ClinVar Miner

Submissions for variant NM_013382.5(POMT2):c.1627C>A (p.Leu543Met) (rs367552151)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000658417 SCV000780189 uncertain significance not provided 2018-05-29 criteria provided, single submitter clinical testing The L543M variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The L543M variant is observed in 18/24,030 (0.075%) alleles from individuals of African background (Lek et al., 2016). This variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function.
Invitae RCV001065039 SCV001229977 uncertain significance Congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies, type A2; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B2; Limb-girdle muscular dystrophy-dystroglycanopathy, type C2 2019-11-05 criteria provided, single submitter clinical testing This sequence change replaces leucine with methionine at codon 543 of the POMT2 protein (p.Leu543Met). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and methionine. This variant is present in population databases (rs367552151, ExAC 0.04%). This variant has not been reported in the literature in individuals with POMT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 546524). 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 tolerated, but 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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