CAPN3 Gene (Protein Coding)

Calpain 3

GC15P042359
GIFtS:
48
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 alte... See more...

Aliases for CAPN3 Gene

Aliases for CAPN3 Gene

  • Calpain 3 2 3 5
  • CANP3 2 3 4
  • NCL-1 2 3 4
  • New Calpain 1 3 4
  • EC 3.4.22.54 4 50
  • Calpain-3 3 4
  • CANPL3 3 4
  • P94 2 3
  • 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
  • EC 3.4.22 50
  • LGMD2A 3
  • LGMDD4 3
  • LGMDR1 3
  • CANP 3 4
  • LGMD2 3
  • CAPN3 5
  • NCL1 4

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, Autosomal Recessive 1 and Muscular Dystrophy, Limb-Girdle, Autosomal Dominant 4. Among its related pathways are B Cell Receptor Signaling Pathway (sino) and Degradation of the extracellular matrix. 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 Summary for CAPN3 Gene

  • Calcium-regulated non-lysosomal thiol-protease. Proteolytically cleaves CTBP1 at 'His-409'.

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 , Rfam classification and piRNA Summary for CAPN3 Gene

Genomics for CAPN3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CAPN3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH15J042403 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE dbSUPER 260.8 +45.7 45709 3.6 RXRA SMAD4 HNF4A RXRB SP1 ZNF644 ATF1 RAD21 ZNF24 ATF2 CAPN3 HSALNG0105438 HSALNG0105439 GANC TMEM87A ADAL VPS39 piR-43483 ENSG00000258461 ZNF106
GH15J042401 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE dbSUPER 250.3 +42.6 42570 1.6 NR2C1 SPI1 EHMT2 ETV1 ELF1 ZBTB40 L3MBTL2 POLR2A GABPB1 ZFX CAPN3 TMEM87A GANC ADAL VPS39 HSALNG0105435 HSALNG0105438 ENSG00000258461 ZNF106
GH15J042359 Promoter/Enhancer 1.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 264.6 +0.7 682 1.6 SPI1 CAPN3 LRRC57 PLA2G4F ZNF106 STARD9 ENSG00000288667-002 ENSG00000258461
GH15J042404 Promoter/Enhancer 0.8 EPDnew dbSUPER 250.3 +43.5 43547 0.1 MAX L3MBTL2 ZNF24 ZKSCAN1 HSALNG0105438 HSALNG0105439 CAPN3 TMEM87A GANC HSALNG0105435 ENSG00000258461 ZNF106
GH15J042410 Promoter 0.6 EPDnew 260.8 +51.4 51444 0.1 ATF2 ATF7 PRDM1 CAPN3 HSALNG0105440 piR-58732 ENSG00000258461 ZNF106
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CAPN3

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

Genomic Locations for CAPN3 Gene

Latest Assembly
chr15:42,359,498-42,412,949
(GRCh38/hg38)
Size:
53,452 bases
Orientation:
Plus strand

Previous Assembly
chr15:42,651,699-42,704,515
(GRCh37/hg19 by Entrez Gene)
Size:
52,817 bases
Orientation:
Plus strand

chr15:42,640,301-42,704,516
(GRCh37/hg19 by Ensembl)
Size:
64,216 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 Structure • Gene Density

RefSeq DNA sequence for CAPN3 Gene

Proteins for CAPN3 Gene

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  • 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:
    • 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). Interacts with SIMC1 (PubMed:23707407).

    Three dimensional structures from OCA and Proteopedia for CAPN3 Gene

    Alternative splice isoforms for CAPN3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CAPN3 Gene

Protein Expression for CAPN3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for CAPN3 Gene

P20807:
  • PVQYETRMACGLV
  • WQKIFKHYD
  • LSEEVEN
  • RFRLPPSEYVI
  • DKLQTWTVSVNEGRWVRGCSAGGCRN
  • KLLEEDDDP
  • LNLQEFHHLW
  • PSTYEPH
  • DQESEEQQQFRNIF
  • TIGFAIYEVPKEMHG
  • WNGSWSD
  • RLRNPWG
  • KCLEKKVL
  • RTDICQG
  • LLEKAYAKLHGSYE
  • AGFHLNNQL
  • QLYDIITMRYADK
  • EVICSFLVALMQKNRRK
  • WKDWSFVDKDEKARLQHQVTEDGEFWMSY
  • EAMEDFTGGV
  • RVIPHDQSF
  • TFWTNPQ
  • IDFDSFI
  • YAGIFHF
  • KIMKKAIERGSLMGCSIDDGTNMTYGTSPSGL
  • LLEKAYAK
  • RSMIALMDTDGSG
  • ETSLFYSQK
  • IDDCLPTYNNQLVFTKS
  • WVDVVIDD
  • LHKKCLE
  • TIGFAIY
  • RNPWGQVEW
  • PDTFWTNPQYRLKLLEEDDDP
  • EDFTGGV
  • QIAGDDMEICADELK
  • FWMSYEDF
  • YEMRNAV

