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GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CAPN3
calpain 3
Chromosome 15 Β· 15q15.1
NCBI Gene: 825Ensembl: ENSG00000092529.26HGNC: HGNC:1480UniProt: A0A0S2Z3E1
159PubMed Papers
22Diseases
0Drugs
518Pathogenic Variants
FUNCTIONAL ROLE
Protease
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein destabilizationnegative regulation of protein sumoylationnegative regulation of apoptotic processregulation of canonical NF-kappaB signal transductionautosomal recessive limb-girdle muscular dystrophy type 2Amuscular dystrophy, limb-girdle, autosomal dominant 4autosomal recessive limb-girdle muscular dystrophyAbnormality of the musculature
✦AI Summary

CAPN3 (calpain 3) is a calcium-regulated cysteine protease with unique characteristics among human calpains, including rapid autodegradation and dependence on sodium for activation 1. The protein possesses both proteolytic and non-proteolytic functions, with the distinctive ability to regain protease activity after autolytic dissociation through intermolecular complementation 1. CAPN3 mediates proteasome-independent degradation of p53 and cleaves CTBP1, contributing to protein quality control and transcriptional regulation. CAPN3 mutations cause limb-girdle muscular dystrophy type 2A (LGMD2A), an autosomal recessive disorder characterized by progressive proximal muscle weakness. Among large diagnostic cohorts, CAPN3 mutations represent a major genetic cause of LGMD, accounting for approximately 17-19% of molecularly diagnosed cases 23. Patients typically present between ages 6-18 years, with wheelchair dependence by age 32 years 4. Over 100 distinct mutations have been identified throughout the CAPN3 gene, with the 2362AG→TCATCT mutation being most frequent 4. Two null mutations correlate with more severe phenotypes, though mutation type alone does not predict disease progression 4. CAPN3 dysfunction impairs satellite cell function, affecting muscle regeneration capacity 5. Combined clinical and biochemical assessment provides ~91% diagnostic accuracy for calpainopathy 4.

Sources cited
1
CAPN3 is a calcium-regulated protease with unique features including rapid autodegradation, sodium dependence for activation, and ability to regain protease function through intermolecular complementation
PMID: 26363099
2
CAPN3 mutations account for 17% of molecularly diagnosed LGMD cases in a large US cohort of 4656 patients
PMID: 30564623
3
CAPN3 mutations account for 19% of definitive molecular diagnoses in a cohort of 207 inherited myopathy patients from the Indian subcontinent
PMID: 33250842
4
LGMD2A patients present with mean age at onset of 14 years, become wheelchair-bound by mean age 32.2 years, and show 105 different CAPN3 mutations with the 2362AG→TCATCT mutation in 30.7% of chromosomes
PMID: 15689361
5
Two null CAPN3 mutations correlate with significantly reduced walking ability compared to at least one missense mutation, and combined clinical and biochemical assessment achieves 90.8% diagnostic accuracy
PMID: 15689361
6
CAPN3 is among myopathogenes differentially expressed during satellite cell activation, suggesting impairment of muscle regeneration capacity in CAPN3-related disorders
PMID: 35302338
Disease Associationsβ“˜22
autosomal recessive limb-girdle muscular dystrophy type 2AOpen Targets
0.84Strong
muscular dystrophy, limb-girdle, autosomal dominant 4Open Targets
0.77Strong
autosomal recessive limb-girdle muscular dystrophyOpen Targets
0.68Moderate
Abnormality of the musculatureOpen Targets
0.54Moderate
muscular dystrophyOpen Targets
0.49Moderate
Muscle weaknessOpen Targets
0.48Moderate
limb-girdle muscular dystrophyOpen Targets
0.47Moderate
Shoulder girdle muscle weaknessOpen Targets
0.46Moderate
genetic disorderOpen Targets
0.45Moderate
cardiac arrhythmiaOpen Targets
0.43Moderate
Elbow flexion contractureOpen Targets
0.43Moderate
Lower-limb joint contractureOpen Targets
0.43Moderate
myopathyOpen Targets
0.42Moderate
Absent Achilles reflexOpen Targets
0.41Moderate
Autosomal dominant limb-girdle muscular dystrophyOpen Targets
0.37Weak
muscular dystrophy, limb-girdle, autosomal dominantOpen Targets
0.37Weak
alcohol drinkingOpen Targets
0.36Weak
Elevated circulating creatine kinase concentrationOpen Targets
0.36Weak
congenital muscular dystrophyOpen Targets
0.34Weak
Limb-girdle muscle weaknessOpen Targets
0.34Weak
Muscular dystrophy, limb-girdle, autosomal dominant 4UniProt
Muscular dystrophy, limb-girdle, autosomal recessive 1UniProt
Pathogenic Variants518
NM_000070.3(CAPN3):c.327_328dup (p.Arg110fs)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 110
NM_000070.3(CAPN3):c.1343G>T (p.Arg448Leu)Likely pathogenic
Abnormality of the musculature|Autosomal recessive limb-girdle muscular dystrophy|Muscular dystrophy, limb-girdle, autosomal dominant 4
β˜…β˜…β˜…β˜†2026β†’ Residue 448
NM_000070.3(CAPN3):c.2306G>C (p.Arg769Pro)Likely pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 769
NM_000070.3(CAPN3):c.2243G>A (p.Arg748Gln)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Abnormality of the musculature|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy type 2A;Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 748
