ClinVar Miner

Submissions for variant NM_013382.5(POMT2):c.134C>G (p.Pro45Arg) (rs753037500)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000522834 SCV000619902 uncertain significance not provided 2017-08-03 criteria provided, single submitter clinical testing The P45R variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The P45R variant is observed in 5/1272 (0.4%) alleles from individuals of Latino background; however, limited data are available (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The P45R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved. 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 RCV000707422 SCV000836520 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 2018-05-09 criteria provided, single submitter clinical testing This sequence change replaces proline with arginine at codon 45 of the POMT2 protein (p.Pro45Arg). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and arginine. This variant is present in population databases (rs753037500, ExAC 0.4%). This variant has not been reported in the literature in individuals with POMT2-related disease. ClinVar contains an entry for this variant (Variation ID: 451230). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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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