ACTA1 p.Glu95Lys

The c.283G>A variant in ACTA1 is a missense variant predicted to cause substitution of glutamic acid by lysine at amino acid 95 (legacy nomenclature: p.Glu93Lys). This variant is absent from gnomAD v4.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.933, which is above the threshold of 0.7, evidence that correlates with impact to ACTA1 function (PP3). ACTA1, in which the variant was identified, is defined by the ClinGen Congenital Myopathies VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant has been reported in 4 probands with severe hypotonia and/or congenital myopathy (PS4_Moderate; PMID: 35810298, Invitae, ClinVar SCV:SCV000950636.2). In one of those four individuals, the variant has been identified as a de novo occurrence with confirmed parental relationships (PS2; Invitae, ClinVar SCV:SCV000950636.2). At least one patient with this variant displayed intranuclear rods and type 1 muscle fiber predominance, which is highly specific for alpha-actinopathy and has had exome testing that is negative for all other causes of myopathy (PP4_Strong, PMID: 35810298). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant alpha-actinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PP4_Strong, PS4_Moderate, PS2_Supporting, PM2_Supporting, PP2, PP3 (Congenital Myopathies VCEP specifications version 2; 08/27/2024).