ClinVar Miner

Submissions for variant NM_013382.7(POMT2):c.275T>C (p.Met92Thr)

gnomAD frequency: 0.00001  dbSNP: rs775489616
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000712839 SCV000843374 uncertain significance not provided 2018-01-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002532939 SCV003239411 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2; Autosomal recessive limb-girdle muscular dystrophy type 2N 2022-02-04 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 92 of the POMT2 protein (p.Met92Thr). This variant is present in population databases (rs775489616, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with POMT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 586372). 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003987678 SCV004803281 uncertain significance not specified 2024-01-12 criteria provided, single submitter clinical testing Variant summary: POMT2 c.275T>C (p.Met92Thr) results in a non-conservative amino acid change located in the Glycosyl transferase family 39/83 (IPR003342) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251336 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.275T>C in individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 586372). Based on the evidence outlined above, the variant was classified as uncertain significance.

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