Submission Details

The CAPN3 gene encodes calpain-3, a calcium-activated protease that is expressed predominantly in skeletal muscle. Upon stimulation, calpain-3 activates and inactivates itself rapidly through autocatalysis. CAPN3 was first reported in relation to autosomal dominant (AD) limb-girdle muscular dystrophy (LGMD) in 2016 (Vissing et al., PMID: 27259757). CAPN3-related AD LGMD is also known as LGMDD4 (MIM #618129). This gene is also associated with CAPN3-related autosomal recessive (AR) LGMD, which is also known as LGMDR1 (MIM #253600). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we identified differences in inheritance pattern and presumed molecular mechanism. We therefore split the curations and separately assessed the causative relationship between CAPN3 and AR LGMD (MONDO:0015152) and AD LGMD (MONDO:0015151).

The clinical phenotypes associated with CAPN3-related AD LGMD are often less severe and of later onset compared to those found in patients with CAPN3-related AR LGMD. Onset ranges from late childhood/early adolescence to the seventh decade, with some individuals presenting as clinically asymptomatic. Not all affected individuals experience proximal muscle weakness, though most have elevated serum CK. Camptocormia, waddling gait, low back pain and other myalgia, fatigability, and scapular winging are also reported. Muscle imaging may show signs of fat infiltration or atrophy, and myopathic or dystrophic patterns may be present on muscle biopsy. Among evaluated patients, calpain-3 protein expression in skeletal muscle is variable, with a near-absence reported in some patients and seemingly normal expression in others. Additional cases may help clarify whether AD calpainopathy should be considered part of or distinct from the spectrum of LGMD.

The genetic evidence for this curation included review of 34 families with a total of 15 reported variants described in 12 publications (PMID: 27259757, 28881388, 32557990, 32342993, 33107701, 32896923, 33741228, 37589857, 38812636, 39703226, 38356676, 40226307). Among these reports, 6 variants identified in 10 probands with sufficient indication of AD inheritance were scored a total of 7 pts. The c.643_663del p.(Ser215_Gly221del) variant is a founder variant in the Scandinavian population (PMID: 27259757). Segregation with the disease in an AD manner observed in four families was awarded 2.2 pts, with a summed estimated LOD score of 9.63 (PMID: 27259757, 32896923, 32342993). All scored variants were shown to impair calpain-3 autolytic and proteolytic activity but retain susceptibility to cleavage by wild-type calpain-3 in vitro (PMID: 18337726, 32557990, 32342993, 33741228; https://doi.org/10.1016/j.nmd.2022.07.220. The mechanism of pathogenicity is not well understood but is presumed to involve a dominant-negative effect on wild-type calpain-3, though this has not yet been demonstrated in vitro. Haploinsufficiency is not a mechanism for CAPN3-related AD LGMD, and all variants reported to date are expected to result in an altered rather than absent protein product. Reported variants include missense variants, in-frame deletions, and variants shown to alter splicing, producing a prematurely truncated protein or in-frame deletion. This gene-disease relationship is also supported by experimental evidence (2.5 pts), including expression of the gene product in skeletal muscle and a function in sarcomeric repair and maintenance consistent with a role in muscle disease as well as reduced calpain-3 protein expression and absent proteolytic activity in patient muscle tissue (PMID: 9777948, 9521867, 18974005, 32557990, 2725975). In summary, there is Definitive evidence supporting the relationship between CAPN3 and autosomal dominant limb girdle muscular dystrophy. This relationship has been repeatedly demonstrated in both the research and clinical diagnostic settings and upheld over time. This classification was approved by the ClinGen Muscular Dystrophies and Myopathies GCEP on May 13, 2025 (SOP Version 11).

This gene-disease pair was originally evaluated by the Muscular Dystrophies and Myopathies GCEP in May 2022. It was re-evaluated in May 2025 and upgraded from Limited to Definitive with the addition of new case data and incorporation of variant-level functional impact.

Of note: Only a small minority of variants in CAPN3 have convincing evidence for a role in disease in the single heterozygous state. Most variants, including all of those expected to result in an absent rather than altered protein product, have evidence only for AR inheritance. Accordingly, disease-causing variants will be present on both alleles in the vast majority of patients with CAPN3-related LGMD. Caution is warranted before attributing a patient's muscle disease to the presence of a single heterozygous variant in CAPN3, particularly in the absence of a positive family history suggestive of AD inheritance. Importantly, in some patients, "dominant" variants are identified in trans with a second CAPN3 pathogenic variant (e.g., PMID: 32896923, 34863162). Depending on the functional impact of the second variant, such patients may, or may not, exhibit more severe disease. In patients in whom a single pathogenic CAPN3 variant is identified, clinical severity, age of onset, family history, and previous reports of the variant should be carefully considered. In most cases, further genetic testing to identify a second variant should be pursued.