CAPN1 calpain 1 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 11q13.1

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (65181373..65212006)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (65174678..65205290)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (64948844..64979477)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
Calpain-Mediated Mitochondrial Damage: An Emerging Mechanism Contributing to Cardiac Disease.
Title: Calpain-Mediated Mitochondrial Damage: An Emerging Mechanism Contributing to Cardiac Disease.
Increasing involvement of CAPN1 variants in spastic ataxias and phenotype-genotype correlations.
Title: Increasing involvement of CAPN1 variants in spastic ataxias and phenotype-genotype correlations.

Submit: New GeneRIF Correction See all GeneRIFs (144)

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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH11707 (e-PCR)
- UniSTS:63308

SGC31567 (e-PCR)
- UniSTS:35721

D11S3744 (e-PCR)
- UniSTS:152974

G33105 (e-PCR)
- UniSTS:18639

GDB:631802 (e-PCR)
- UniSTS:158429

RH48703 (e-PCR)
- UniSTS:58082

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
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 NMDA receptor activity	TAS Traceable Author Statement more info	PubMed
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 more info	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 more info	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

EC 3.4.22.52

NP_001185798.1

EC 3.4.22.52

NP_005177.2

EC 3.4.22.52

XP_006718761.1

EC 3.4.22.52

XP_011543594.1

EC 3.4.22.52

XP_054226070.1

EC 3.4.22.52

XP_054226071.1

EC 3.4.22.52

NCBI Reference Sequences (RefSeq)

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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

NG_052817.1 RefSeqGene

Range

5714..35792

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

65181373..65212006

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)