Post-translational modifications for CAPN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CAPN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

Domains & Families for CAPN3 Gene

Gene Families for CAPN3 Gene

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

Protein Domains for CAPN3 Gene

InterPro:
Blocks:
  • Calpain cysteine protease (C2) family signature

Suggested Antigen Peptide Sequences for CAPN3 Gene

GenScript: Design optimal peptide antigens:
  • CAPN3 protein (A4FTZ9_HUMAN)
  • Calpain 3 transcription variant 10 (C6EVS3_HUMAN)
  • Calpain 3 transcription variant 11 (C6EVS4_HUMAN)
  • New calpain 1 (CAN3_HUMAN)
  • Calpain 3, (P94) (Q496N2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P20807

UniProtKB/Swiss-Prot:

CAN3_HUMAN :
  • Belongs to the peptidase C2 family.
Family:
  • Belongs to the peptidase C2 family.
genes like me logo Genes that share domains with CAPN3: view

Function for CAPN3 Gene

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  6. Cell Lines for research

Molecular function for CAPN3 Gene

UniProtKB/Swiss-Prot Function:
Calcium-regulated non-lysosomal thiol-protease. Proteolytically cleaves CTBP1 at 'His-409'.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Broad endopeptidase activity.; EC=3.4.22.54;.
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 IEA,TAS 9642272
GO:0005509 calcium ion binding IEA,ISS --
GO:0005515 protein binding IPI 20860623
GO:0008233 peptidase activity IEA,IDA 9642272
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 Models for research

  • Taconic Biosciences Mouse Models for CAPN3

miRNA for CAPN3 Gene

miRTarBase miRNAs that target CAPN3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CAPN3

Clone products for research

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
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
nucleus 5
cytosol 5
plasma membrane 4
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
lysosome 2
endosome 1
golgi apparatus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for CAPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular TAS 7720071
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

PathCards logo

SuperPathways for CAPN3 Gene

SuperPathway Contained pathways
1 DREAM Repression and Dynorphin Expression
nNOS Signaling in Skeletal Muscle
.37
Caspase Cascade
.36
Calpain Protease Regulates Cellular Mechanics
.31
2 Degradation of the extracellular matrix
Degradation of the extracellular matrix
.38
Extracellular matrix organization
.38
3 Apoptosis Pathway
Apoptosis Pathway
.45
4 B Cell Receptor Signaling Pathway (sino)
T Cell Receptor Signaling Pathway
.38
5 ERK Signaling
ERK Signaling
.61
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
1 Tocris pathway for CAPN3 Gene
5 Qiagen pathways for CAPN3 Gene
  • Calpain Protease Regulates Cellular Mechanics
  • Caspase Cascade
  • ERK Signaling
  • FAK1 Signaling
  • nNOS Signaling in Skeletal Muscle

SIGNOR curated interactions for CAPN3 Gene

Activates:
Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for CAPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA,IDA 9642272
GO:0006915 apoptotic process TAS 19386580
GO:0007517 muscle organ development TAS 9642272
GO:0012501 programmed cell death IEA --
GO:0014718 positive regulation of satellite cell activation involved in skeletal muscle regeneration ISS --
genes like me logo Genes that share ontologies with CAPN3: view

Drugs & Compounds for CAPN3 Gene

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-aminocarnityl-succinyl-leucyl-argininal-diethylacetal Investigational Pharma Target 0
Calcium Nutra 6959
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

(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

Drug products for research

Transcripts for CAPN3 Gene

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mRNA/cDNA for CAPN3 Gene

7 REFSEQ mRNAs :
25 NCBI additional mRNA sequence :
59 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CAPN3

Clone products for research

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

Expression for CAPN3 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

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

mRNA expression in normal human tissues for CAPN3 Gene
mRNA expression by GTEx for CAPN3 GenemRNA expression by BioGPS 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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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.

