ClinVar Miner

Submissions for variant NM_003906.5(MCM3AP):c.2407G>A (p.Glu803Lys)

gnomAD frequency: 0.00006  dbSNP: rs146488499
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001883410 SCV002140820 uncertain significance not provided 2022-04-25 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 803 of the MCM3AP protein (p.Glu803Lys). This variant is present in population databases (rs146488499, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with MCM3AP-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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.
GeneDx RCV001883410 SCV002578482 uncertain significance not provided 2022-04-09 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV003130570 SCV003810826 uncertain significance Peripheral neuropathy, autosomal recessive, with or without impaired intellectual development 2022-09-14 criteria provided, single submitter clinical testing
Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center RCV003130570 SCV004190158 uncertain significance Peripheral neuropathy, autosomal recessive, with or without impaired intellectual development 2021-04-23 criteria provided, single submitter clinical testing Variant in the MCM3AP gene, c.2407G>A is a missense variant, which results in a substitution of glutamine residue at the 803 position to lysine (p.Glu803Lys). This variant localizes to coding exon 8 of the MCM3AP gene (28 exons in total; NM_003906.5) and is within the Sac3 domain of the protein. It is predicted to be deleterious and damaging to protein structure and/or function based on in silico analyses (PROVEAN and SIFT). This variant has been observed inthe Genome Aggregation Database (gnomAD) at a very low frequency (14/282862, 0 homozygotes), indicating it is not acommon benign variant in the populations represented in this database. To the best of our knowledge, this specific variant has not been reported in the literature to be associated with disease. However, missense variants have been reported to cluster in the Sac3 domain (amino acid 366-990) (PMID: 29982295, 32202298).

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