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
  • EC 3.4.22.54 4 61
  • 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
  • Calpain P94 4
  • Calpain L3 4
  • Calpain-3 3
  • EC 3.4.22 61
  • 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 Calpainopathy. Among its related pathways are Arrhythmogenic right ventricular cardiomyopathy (ARVC) and DREAM Repression and Dynorphin Expression. 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

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

Genomics for CAPN3 Gene

Regulatory Elements for CAPN3 Gene

Enhancers for CAPN3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15F042359 0.8 Ensembl ENCODE 13.5 +0.3 302 1.2 CAPN3 LRRC57 PLA2G4F GC15M042373
GH15F042286 0.7 ENCODE 10.9 -72.3 -72252 2.3 ELF3 HDAC1 PKNOX1 CBX3 MLX ARID4B ZSCAN9 RARA YY1 ZNF366 GANC CAPN3 PLA2G4F VPS39 TMEM87A BNIP3P5
GH15F042403 1 ENCODE 10.8 +45.7 45708 3.6 HNF4G SMAD4 ZNF24 HNF4A RAD21 ZNF644 RXRB GANC CAPN3 TMEM87A ADAL VPS39 GC15P042409 PIR36482 PIR50861
GH15F042449 0.7 Ensembl 10.7 +90.4 90401 0.2 CAPN3 GANC TMEM87A GC15P042438 ZNF106
GH15F042461 0.2 ENCODE 10.4 +102.1 102076 0.4 LRRC57 SNAP23 CAPN3 GANC TMEM87A GC15P042438 ZNF106
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around CAPN3 on UCSC Golden Path with GeneCards custom track

Genomic Location for CAPN3 Gene

Chromosome:
15
Start:
42,359,500 bp from pter
End:
42,412,318 bp from pter
Size:
52,819 bases
Orientation:
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:
    P20807-CAN3_HUMAN
    Recommended name:
    Calpain-3
    Protein Accession:
    P20807
    Secondary Accessions:
    • A6H8K6
    • Q7L4R0
    • Q9BQC8
    • Q9BTU4
    • Q9Y5S6
    • Q9Y5S7

    Protein attributes for CAPN3 Gene

    Size:
    821 amino acids
    Molecular mass:
    94254 Da
    Quaternary structure:
    • Interacts with TTN/titin. Interacts with CMYA5; this interaction, which results in CMYA5 proteolysis, may protect CAPN3 from autolysis.

    Three dimensional structures from OCA and Proteopedia for CAPN3 Gene

    Alternative splice isoforms for CAPN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CAPN3 Gene

Post-translational modifications for CAPN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cloud-Clone Corp. Antibodies for CAPN3

Domains & Families for CAPN3 Gene

Gene Families for CAPN3 Gene

Graphical View of Domain Structure for InterPro Entry

P20807

UniProtKB/Swiss-Prot:

CAN3_HUMAN :
  • Contains 1 calpain catalytic domain.
  • Belongs to the peptidase C2 family.
Domain:
  • Contains 1 calpain catalytic domain.
  • Contains 4 EF-hand domains.
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

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)
UniProtKB/Swiss-Prot CatalyticActivity:
Broad endopeptidase activity.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by micromolar concentrations of calcium and inhibited by calpastatin.
UniProtKB/Swiss-Prot Function:
Calcium-regulated non-lysosomal thiol-protease.

Enzyme Numbers (IUBMB) 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 IEA,TAS 9642272
GO:0004871 signal transducer activity TAS 7720071
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

Flow Cytometry 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

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CAPN3 Gene COMPARTMENTS Subcellular localization image for CAPN3 gene
Compartment Confidence
cytosol 5
nucleus 5
plasma membrane 5
mitochondrion 2
cytoskeleton 1
endoplasmic reticulum 1
extracellular 1
lysosome 1
peroxisome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for CAPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA,TAS 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

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:0006461 protein complex assembly ISS --
GO:0006508 proteolysis IEA,IDA 9642272
GO:0006915 apoptotic process TAS 19386580
GO:0007165 signal transduction IEA --
GO:0007517 muscle organ development TAS 9642272
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

(5) Drugs for CAPN3 Gene - From: ApexBio, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
PD 150606 Pharma Non-peptide calpain inhibitor, Cell permeable calpain inhibitor 0
PD 151746 Pharma calpain inhibitor, cell-permeable 0
Acetyl-Calpastatin (184-210) (human) Pharma Calpain I/II inhibitor, Selective calpain inhibitor 0

(2) Additional Compounds for CAPN3 Gene - From: Novoseek and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
MG 132
133407-82-6

(2) Tocris Compounds for CAPN3 Gene

Compound Action Cas Number
Acetyl-Calpastatin (184-210) (human) Selective calpain inhibitor 123714-50-1
MG 132 Proteasome and calpain inhibitor. Inhibits NF-kappaB activation 133407-82-6

(2) ApexBio Compounds for CAPN3 Gene

Compound Action Cas Number
PD 150606 Non-peptide calpain inhibitor 179528-45-1
PD 151746 calpain inhibitor, cell-permeable 179461-52-0
genes like me logo Genes that share compounds with CAPN3: view

Transcripts for CAPN3 Gene

Unigene Clusters for CAPN3 Gene

Calpain 3, (p94):
Representative Sequences:

