Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CAPN3 Gene

Aliases for CAPN3 Gene

  • Calpain 3 2 3 5
  • New Calpain 1 3 4
  • CANPL3 3 4
  • CANP3 3 4
  • NCL-1 3 4
  • Muscle-Specific Calcium-Activated Neutral Protease 3 Large Subunit 3
  • Muscle-Specific Calcium-Activated Neutral Protease 3 4
  • Calpain P94, Large [Catalytic] Subunit 3
  • Calcium-Activated Neutral Proteinase 3 4
  • Calpain, Large Polypeptide L3 3
  • EC 4
  • Calpain P94 4
  • Calpain L3 4
  • Calpain-3 3
  • LGMD2A 3
  • CANP 3 4
  • LGMD2 3
  • NCL1 4
  • P94 3

External Ids for CAPN3 Gene

Previous HGNC Symbols for CAPN3 Gene

  • LGMD2
  • LGMD2A

Previous GeneCards Identifiers for CAPN3 Gene

  • GC15P038019
  • GC15P035547
  • GC15P040144
  • GC15P040367
  • GC15P040283
  • GC15P040353
  • GC15P040427
  • GC15P042640
  • GC15P019488

Summaries for CAPN3 Gene

Entrez Gene Summary for CAPN3 Gene

  • Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit family that specifically binds to titin. Mutations in this gene are associated with limb-girdle muscular dystrophies type 2A. Alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms and some variants are ubiquitously expressed. [provided by RefSeq, Jul 2008]

GeneCards Summary for CAPN3 Gene

CAPN3 (Calpain 3) is a Protein Coding gene. Diseases associated with CAPN3 include Muscular Dystrophy, Limb-Girdle, Type 2A and Muscular Dystrophy. Among its related pathways are B Cell Receptor Signaling Pathway (sino) and Focal Adhesion. Gene Ontology (GO) annotations related to this gene include calcium ion binding and peptidase activity. An important paralog of this gene is CAPN9.

UniProtKB/Swiss-Prot for CAPN3 Gene

  • Calcium-regulated non-lysosomal thiol-protease.

Tocris Summary for CAPN3 Gene

  • Calpains are a group of calcium-sensitive cysteine proteases that are ubiquitously expressed in mammals. Structurally, calpains contain two subunits; an 80 kDa catalytic subunit and a 28 kDa regulatory subunit that functions as a chaperone to stabilize the 80 kDa structure.

Gene Wiki entry for CAPN3 Gene

Additional gene information for CAPN3 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CAPN3 Gene

Genomics for CAPN3 Gene

GeneHancer (GH) Regulatory Elements for CAPN3 Gene

Promoters and enhancers for CAPN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J042401 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 650.3 +42.6 42568 1.6 L3MBTL2 ELF1 ZBTB40 GABPA POLR2A GABPB1 NR2C1 EHMT2 MLLT1 ZNF24 CAPN3 GANC TMEM87A ADAL VPS39 PIR36482 GC15P042409 PIR50861 ENSG00000258461
GH15J042403 Promoter/Enhancer 1.3 EPDnew ENCODE dbSUPER 660.8 +45.7 45707 3.6 ATF1 RXRA ZNF644 RAD21 ATF2 MITF SP1 HNF4G CREB1 ZNF24 CAPN3 GANC TMEM87A ADAL VPS39 PIR36482 GC15P042409 PIR50861 ENSG00000258461
GH15J042359 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE dbSUPER 663.4 +0.4 380 1 CAPN3 LRRC57 PLA2G4F ENSG00000258461 GC15M042373
GH15J042404 Promoter/Enhancer 1 EPDnew dbSUPER 650.3 +43.5 43545 0.1 L3MBTL2 MAX ZNF24 ZKSCAN1 CAPN3 TMEM87A GANC PIR36482 GC15P042409 PIR50861 ENSG00000258461
GH15J042410 Promoter 0.7 EPDnew 660.8 +51.4 51442 0.1 ATF7 PRDM1 ATF2 CAPN3 PIR36482 PIR52731 GC15P042409 ENSG00000258461
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CAPN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CAPN3 gene promoter:
  • GR-alpha
  • MIF-1
  • CUTL1
  • GR
  • GR-beta
  • Nkx2-5
  • Sox5
  • GATA-3

