U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

CAPN5 calpain 5 [ Homo sapiens (human) ]

Gene ID: 726, updated on 3-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
CAPN5provided by HGNC
Official Full Name
calpain 5provided by HGNC
Primary source
HGNC:HGNC:1482
See related
Ensembl:ENSG00000149260 MIM:602537; AllianceGenome:HGNC:1482
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
VRNI; ADNIV; HTRA3; nCL-3
Summary
Calpains are calcium-dependent cysteine proteases involved in signal transduction in a variety of cellular processes. A functional calpain protein consists of an invariant small subunit and 1 of a family of large subunits. CAPN5 is one of the large subunits. Unlike some of the calpains, CAPN5 and CAPN6 lack a calmodulin-like domain IV. Because of the significant similarity to Caenorhabditis elegans sex determination gene tra-3, CAPN5 is also called as HTRA3. [provided by RefSeq, Jul 2008]
Expression
Broad expression in colon (RPKM 33.5), duodenum (RPKM 28.3) and 19 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See CAPN5 in Genome Data Viewer
Location:
11q13.5
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (77066971..77126155)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (76997312..77056732)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (76778018..76837201)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369399 Neighboring gene uncharacterized LOC105369400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76777177-76777677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76797624-76798572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76824170-76824764 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76824765-76825360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76825361-76825954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76837978-76838700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76838701-76839424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76840147-76840870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76842316-76843037 Neighboring gene olfactory marker protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76851056-76851622 Neighboring gene myosin VIIA Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:76893658-76894158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76902287-76902788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76902789-76903288 Neighboring gene glycerophosphodiester phosphodiesterase domain containing 4

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. The C2 domain of calpain 5 contributes to enzyme activation and membrane localization. Bondada V, et al. Biochim Biophys Acta Mol Cell Res, 2021 Jun. PMID 33811937, Free PMC Article
  2. Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. Velez G, et al. Cell Rep, 2020 Jan 21. PMID 31968260, Free PMC Article
  3. Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy. Velez G, et al. Sci Rep, 2019 May 20. PMID 31110225, Free PMC Article
  4. A novel de novo CAPN5 mutation in a patient with inflammatory vitreoretinopathy, hearing loss, and developmental delay. Velez G, et al. Cold Spring Harb Mol Case Stud, 2018 Jun. PMID 29472286, Free PMC Article
  5. Small-angle X-ray scattering of calpain-5 reveals a highly open conformation among calpains. Gakhar L, et al. J Struct Biol, 2016 Dec. PMID 27474374, Free PMC Article

See all (51) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of calpain-5 in cerebral ischemia and reperfusion injury.
    Title: Role of calpain-5 in cerebral ischemia and reperfusion injury.
  2. Early-onset Neovascular Inflammatory Vitreoretinopathy Due to Two de Novo CAPN5 Mutations in Chinese Patients: A Case Series.
    Title: Early-onset Neovascular Inflammatory Vitreoretinopathy Due to Two de Novo CAPN5 Mutations in Chinese Patients: A Case Series.
  3. Mitochondrial calpain-5 truncates caspase-4 during endoplasmic reticulum stress.
    Title: Mitochondrial calpain-5 truncates caspase-4 during endoplasmic reticulum stress.
  4. The C2 domain of calpain 5 contributes to enzyme activation and membrane localization.
    Title: The C2 domain of calpain 5 contributes to enzyme activation and membrane localization.
  5. Characterization of mitochondrial calpain-5.
    Title: Characterization of mitochondrial calpain-5.
  6. Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants.
    Title: Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants.
  7. Whole-Exome Sequencing of Patients With Posterior Segment Uveitis.
    Title: Whole-Exome Sequencing of Patients With Posterior Segment Uveitis.
  8. Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy.
    Title: Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy.
  9. Study found 22 loss-of-function (LOF) CAPN5 variants located throughout the gene and in all major protein domains. Structural modeling of coding variants showed these LOF variants were nearby known vitreoretinopathy-causing variants within the proteolytic core and in regions of high homology between human CAPN5 and 150 homologs, yet the LOF of CAPN5 was tolerated as opposed to gain-of-function disease-causing variants.
    Title: CAPN5 genetic inactivation phenotype supports therapeutic inhibition trials.
  10. We describe a pediatric patient with severe inflammatory vitreoretinopathy accompanied by hearing loss and developmental delay associated with a novel, de novo CAPN5 missense mutation (c.865C>T, p.Arg289Trp) that shows greater hyperactivation of the calpain protease, indicating a genotype-phenotype correlation.
    Title: A novel de novo CAPN5 mutation in a patient with inflammatory vitreoretinopathy, hearing loss, and developmental delay.
Submit: New GeneRIF Correction See all GeneRIFs (29)

Phenotypes

Go to the top of the page Help

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
Proliferative vitreoretinopathy
MedGen: C0242852 OMIM: 193235 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
EBI GWAS Catalog
Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ46245

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium-dependent cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in proteolysis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular exosome HDA PubMed 
located_in focal adhesion HDA PubMed 
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
calpain-5
Names
calpain htra-3
new calpain 3
testis tissue sperm-binding protein Li 91mP

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_033002.2 RefSeqGene

    Range
    5002..64186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001425321.1 → NP_001412250.1  calpain-5 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AP000752
    UniProtKB/TrEMBL
    E7EV01

  2. NM_001425322.1 → NP_001412251.1  calpain-5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000752
    UniProtKB/Swiss-Prot
    O00263, O15484
    UniProtKB/TrEMBL
    A0A140VKH4

  3. NM_001425323.1 → NP_001412252.1  calpain-5 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AP000752

  4. NM_004055.5 → NP_004046.2  calpain-5 isoform 1

    See identical proteins and their annotated locations for NP_004046.2

    Status: REVIEWED

    Source sequence(s)
    AP000752, BC018123
    Consensus CDS
    CCDS8248.1
    UniProtKB/Swiss-Prot
    O00263, O15484
    UniProtKB/TrEMBL
    A0A140VKH4, Q59GM2
    Related
    ENSP00000498132.1, ENST00000648180.1
    Conserved Domains (3) summary
    cd04046
    Location:515 → 638
    C2_Calpain; C2 domain present in Calpain proteins
    cd00214
    Location:352 → 498
    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:27 → 341
    Peptidase_C2; Calpain family cysteine protease

RNA

  1. NR_189161.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000752

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

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    77066971..77126155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545225.1 → XP_011543527.1  calpain-5 isoform X1

    See identical proteins and their annotated locations for XP_011543527.1

    UniProtKB/TrEMBL
    Q6ZRM8
    Conserved Domains (3) summary
    smart00230
    Location:53 → 391
    CysPc; Calpain-like thiol protease family
    cd04046
    Location:555 → 678
    C2_Calpain; C2 domain present in Calpain proteins
    pfam01067
    Location:394 → 533
    Calpain_III; Calpain large subunit, domain III

  2. XM_017018223.3 → XP_016873712.3  calpain-5 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    76997312..77056732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369805.1 → XP_054225780.1  calpain-5 isoform X1

  2. XM_054369806.1 → XP_054225781.1  calpain-5 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15484.2 GenPept UniProtKB/Swiss-Prot:O15484

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous