ClinVar Miner

Submissions for variant NM_002180.2(IGHMBP2):c.1754A>G (p.Lys585Arg) (rs146450269)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000221451 SCV000280006 uncertain significance not provided 2017-03-19 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the IGHMBP2 gene. The K585R variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The K585R variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The K585R variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species. Additionally, missense variants in nearby residues (V580I, R581S, N583I, G586C) have been reported in the Human Gene Mutation Database in association with IGHMBP2-related disorders (Stenson et al., 2014), supporting the functional importance of this region of the protein. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV001226844 SCV001399171 uncertain significance Spinal muscular atrophy, distal, autosomal recessive, 1; Charcot-Marie-Tooth disease, axonal, type 2S 2019-11-04 criteria provided, single submitter clinical testing This sequence change replaces lysine with arginine at codon 585 of the IGHMBP2 protein (p.Lys585Arg). The lysine residue is highly conserved and there is a small physicochemical difference between lysine and arginine. This variant is present in population databases (rs146450269, ExAC 0.03%). This variant has not been reported in the literature in individuals with IGHMBP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 234918). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The arginine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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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