CAPN3

Inheritance Pattern: AR

Disease ID:MONDO:0009675

Submitter: Natera

Inheritance Pattern: AD

Disease ID:MONDO:0029133

Submitter: Labcorp Genetics (formerly Invitae)

Inheritance Pattern: AD

Disease ID:MONDO:0015151

Submitter: ClinGen

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.

Inheritance Pattern: AR

Disease ID:MONDO:0009675

Submitter: Labcorp Genetics (formerly Invitae)

Inheritance Pattern: AD

Disease ID:MONDO:0029133

Submitter: Ambry Genetics

Inheritance Pattern: AR

Disease ID:MONDO:0009675

Submitter: Myriad Women's Health

Inheritance Pattern: AD

Disease ID:MONDO:0029133

Submitter: Natera

Inheritance Pattern: AR

Disease ID:MONDO:0015152

Submitter: ClinGen

The relationship between *CAPN3* and autosomal recessive limb-girdle muscular dystrophy (LGMDR1 included) has been evaluated using the ClinGen Clinical Validity Framework as of May 2022. The *CAPN3* gene is located on chromosome 15q15.q and encodes multiple transcript variants. The longest transcript (NM_000070.3) is 3.5 kb long with 24 exons encoding an 821-amino acid protein. Additional transcripts, derived from alternative splicing and the use of alternative promoter have also been identified. More than 250 pathogenic variants reported in patients with autosomal recessive LGMD are recorded in ClinVar, more than 150 of them being predicted loss of function variants. Limb girdle muscular dystrophy is characterized by progressive weakness in muscles including but not limited to the proximal muscles and affecting the pelvic and shoulder girdle which can lead to difficulty walking or complete loss of ambulation requiring wheelchair use. It is also accompanied by elevated serum creatine kinase and dystrophic and myopathic features. Summary of case level data (12 points): Variants in this gene have been reported in at least 10 probands in 3 publications (PMID: 7720071, 9150160,10330340). Variants in this gene segregated with disease in 24 additional family members. More case-level evidence is available in the literature, but the maximum score for genetic evidence (12 pts) has been reached. The mechanism for disease is expected to be biallelic loss of function. Summary of Experimental Data (6 points): This gene-disease relationship is supported by expression studies, biochemical function, protein interaction, animal models, and rescue evidence. Calpain 3 (*CAPN3*) is a muscle-specific member of the calpain family Ca2+ dependent cysteine proteases and localizes to sarcomere in skeletal muscle (PMID: 9521867, 9777948,15138196, 10229226). Calpain 3 is activated by autolysis. Calpain 3 interacts with multiple skeletal muscle sarcomere and sarcolemma proteins, and many of which are cleaved by active Calpain 3 (PMID: 15138196, 15827562). While the known Calpain 3 substrate list is likely incomplete, Calpine 3 plays important functions in muscle calmodulin pathway, skeletal mTORC1 signaling, mitochondrial biogenesis, and apoptosis (PMID: 10229226, 25389288, 33308300). A number of mouse models by targeted knockout and gene trapping of *CAPN3* are reported with phenotype and muscle histological defects similar to human patients with AR-LGMD (PMID: 33308300, 15138196). And rescue in mouse models are also reported (PMID: 16290124, 34514031). In summary, the *CAPN3* -autosomal recessive limb-girdle muscular dystrophy gene-disease relationship is definitive. This is demonstrated in both research and clinical diagnostic settings and has been upheld over time.

Inheritance Pattern: AR

Disease ID:MONDO:0009675

Submitter: Orphanet