ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.1565C>T (p.Ala522Val)

gnomAD frequency: 0.00005  dbSNP: rs374402055
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001035908 SCV001199248 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2021-08-31 criteria provided, single submitter clinical testing This sequence change replaces alanine with valine at codon 544 of the POMT1 protein (p.Ala544Val). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and valine. This variant is present in population databases (rs374402055, ExAC 0.2%). This variant has not been reported in the literature in individuals affected with POMT1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Revvity Omics, Revvity RCV003141941 SCV003811807 uncertain significance not provided 2020-03-26 criteria provided, single submitter clinical testing
GeneDx RCV003141941 SCV003915374 uncertain significance not provided 2022-10-06 criteria provided, single submitter clinical testing In silico analysis supports a deleterious effect on splicing; In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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