ClinVar Miner

Submissions for variant NM_013382.7(POMT2):c.2197C>T (p.Gln733Ter)

dbSNP: rs1452558347
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000592554 SCV000708146 likely pathogenic not provided 2017-05-11 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001553651 SCV001774588 uncertain significance not specified 2021-07-20 criteria provided, single submitter clinical testing Variant summary: POMT2 c.2197C>T (p.Gln733X) results in a premature termination codon, predicted to cause a truncation of the encoded protein. The variant is not expected to result in nonsense mediated decay but, will be missing the last few amino acids of the protein. However, without further functional evidence, its clinical implication is not clear. The variant allele was found at a frequency of 4e-06 in 251420 control chromosomes (gnomAD). To our knowledge, no occurrence of c.2197C>T in individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance until additional clinical reports supported by functional studies are identified.
Genomic Medicine Lab, University of California San Francisco RCV002286415 SCV002576356 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002532611 SCV003448868 pathogenic 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 2024-03-14 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln733*) in the POMT2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 18 amino acid(s) of the POMT2 protein. This variant is present in population databases (no rsID available, gnomAD 0.006%). 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: 501676). This variant disrupts a region of the POMT2 protein in which other variant(s) (p.Trp748Arg) have been determined to be pathogenic (PMID: 17634419, 17869517). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV002286415 SCV004204114 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 2023-04-01 criteria provided, single submitter clinical testing

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