Evidence on tissue expression from TISSUES for CAPN3 Gene

  • Skin(4.9)
  • Nervous system(4.1)
  • Muscle(3.7)
  • Heart(3)
  • Kidney(2.5)
  • Blood(2)
  • Liver(2)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • immune
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • head
Thorax:
  • scapula
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • 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
Chimpanzee
(Pan troglodytes)
 Mammalia CAPN3 30
  • 98 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CAPN3 29 30
  • 91.35 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CAPN3 29 30
  • 90.5 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Capn3 29
  • 90.38 (n)
Mouse
(Mus musculus)
 Mammalia Capn3 29 16 30
  • 90.13 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia CAPN3 30
  • 86 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CAPN3 29 30
  • 75.68 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CAPN3 30
  • 74 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia LOC100497532 29
  • 72.5 (n)
Zebrafish
(Danio rerio)
 Actinopterygii capn3a 29 30
  • 71.33 (n)
 OneToMany
capn3b 30
  • 63 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta CalpA 31
  • 42 (a)
CalpB 31
  • 40 (a)
CalpC 31
  • 27 (a)
Worm
(Caenorhabditis elegans)
 Secernentea clp-7 31
  • 42 (a)
clp-6 31
  • 41 (a)
clp-3 31
  • 37 (a)
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.4609 30
  • 49 (a)
 OneToMany
Species where no ortholog for CAPN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for CAPN3: view image
Alliance of Genome Resources:
Additional Orthologs for CAPN3

Paralogs for CAPN3 Gene

Paralogs for CAPN3 Gene

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

  • CAN3_HUMAN
  • A4FTZ9_HUMAN
  • C6EVS3_HUMAN
  • C6EVS4_HUMAN
  • F8W8F5_HUMAN
  • H3BMH1_HUMAN
  • H3BNN7_HUMAN
  • H3BS30_HUMAN
  • H3BS77_HUMAN
  • H3BSA2_HUMAN
  • H3BUR3_HUMAN
  • H3BUZ3_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

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CAPN3 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
1001331 Uncertain Significance: Limb-girdle muscular dystrophy, type 2A 42,389,998(+) A/G
NM_000070.3(CAPN3):c.847A>G (p.Met283Val) 		MISSENSE_VARIANT,INTRON
1001385 Uncertain Significance: Limb-girdle muscular dystrophy, type 2A 42,410,501(+) G/A
NM_000070.3(CAPN3):c.2184+5G>A 		INTRON
1003523 Uncertain Significance: Limb-girdle muscular dystrophy, type 2A 42,402,872(+) A/ATGCGGTTTGCTCC
NM_000070.3(CAPN3):c.1615_1616insTGCGGTTTGCTCCTGGCCTTGCAAAGGCCT (p.Asn539delinsMetArgPheAlaProGlyLeuAlaLysAlaTyr) 		INFRAME_INDEL
1004010 Uncertain Significance: Limb-girdle muscular dystrophy, type 2A 42,359,905(+) G/A
NM_000070.3(CAPN3):c.100G>A (p.Ala34Thr) 		MISSENSE
1005896 Uncertain Significance: Limb-girdle muscular dystrophy, type 2A 42,390,010(+) A/G
NM_000070.3(CAPN3):c.859A>G (p.Ile287Val) 		MISSENSE_VARIANT,INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CAPN3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)
CAPN3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CAPN3
Leiden Open Variation Database (LOVD)
CAPN3

SNP Genotyping and Copy Number Assays for research

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

Disorders for CAPN3 Gene

MalaCards: The human disease database

(60) MalaCards diseases for CAPN3 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
muscular dystrophy, limb-girdle, autosomal recessive 1
  • lgmdr1
muscular dystrophy, limb-girdle, autosomal dominant 4
  • lgmdd4
calpain-3-related limb-girdle muscular dystrophy r1
  • autosomal recessive limb-girdle muscular dystrophy type 2a
paresthesia
progressive muscular atrophy
  • progressive spinal muscular atrophy
- 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
  • Muscular dystrophy, limb-girdle, autosomal recessive 1 (LGMDR1) [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 variants affecting the gene represented in this entry.
  • Muscular dystrophy, limb-girdle, autosomal dominant 4 (LGMDD4) [MIM:618129]: A form of autosomal dominant limb-girdle muscular dystrophy, a myopathy characterized by proximal and/or distal muscle weakness and atrophy. The age at onset is variable and can range from the first to the sixth decade, although later onset is less common. LGMDD4 is characterized by onset of proximal muscle weakness in young adulthood, gait difficulties, increased serum creatine kinase, myalgia, and back pain. Some patients may have upper limb involvement. Disease severity and expressivity are highly variable. {ECO:0000269 PubMed:27259757, ECO:0000269 PubMed:28881388}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for CAPN3

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 40 72
  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 40 72
  3. Molecular diagnosis in LGMD2A: mutation analysis or protein testing? (PMID: 15221789) Fanin M … Angelini C (Human mutation 2004) 3 22 40 72
  4. Calpainopathy-a survey of mutations and polymorphisms. (PMID: 10330340) Richard I … Beckmann JS (American journal of human genetics 1999) 3 4 22 72
  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 72

ExternalLinks

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