CAPN3 p.Arg489Gln

The NM_000070.3: c.1466G>A variant in CAPN3 is a missense variant expected to cause the substitution of arginine with glutamine at position 489, p.(Arg489Gln). This variant has been identified in at least 8 individuals with features consistent with LGMD (PMID: 30989743, 10484770, 30564623, 17994539; LOVD CAPN3_000018; ClinVar SCV000645479.8 internal data communication), including confirmed in trans with a likely pathogenic or pathogenic variant in one case with LGMD (c.1711del p.(Leu571SerfsTer23), 1.0 pt, PMID: 17994539, 26404900), one case with hyperCKemia (c.1469G>A p.(Arg490Gln), 1.0 pt, PMID: 18854869, 14578192), and one case with chronic proximal muscle weakness (c.1715G>A (p.Arg572Gln), 1.0 pt, ClinVar SCV000645479.8 internal data communication). It has also been reported in unknown phase with a pathogenic variant in at least two patients (c.2182C>T p.(Gln728Ter), 0.5 pts, PMID: 30919934; c.550del, p.(Thr184ArgfsTer36), 0.5 pts, PMID: 30919934) and in unknown phase with a likely pathogenic variant in one patient (c.2440-1G>A, 0.25 pts, PMID: 30564623, LOVD Individual #00222689) (PM3_Very Strong). At least one individual with this variant and a second presumed diagnostic CAPN3 variant displayed progressive limb girdle muscle weakness and significantly reduced calpain-3 protein expression in skeletal muscle, which is specific for CAPN3-related LGMD (PMID: 17994539; PP4_Moderate). The Grpmax population frequency of this variant is 0.0003738 in gnomAD v4.1.0 (28/74900 African/African American chromosomes), which is greater than the ClinGen LGMD VCEP threshold (≤0.0001) (PM2_Supporting not met). The computational predictor REVEL gives a score of 0.881, which is above the LGMD VCEP threshold of ≥0.70, evidence that correlates with impact to CAPN3 function (PP3). A mini-gene assay showed that this variant may result in exon 11 skipping in a very small minority of transcripts; however, significant expression of transcripts with the normal annotated splice pattern was maintained (PMID: 32668095; PVS1_RNA not met). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (LGMD VCEP specifications version 2.0.0; 04/01/2026): PM3_Very Strong, PP4_Moderate, PP3.