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CAPN1 calpain 1 [ Homo sapiens (human) ]

Gene ID: 823, updated on 28-Oct-2024

Summary

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Official Symbol
CAPN1provided by HGNC
Official Full Name
calpain 1provided by HGNC
Primary source
HGNC:HGNC:1476
See related
Ensembl:ENSG00000014216 MIM:114220; AllianceGenome:HGNC:1476
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CANP; muCL; CANP1; SPG76; CANPL1; muCANP
Summary
The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes the large subunit of the ubiquitous enzyme, calpain 1. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]
Expression
Ubiquitous expression in esophagus (RPKM 94.2), skin (RPKM 48.8) and 24 other tissues See more
Orthologs
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Genomic context

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See CAPN1 in Genome Data Viewer
Location:
11q13.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65181373..65212006)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65174678..65205290)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64948844..64979477)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr11:64949086-64949875 and GRCh37_chr11:64949876-64950664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64950665-64951454 Neighboring gene phosphoglycerate mutase 1 pseudogene 8 Neighboring gene speedy/RINGO cell cycle regulator family member C Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:64952638-64953204 Neighboring gene CAPN1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64953771-64954337 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64955709-64956255 Neighboring gene MPRA-validated peak1300 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64971432-64972419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4949 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:64976880-64978079 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64978770-64978973 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64980323-64981239 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64981240-64982155 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64984183-64984746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64984747-64985310 Neighboring gene solute carrier family 22 member 20, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64989237-64989466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4951 Neighboring gene MPRA-validated peak1301 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:65011321-65011846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3512 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:65028571-65029458 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:65029459-65030344 Neighboring gene DNA polymerase alpha 2, accessory subunit Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:65046741-65047940 Neighboring gene uncharacterized LOC105369344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65068776-65069313 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65069314-65069850

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Mu-calpain binds to lipid bilayers via the exposed hydrophobic surface of its Ca2+-activated conformation. Fernández-Montalván A, et al. Biol Chem, 2006 May. PMID 16740134
  2. Genetic variants in histone modification regions are associated with the prognosis of lung adenocarcinoma. Kang HG, et al. Sci Rep, 2021 Nov 2. PMID 34728688, Free PMC Article
  3. Calpain-Mediated Mitochondrial Damage: An Emerging Mechanism Contributing to Cardiac Disease. Zhang M, et al. Cells, 2021 Aug 8. PMID 34440793, Free PMC Article
  4. Redox-Dependent Calpain Signaling in Airway and Pulmonary Vascular Remodeling in COPD. Kovacs L, et al. Adv Exp Med Biol, 2017. PMID 29047085, Free PMC Article
  5. Calpain activity in plasma of patients with essential tremor and Parkinson's disease: a pilot study. Muruzheva ZM, et al. Neurol Res, 2021 Apr. PMID 33729106

See all (283) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Otud6b induces pulmonary arterial hypertension by mediating the Calpain-1/HIF-1alpha signaling pathway.
    Title: Otud6b induces pulmonary arterial hypertension by mediating the Calpain-1/HIF-1α signaling pathway.
  2. Remote ischemic preconditioning reduces mitochondrial apoptosis mediated by calpain 1 activation in myocardial ischemia-reperfusion injury through calcium channel subunit Cacna2d3.
    Title: Remote ischemic preconditioning reduces mitochondrial apoptosis mediated by calpain 1 activation in myocardial ischemia-reperfusion injury through calcium channel subunit Cacna2d3.
  3. Spastic paraplegia type 76 due to novel CAPN1 mutations: three case reports with literature review.
    Title: Spastic paraplegia type 76 due to novel CAPN1 mutations: three case reports with literature review.
  4. CAPN1 (Calpain1)-Dependent Cleavage of STIM1 (Stromal Interaction Molecule 1) Results in an Enhanced SOCE (Store-Operated Calcium Entry) in Human Neonatal Platelets.
    Title: CAPN1 (Calpain1)-Dependent Cleavage of STIM1 (Stromal Interaction Molecule 1) Results in an Enhanced SOCE (Store-Operated Calcium Entry) in Human Neonatal Platelets.
  5. Immune suppressive function of IL-1alpha release in the tumor microenvironment regulated by calpain 1.
    Title: Immune suppressive function of IL-1α release in the tumor microenvironment regulated by calpain 1.
  6. Calpain-1 inhibition attenuates in vivo thrombosis in a humanized model of sickle cell disease.
    Title: Calpain-1 inhibition attenuates in vivo thrombosis in a humanized model of sickle cell disease.
  7. CAPN1 and hereditary spastic paraplegia: a novel variant in an Iranian family and overview of the genotype-phenotype correlation.
    Title: CAPN1 and hereditary spastic paraplegia: a novel variant in an Iranian family and overview of the genotype-phenotype correlation.
  8. Genetic variants in histone modification regions are associated with the prognosis of lung adenocarcinoma.
    Title: Genetic variants in histone modification regions are associated with the prognosis of lung adenocarcinoma.
  9. Relationship of intracellular proteolysis with CAP1 and cofilin1 in non-small-cell lung cancer.
    Title: Relationship of intracellular proteolysis with CAP1 and cofilin1 in non-small-cell lung cancer.
  10. Calpain-Mediated Mitochondrial Damage: An Emerging Mechanism Contributing to Cardiac Disease.
    Title: Calpain-Mediated Mitochondrial Damage: An Emerging Mechanism Contributing to Cardiac Disease.
Submit: New GeneRIF Correction See all GeneRIFs (145)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal recessive spastic paraplegia type 76
MedGen: C5567483 OMIM: 616907 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Activation of the Ca(2+)-dependent protease, calpain, is involved in cytotoxic effects mediated by HIV-1 gp120 in neuroblastoma cultures PubMed
Tat tat Calpain-mediated cleavage of HIV-1 Tat occurs in the C-terminus of this viral protein, between amino acids 68 and 69. The cleavage of Tat by calpain 1 increases neurotoxic effect of this viral protein PubMed
tat HIV-1 Tat increases plasma membrane (PM) dopamine transporter (DAT) activity and calpain protease activity at the PM PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ56829