Genomic Locations for CAPN3 Gene

Genomic Locations for CAPN3 Gene
52,819 bases
Plus strand
64,216 bases
Plus strand

Genomic View for CAPN3 Gene

Genes around CAPN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CAPN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CAPN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CAPN3 Gene

Proteins for CAPN3 Gene

  • Protein details for CAPN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A6H8K6
    • Q7L4R0
    • Q9BQC8
    • Q9BTU4
    • Q9Y5S6
    • Q9Y5S7

    Protein attributes for CAPN3 Gene

    821 amino acids
    Molecular mass:
    94254 Da
    Quaternary structure:
    • Homodimer; via EF-hand domain 4 (PubMed:24846670). Interacts with TTN/titin (PubMed:14583192). Interacts with CMYA5; this interaction, which results in CMYA5 proteolysis, may protect CAPN3 from autolysis (PubMed:20634290).

    Three dimensional structures from OCA and Proteopedia for CAPN3 Gene

    Alternative splice isoforms for CAPN3 Gene


neXtProt entry for CAPN3 Gene

Post-translational modifications for CAPN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CAPN3 Gene

Domains & Families for CAPN3 Gene

Gene Families for CAPN3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase C2 family.
  • Belongs to the peptidase C2 family.
genes like me logo Genes that share domains with CAPN3: view

Function for CAPN3 Gene

Molecular function for CAPN3 Gene

UniProtKB/Swiss-Prot Function:
Calcium-regulated non-lysosomal thiol-protease.
UniProtKB/Swiss-Prot CatalyticActivity:
Broad endopeptidase activity.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by micromolar concentrations of calcium and inhibited by calpastatin.
GENATLAS Biochemistry:
calpain,large polypeptide L3,calcium dependent neutral cysteine proteinase,papain superfamily (subunit p94,muscle-specific,possessing a proteolytic activity against a potential substrat,fodrin)

Enzyme Numbers (IUBMB) for CAPN3 Gene

Phenotypes From GWAS Catalog for CAPN3 Gene

Gene Ontology (GO) - Molecular Function for CAPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IDA 9642272
GO:0004198 calcium-dependent cysteine-type endopeptidase activity TAS,IEA 9642272
GO:0004871 obsolete signal transducer activity TAS --
GO:0005509 calcium ion binding IEA,ISS --
GO:0005515 protein binding IPI 20860623
genes like me logo Genes that share ontologies with CAPN3: view
genes like me logo Genes that share phenotypes with CAPN3: view

Human Phenotype Ontology for CAPN3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CAPN3 Gene

MGI Knock Outs for CAPN3:

Animal Model Products

  • Taconic Biosciences Mouse Models for CAPN3

miRNA for CAPN3 Gene

miRTarBase miRNAs that target CAPN3

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for CAPN3 Gene

Localization for CAPN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CAPN3 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CAPN3 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5
mitochondrion 2
extracellular 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for CAPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular TAS,IEA 9642272
GO:0005634 nucleus IDA 19386580
GO:0005737 cytoplasm IEA,IDA 19386580
GO:0005829 cytosol ISS --
GO:0005886 plasma membrane ISS --
genes like me logo Genes that share ontologies with CAPN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CAPN3 Gene

Pathways & Interactions for CAPN3 Gene

genes like me logo Genes that share pathways with CAPN3: view

Pathways by source for CAPN3 Gene

1 Sino Biological pathway for CAPN3 Gene
1 BioSystems pathway for CAPN3 Gene

Gene Ontology (GO) - Biological Process for CAPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IDA,IEA 9642272
GO:0006915 apoptotic process TAS 19386580
GO:0007165 signal transduction IEA --
GO:0007517 muscle organ development TAS 9642272
GO:0012501 programmed cell death IEA --
genes like me logo Genes that share ontologies with CAPN3: view

No data available for SIGNOR curated interactions for CAPN3 Gene

Drugs & Compounds for CAPN3 Gene

(8) Drugs for CAPN3 Gene - From: DrugBank, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
L-aminocarnityl-succinyl-leucyl-argininal-diethylacetal Investigational Pharma Target 0
PD 150606 Pharma Non-peptide calpain inhibitor 0
PD 151746 Pharma calpain inhibitor, cell-permeable 0
Calpeptin Pharma Ca2+-dependent protease,calpain inhibitor, Calpain and cathepsin L inhibitor 0