Clone Products

Flow Cytometry 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 ^
SP1:
SP2: - - - - - - - - -
SP3:
SP4: - - - - - - - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13: - - -
SP14: - - - - - - - -
SP15: - - - -
SP16: - - - - - -
SP17:
SP18: -
SP19: -
SP20:
SP21:
SP22:

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: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:

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: - - - - - - -
SP2:
SP3: -
SP4:
SP5: - -
SP6: - - - - - - - -
SP7: - - -
SP8: - - - - -
SP9:
SP10: -
SP11: -
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:

Relevant External Links for CAPN3 Gene

GeneLoc Exon Structure for
CAPN3
ECgene alternative splicing isoforms for
CAPN3

Expression for CAPN3 Gene

mRNA expression in normal human tissues 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, PaxDb, and MOPED for CAPN3 Gene



NURSA nuclear receptor signaling pathways regulating expression of CAPN3 Gene:

CAPN3

SOURCE GeneReport for Unigene cluster for CAPN3 Gene:

Hs.143261

mRNA Expression by UniProt/SwissProt for CAPN3 Gene:

P20807-CAN3_HUMAN
Tissue specificity: Isoform I is skeletal muscle specific.
genes like me logo Genes that share expression patterns with CAPN3: view

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia CAPN3 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CAPN3 34 35
  • 91.35 (n)
cow
(Bos Taurus)
Mammalia CAPN3 34 35
  • 90.5 (n)
rat
(Rattus norvegicus)
Mammalia Capn3 34
  • 90.38 (n)
mouse
(Mus musculus)
Mammalia Capn3 34 16 35
  • 90.13 (n)
oppossum
(Monodelphis domestica)
Mammalia CAPN3 35
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves CAPN3 34 35
  • 75.68 (n)
lizard
(Anolis carolinensis)
Reptilia CAPN3 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497532 34
  • 72.5 (n)
zebrafish
(Danio rerio)
Actinopterygii capn3a 34 35
  • 71.33 (n)
capn3b 35
  • 63 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CalpA 36
  • 42 (a)
CalpB 36
  • 40 (a)
CalpC 36
  • 27 (a)
worm
(Caenorhabditis elegans)
Secernentea clp-7 36
  • 42 (a)
clp-6 36
  • 41 (a)
clp-3 36
  • 37 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4609 35
  • 49 (a)
OneToMany
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

ENSEMBL:
Gene Tree for CAPN3 (if available)
TreeFam:
Gene Tree for CAPN3 (if available)

Paralogs for CAPN3 Gene

Variants for CAPN3 Gene

Sequence variations from dbSNP and Humsavar for CAPN3 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs121434544 Limb-girdle muscular dystrophy 2A (LGMD2A) [MIM:253600], Pathogenic 42,402,972(+) CCTCC(A/G/T)GGTCT upstream-variant-2KB, reference, missense
rs121434546 Limb-girdle muscular dystrophy 2A (LGMD2A) [MIM:253600], Pathogenic 42,360,062(+) GACCT(C/T)TCTCT reference, missense
rs121434547 Limb-girdle muscular dystrophy 2A (LGMD2A) [MIM:253600], Pathogenic 42,392,649(+) CATTC(C/T)GGTTC reference, missense
rs121434548 Limb-girdle muscular dystrophy 2A (LGMD2A) [MIM:253600], Pathogenic 42,401,755(+) CCGGC(A/C/G)GAAGG upstream-variant-2KB, reference, missense
rs140660066 Limb-girdle muscular dystrophy 2A (LGMD2A) [MIM:253600] 42,359,815(+) CGACC(A/G)TCATT reference, missense

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)

Relevant External Links for CAPN3 Gene

Human Gene Mutation Database (HGMD)
CAPN3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CAPN3

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

Disorders for CAPN3 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
muscular dystrophy, limb-girdle, type 2a
  • calpainopathy
calpainopathy
  • leyden-moebius muscular dystrophy
limb-girdle muscular dystrophy
  • lgmd
idiopathic eosinophilic myositis
isolated hyperckemia
  • elevated serum cpk
- elite association - COSMIC cancer census association via MalaCards
Search CAPN3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CAN3_HUMAN
  • 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.

Relevant External Links for CAPN3

Genetic Association Database (GAD)
CAPN3
Human Genome Epidemiology (HuGE) Navigator
CAPN3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CAPN3
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) SA!enz A. … LA^pez de Munain A. (Brain 2005) 3 22 46 64
  2. Prevalence of the 550delA mutation in calpainopathy (LGMD 2A) in Croatia. (PMID: 14981715) Canki-Klain N. … Feingold J. (Am. J. Med. Genet. A 2004) 3 22 46 64
  3. Molecular diagnosis in LGMD2A: mutation analysis or protein testing? (PMID: 15221789) Fanin M. … Angelini C. (Hum. Mutat. 2004) 3 22 46 64
  4. Calpainopathy -- a survey of mutations and polymorphisms. (PMID: 10330340) Richard I. … Beckmann J.S. (Am. J. Hum. Genet. 1999) 3 4 22 64
  5. A biochemical, genetic, and clinical survey of autosomal recessive limb girdle muscular dystrophies in Turkey. (PMID: 9266733) Dincer P. … Topaloglu H. (Ann. Neurol. 1997) 3 4 22 64

Products for CAPN3 Gene

Sources for CAPN3 Gene

Content
Loading form....