 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 940 of the MAGEL2 protein (p.Pro940Ser). 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 output the following: SIFT: "Not Available"; PolyPhen-2: "Not Available"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with MAGEL2-related conditions. This variant is present in population databases (rs763578669, gnomAD 0.01%).
Ambry Genetics RCV002615733 SCV003675524 likely benign Inborn genetic diseases 2022-12-27 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.
PreventionGenetics, part of Exact Sciences RCV004750285 SCV005346301 uncertain significance MAGEL2-related disorder 2023-11-09 no assertion criteria provided clinical testing The MAGEL2 c.2818C>T variant is predicted to result in the amino acid substitution p.Pro940Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.013% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/15-23890072-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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