(2) Tocris Compounds for CAPN3 Gene

Compound Action Cas Number
Calpeptin Calpain and cathepsin L inhibitor 117591-20-5
MDL 28170 Potent, selective calpain and cathepsin B inhibitor 88191-84-8
genes like me logo Genes that share compounds with CAPN3: view

Transcripts for CAPN3 Gene

mRNA/cDNA for CAPN3 Gene

Unigene Clusters for CAPN3 Gene

Calpain 3, (p94):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CAPN3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^
SP2: - - - - - - - - -
SP4: - - - - - - - -
SP13: - - -
SP14: - - - - - - - -
SP15: - - - -
SP16: - - - - - -
SP18: -
SP19: -

ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b ^ 32a · 32b ^ 33 ^ 34 ^ 35 ^ 36 ^ 37a · 37b ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^
SP1: - -
SP2: -
SP3: - -

ExUns: 43 ^ 44 ^ 45a · 45b · 45c ^ 46a · 46b ^ 47a · 47b ^ 48a · 48b · 48c ^ 49a · 49b ^ 50 ^ 51 ^ 52 ^ 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58 ^ 59
SP1: - - - - - - -
SP3: -
SP5: - -
SP6: - - - - - - - -
SP7: - - -
SP8: - - - - -
SP10: -
SP11: -

Relevant External Links for CAPN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CAPN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CAPN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CAPN3 Gene

This gene is overexpressed in Muscle - Skeletal (x14.4) and Brain - Spinal cord (cervical c-1) (x4.4).

Protein differential expression in normal tissues from HIPED for CAPN3 Gene

This gene is overexpressed in Islet of Langerhans (36.5), Bone marrow mesenchymal stem cell (18.2), and Tonsil (13.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CAPN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of CAPN3 Gene:


SOURCE GeneReport for Unigene cluster for CAPN3 Gene:


mRNA Expression by UniProt/SwissProt for CAPN3 Gene:

Tissue specificity: Isoform I is skeletal muscle specific.

Evidence on tissue expression from TISSUES for CAPN3 Gene

  • Skin(4.9)
  • Nervous system(3.9)
  • Muscle(3.8)
  • Heart(2.5)
  • Kidney(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CAPN3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • immune
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • head
  • scapula
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood
  • white blood cell
genes like me logo Genes that share expression patterns with CAPN3: view

No data available for Protein tissue co-expression partners for CAPN3 Gene

Orthologs for CAPN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for CAPN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CAPN3 34
  • 98 (a)
(Canis familiaris)
Mammalia CAPN3 34 33
  • 91.35 (n)
(Bos Taurus)
Mammalia CAPN3 34 33
  • 90.5 (n)
(Rattus norvegicus)
Mammalia Capn3 33
  • 90.38 (n)
(Mus musculus)
Mammalia Capn3 16 34 33
  • 90.13 (n)
(Monodelphis domestica)
Mammalia CAPN3 34
  • 86 (a)
(Gallus gallus)
Aves CAPN3 34 33
  • 75.68 (n)
(Anolis carolinensis)
Reptilia CAPN3 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497532 33
  • 72.5 (n)
(Danio rerio)
Actinopterygii capn3a 34 33
  • 71.33 (n)
capn3b 34
  • 63 (a)
fruit fly
(Drosophila melanogaster)
Insecta CalpA 35
  • 42 (a)
CalpB 35
  • 40 (a)
CalpC 35
  • 27 (a)
(Caenorhabditis elegans)
Secernentea clp-7 35
  • 42 (a)
clp-6 35
  • 41 (a)
clp-3 35
  • 37 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4609 34
  • 49 (a)
Species where no ortholog for CAPN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CAPN3 Gene

Gene Tree for CAPN3 (if available)
Gene Tree for CAPN3 (if available)
Evolutionary constrained regions (ECRs) for CAPN3: view image

Paralogs for CAPN3 Gene

Paralogs for CAPN3 Gene

(15) SIMAP similar genes for CAPN3 Gene using alignment to 17 proteins:

