ClinVar Miner

Submissions for variant NM_013382.7(POMT2):c.1976G>A (p.Arg659Gln)

gnomAD frequency: 0.00001  dbSNP: rs770606360
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001331801 SCV001523924 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 2020-07-15 criteria provided, single submitter clinical testing This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Genomic Medicine Lab, University of California San Francisco RCV001331801 SCV001572979 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 2019-11-07 criteria provided, single submitter clinical testing
Invitae RCV001871825 SCV002223381 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 2022-06-27 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 659 of the POMT2 protein (p.Arg659Gln). This variant is present in population databases (rs770606360, gnomAD 0.02%). 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: 1030284). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
GeneDx RCV003327506 SCV004034422 uncertain significance not provided 2023-03-07 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV001331801 SCV004809658 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 2024-04-04 criteria provided, single submitter clinical testing

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