NM_000070.3(CAPN3):c.1435A>G (p.Ser479Gly)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Autosomal recessive limb-girdle muscular dystrophy|Autosomal recessive limb-girdle muscular dystrophy type 2A;Muscular dystrophy, limb-girdle, autosomal dominant 4|Muscular dystrophy, limb-girdle, autosomal dominant 4|CAPN3-related disorder
β˜…β˜…β˜…β˜†2026β†’ Residue 479
NM_000070.3(CAPN3):c.2288A>G (p.Tyr763Cys)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy|Muscular dystrophy, limb-girdle, autosomal dominant 4;Autosomal recessive limb-girdle muscular dystrophy type 2A
β˜…β˜…β˜…β˜†2026β†’ Residue 763
NM_000070.3(CAPN3):c.1622G>A (p.Arg541Gln)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 541
NM_000070.3(CAPN3):c.2393C>A (p.Ala798Glu)Pathogenic
not provided|Autosomal recessive limb-girdle muscular dystrophy type 2A|Autosomal recessive limb-girdle muscular dystrophy|Autosomal recessive limb-girdle muscular dystrophy type 2A;Muscular dystrophy, limb-girdle, autosomal dominant 4|Muscular dystrophy, limb-girdle, autosomal dominant 4
β˜…β˜…β˜…β˜†2026β†’ Residue 798
NM_000070.3(CAPN3):c.1743_1744del (p.Glu582fs)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 582
NM_000070.3(CAPN3):c.258dup (p.Leu87fs)Pathogenic
not provided|Autosomal recessive limb-girdle muscular dystrophy type 2A|Muscular dystrophy, limb-girdle, autosomal dominant 4|Muscular dystrophy, limb-girdle, autosomal dominant 4;Autosomal recessive limb-girdle muscular dystrophy type 2A|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 87
NM_000070.3(CAPN3):c.1711del (p.Leu571fs)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|Autosomal recessive limb-girdle muscular dystrophy type 2A;Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 571
NM_000070.3(CAPN3):c.2182C>T (p.Gln728Ter)Pathogenic
not provided|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 728
NM_000070.3(CAPN3):c.1715G>A (p.Arg572Gln)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy|Muscular dystrophy, limb-girdle, autosomal dominant 4;Autosomal recessive limb-girdle muscular dystrophy type 2A
β˜…β˜…β˜…β˜†2026β†’ Residue 572
NM_000070.3(CAPN3):c.1342C>T (p.Arg448Cys)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Muscular dystrophy, limb-girdle, autosomal dominant 4|Muscular dystrophy, limb-girdle, autosomal dominant 4;Autosomal recessive limb-girdle muscular dystrophy type 2A|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2026β†’ Residue 448
NM_000070.3(CAPN3):c.1343G>A (p.Arg448His)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Autosomal recessive limb-girdle muscular dystrophy|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy type 2A;Muscular dystrophy, limb-girdle, autosomal dominant 4
β˜…β˜…β˜…β˜†2026β†’ Residue 448
NM_000070.3(CAPN3):c.1621C>T (p.Arg541Trp)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|Autosomal recessive limb-girdle muscular dystrophy type 2A;Muscular dystrophy, limb-girdle, autosomal dominant 4|not provided|Autosomal recessive limb-girdle muscular dystrophy|Muscular dystrophy, limb-girdle, autosomal dominant 4|CAPN3-related disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 541
NM_000070.3(CAPN3):c.1611C>A (p.Tyr537Ter)Pathogenic
not provided|Autosomal recessive limb-girdle muscular dystrophy type 2A|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2025β†’ Residue 537
NM_000070.3(CAPN3):c.734dup (p.Pro245_Ser246insTer)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2025β†’ Residue 245
NM_000070.3(CAPN3):c.1714C>T (p.Arg572Trp)Pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Abnormality of the musculature|Autosomal recessive limb-girdle muscular dystrophy type 2A;Muscular dystrophy, limb-girdle, autosomal dominant 4|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2025β†’ Residue 572
NM_000070.3(CAPN3):c.1322G>A (p.Gly441Asp)Likely pathogenic
Autosomal recessive limb-girdle muscular dystrophy type 2A|Autosomal recessive limb-girdle muscular dystrophy
β˜…β˜…β˜…β˜†2025β†’ Residue 441
View on ClinVar β†—
Related Genes
DMDProtein interaction98%SGCBProtein interaction96%TRIM63Protein interaction95%FLNCProtein interaction95%CASTProtein interaction92%DYSFProtein interaction89%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
53%
Lung
52%
Liver
47%
Ovary
34%
Heart
29%
Gene Interaction Network
Click a node to explore
CAPN3DMDSGCBTRIM63FLNCCASTDYSF
PROTEIN STRUCTURE
Preparing viewer…
PDB6BDT Β· 2.30 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.90LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.74 [0.61–0.90]
RankingsWhere CAPN3 stands among ~20K protein-coding genes
  • #2,822of 20,598
    Most Researched159 Β· top quartile
  • #104of 5,498
    Most Pathogenic Variants518 Β· top 5%
  • #8,058of 17,882
    Most Constrained (LOEUF)0.90
Genes detectedCAPN3
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
Genetic landscape and novel disease mechanisms from a large LGMD cohort of 4656 patients.
PMID: 30564623
Ann Clin Transl Neurol Β· 2018
1.00
2
Sequential targeted exome sequencing of 1001 patients affected by unexplained limb-girdle weakness.
PMID: 32528171
Genet Med Β· 2020
0.90
3
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis Β· 2022
0.80
4
Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent.
PMID: 33250842
Front Neurol Β· 2020
0.70
5
Autosomal recessive limb-girdle and Miyoshi muscular dystrophies in the Netherlands: The clinical and molecular spectrum of 244 patients.
PMID: 30919934
Clin Genet Β· 2019
0.64