  • F8W8F5_HUMAN
  • H3BS30_HUMAN
  • H3BS77_HUMAN
  • H3BV08_HUMAN
  • Q496N2_HUMAN
  • Q762C6_HUMAN
  • Q762C7_HUMAN
  • Q762C8_HUMAN
genes like me logo Genes that share paralogs with CAPN3: view

Variants for CAPN3 Gene

Sequence variations from dbSNP and Humsavar for CAPN3 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs112661890 uncertain-significance, Limb-Girdle Muscular Dystrophy, Recessive, Limb-girdle muscular dystrophy, type 2A 42,411,984(+) G/A 3_prime_UTR_variant
rs113881834 uncertain-significance, Limb-Girdle Muscular Dystrophy, Recessive, Limb-girdle muscular dystrophy, type 2A 42,359,675(+) G/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs115311625 conflicting-interpretations-of-pathogenicity, not specified, Limb-girdle muscular dystrophy, type 2A 42,410,952(+) G/A/C coding_sequence_variant, missense_variant
rs117609395 conflicting-interpretations-of-pathogenicity, benign, not specified, Limb-girdle muscular dystrophy, type 2A 42,384,491(+) C/T coding_sequence_variant, genic_upstream_transcript_variant, synonymous_variant
rs121434544 pathogenic, uncertain-significance, Limb-girdle muscular dystrophy, type 2A, not provided, not specified, Limb-girdle muscular dystrophy 2A (LGMD2A) [MIM:253600] 42,402,972(+) G/A/C/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CAPN3 Gene

Variant ID Type Subtype PubMed ID
nsv1108951 CNV deletion 24896259
nsv1113707 CNV deletion 24896259
nsv1138360 CNV deletion 24896259
nsv832986 CNV loss 17160897
nsv832987 CNV gain 17160897

Variation tolerance for CAPN3 Gene

Residual Variation Intolerance Score: 19.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.13; 90.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CAPN3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CAPN3 Gene

Disorders for CAPN3 Gene

MalaCards: The human disease database

(27) MalaCards diseases for CAPN3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CAPN3 in MalaCards View complete list of genes associated with diseases


  • Limb-girdle muscular dystrophy 2A (LGMD2A) [MIM:253600]: An autosomal recessive degenerative myopathy characterized by progressive symmetrical atrophy and weakness of the proximal limb muscles and elevated serum creatine kinase. The symptoms usually begin during the first two decades of life, and the disease gradually worsens, often resulting in loss of walking ability 10 or 20 years after onset. {ECO:0000269 PubMed:27020652, ECO:0000269 PubMed:27234031, ECO:0000269 PubMed:7720071, ECO:0000269 PubMed:8624690, ECO:0000269 PubMed:9150160, ECO:0000269 PubMed:9266733, ECO:0000269 PubMed:9452114, ECO:0000269 PubMed:9655129, ECO:0000269 PubMed:9762961, ECO:0000269 PubMed:9771675}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CAPN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CAPN3: view

No data available for Genatlas for CAPN3 Gene

Publications for CAPN3 Gene

  1. LGMD2A: genotype-phenotype correlations based on a large mutational survey on the calpain 3 gene. (PMID: 15689361) Sáenz A … López de Munain A (Brain : a journal of neurology 2005) 3 22 44 58
  2. Prevalence of the 550delA mutation in calpainopathy (LGMD 2A) in Croatia. (PMID: 14981715) Canki-Klain N … Feingold J (American journal of medical genetics. Part A 2004) 3 22 44 58
  3. Molecular diagnosis in LGMD2A: mutation analysis or protein testing? (PMID: 15221789) Fanin M … Angelini C (Human mutation 2004) 3 22 44 58
  4. Calpainopathy-a survey of mutations and polymorphisms. (PMID: 10330340) Richard I … Beckmann JS (American journal of human genetics 1999) 3 4 22 58
  5. A biochemical, genetic, and clinical survey of autosomal recessive limb girdle muscular dystrophies in Turkey. (PMID: 9266733) Dinçer P … Topaloglu H (Annals of neurology 1997) 3 4 22 58

Products for CAPN3 Gene

Sources for CAPN3 Gene

Loading form....