ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.699+85C>G

gnomAD frequency: 0.00004  dbSNP: rs369000699
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000610404 SCV000716127 likely benign not specified 2017-02-28 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV002062955 SCV002450165 likely benign Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2024-01-09 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000610404 SCV003923009 uncertain significance not specified 2023-03-16 criteria provided, single submitter clinical testing Variant summary: POMT1 c.765+19C>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant causes a missense change in an alternate transcript (NM_001374689.1: c.622C>G, p.Pro208Ala). The variant allele was found at a frequency of 8e-05 in 250846 control chromosomes (gnomAD). This frequency is not higher than estimated for a pathogenic variant in POMT1 causing Limb-Girdle Muscular Dystrophy, Autosomal Recessive (8e-05 vs 0.00072), allowing no conclusion about variant significance. To our knowledge, no occurrence of the variant in individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.

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