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables calcium-dependent cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calcium-dependent cysteine-type endopeptidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables calcium-dependent cysteine-type endopeptidase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables calcium-dependent cysteine-type endopeptidase activity TAS
Traceable Author Statement
more info
 PubMed 
enables peptidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of NMDA selective glutamate receptor signaling pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in mammary gland involution IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell population proliferation TAS
Traceable Author Statement
more info
 PubMed 
involved_in proteolysis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteolysis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteolysis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in proteolysis NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in receptor catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of catalytic activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of macroautophagy NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in self proteolysis IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of calpain complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cornified envelope IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
  
located_in focal adhesion HDA PubMed 
located_in lysosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
calpain-1 catalytic subunit
Names
CANP 1
calcium-activated neutral proteinase 1
calpain 1, (mu/I) large subunit
calpain mu-type
calpain, large polypeptide L1
calpain-1 large subunit
cell proliferation-inducing gene 30 protein
cell proliferation-inducing protein 30
micromolar-calpain
NP_001185797.1
NP_001185798.1
NP_005177.2
XP_006718761.1
XP_011543594.1
XP_054226070.1
XP_054226071.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_052817.1 RefSeqGene

    Range
    5714..35792
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001198868.2 → NP_001185797.1  calpain-1 catalytic subunit

    See identical proteins and their annotated locations for NP_001185797.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2, and 3 all encode the same protein.
    Source sequence(s)
    AK315556, BC008751, X04366
    Consensus CDS
    CCDS44644.1
    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Related
    ENSP00000435272.1, ENST00000533820.5
    Conserved Domains (3) summary
    cd00214
    Location:364 → 524
    Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
    pfam00648
    Location:56 → 352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546 → 714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)

  2. NM_001198869.2 → NP_001185798.1  calpain-1 catalytic subunit

    See identical proteins and their annotated locations for NP_001185798.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same protein.
    Source sequence(s)
    AK301538, BC008751, BC075862
    Consensus CDS
    CCDS44644.1
    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Related
    ENSP00000434176.1, ENST00000524773.5
    Conserved Domains (3) summary
    cd00214
    Location:364 → 524
    Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
    pfam00648
    Location:56 → 352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546 → 714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)

  3. NM_005186.4 → NP_005177.2  calpain-1 catalytic subunit

    See identical proteins and their annotated locations for NP_005177.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode the same protein.
    Source sequence(s)
    BC008751, X04366
    Consensus CDS
    CCDS44644.1
    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Related
    ENSP00000279247.7, ENST00000279247.11
    Conserved Domains (3) summary
    cd00214
    Location:364 → 524
    Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
    pfam00648
    Location:56 → 352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546 → 714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)

RNA

  1. NR_040008.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate 5' splice pattern, compared to variant 1. It is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK315556, BC008751, BE018156, DC365116, X04366

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    65181373..65212006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006718698.3 → XP_006718761.1  calpain-1 catalytic subunit isoform X1

    See identical proteins and their annotated locations for XP_006718761.1

    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Conserved Domains (3) summary
    cd00214
    Location:364 → 524
    Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
    pfam00648
    Location:56 → 352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546 → 714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)

  2. XM_011545292.2 → XP_011543594.1  calpain-1 catalytic subunit isoform X1

    See identical proteins and their annotated locations for XP_011543594.1

    UniProtKB/Swiss-Prot
    P07384, Q2TTR0, Q6DHV4
    UniProtKB/TrEMBL
    B2RDI5
    Related
    ENSP00000431984.1, ENST00000527323.5
    Conserved Domains (3) summary
    cd00214
    Location:364 → 524
    Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...
    pfam00648
    Location:56 → 352
    Peptidase_C2; Calpain family cysteine protease
    cd16198
    Location:546 → 714
    EFh_PEF_CAPN1; Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65174678..65205290
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370095.1 → XP_054226070.1  calpain-1 catalytic subunit isoform X1

  2. XM_054370096.1 → XP_054226071.1  calpain-1 catalytic subunit isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P07384.1 GenPept UniProtKB/Swiss-Prot:P07384

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