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Aliases for CAPN5 Gene

Aliases for CAPN5 Gene

  • Calpain 5 2 3 5
  • Calpain Htra-3 3 4
  • New Calpain 3 3 4
  • NCL-3 3 4
  • Testis Tissue Sperm-Binding Protein Li 91mP 3
  • Vitreoretinopathy, Neovascular Inflammatory 2
  • EC 3.4.22.- 4
  • Calpain-5 3
  • ADNIV 3
  • HTRA3 3
  • VRNI 3
  • NCL3 4

External Ids for CAPN5 Gene

Previous HGNC Symbols for CAPN5 Gene

  • VRNI

Previous GeneCards Identifiers for CAPN5 Gene

  • GC11P079104
  • GC11P078317
  • GC11P077000
  • GC11P076504
  • GC11P076455
  • GC11P076777
  • GC11P073075

Summaries for CAPN5 Gene

Entrez Gene Summary for CAPN5 Gene

  • 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]

GeneCards Summary for CAPN5 Gene

CAPN5 (Calpain 5) is a Protein Coding gene. Diseases associated with CAPN5 include Vitreoretinopathy, Neovascular Inflammatory and Posterior Uveitis. Among its related pathways are B Cell Receptor Signaling Pathway (sino) and Focal Adhesion. Gene Ontology (GO) annotations related to this gene include calcium-dependent cysteine-type endopeptidase activity. An important paralog of this gene is CAPN6.

UniProtKB/Swiss-Prot for CAPN5 Gene

  • Calcium-regulated non-lysosomal thiol-protease.

Tocris Summary for CAPN5 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 CAPN5 Gene

Additional gene information for CAPN5 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CAPN5 Gene

Genomics for CAPN5 Gene

GeneHancer (GH) Regulatory Elements for CAPN5 Gene

Promoters and enhancers for CAPN5 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J077065 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 658.2 -0.2 -153 2.7 HDGF FOXA2 ARID4B SIN3A ETS1 YY1 GLIS2 ELK1 ATF7 RUNX3 CAPN5 EMSY ENSG00000254459 RSF1 INTS4 LOC105369400
GH11J077034 Promoter/Enhancer 1.6 EPDnew ENCODE dbSUPER 7.3 -31.2 -31164 3.2 PKNOX1 FOXA2 MLX ZFP64 NEUROD1 FOS ATF7 RUNX3 NFKBIZ SP5 B3GNT6 OMP MYO7A ACER3 CAPN5 LOC105369399
GH11J077071 Enhancer 1.1 Ensembl ENCODE dbSUPER 10.5 +7.2 7155 5.6 CTCF TFAP4 PKNOX1 CLOCK JUN SIN3A TSC22D4 ZMYM3 ZIC2 RAD21 CAPN5 ACER3 OMP
GH11J077045 Enhancer 1.3 Ensembl ENCODE dbSUPER 6.1 -19.8 -19843 2.6 PKNOX1 ARID4B SIN3A YY1 ELK1 ARID2 ZNF143 ATF7 RUNX3 RXRA LOC105369399 OMP CAPN5 B3GNT6
GH11J077081 Enhancer 0.8 Ensembl ENCODE dbSUPER 9.6 +16.0 16035 2 ZNF530 HNF4A CAPN5 OMP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CAPN5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CAPN5 gene promoter:
  • Ik-2
  • AREB6
  • STAT1
  • ZIC2
  • Arnt
  • AhR
  • E47
  • AP-1

Genomic Locations for CAPN5 Gene

Genomic Locations for CAPN5 Gene
59,224 bases
Plus strand
59,223 bases
Plus strand

Genomic View for CAPN5 Gene

Genes around CAPN5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CAPN5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CAPN5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CAPN5 Gene

Proteins for CAPN5 Gene

  • Protein details for CAPN5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • O00263

    Protein attributes for CAPN5 Gene

    640 amino acids
    Molecular mass:
    73169 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CAPN5 Gene

Post-translational modifications for CAPN5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CAPN5 Gene

No data available for DME Specific Peptides for CAPN5 Gene

Domains & Families for CAPN5 Gene

Gene Families for CAPN5 Gene

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

Suggested Antigen Peptide Sequences for CAPN5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase C2 family.
  • Belongs to the peptidase C2 family.
genes like me logo Genes that share domains with CAPN5: view

Function for CAPN5 Gene

Molecular function for CAPN5 Gene

UniProtKB/Swiss-Prot Function:
Calcium-regulated non-lysosomal thiol-protease.
GENATLAS Biochemistry:
calpain,class B,large polypeptide,calcium independent cysteine proteinase,papain superfamily,nCL-3 type,specifically expressed in colon,small intestine,testis homolog to C elegans sex determination gene tra3

Enzyme Numbers (IUBMB) for CAPN5 Gene

Phenotypes From GWAS Catalog for CAPN5 Gene

Gene Ontology (GO) - Molecular Function for CAPN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004198 calcium-dependent cysteine-type endopeptidase activity IBA --
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with CAPN5: view
genes like me logo Genes that share phenotypes with CAPN5: view

Human Phenotype Ontology for CAPN5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CAPN5 Gene

MGI Knock Outs for CAPN5:

Animal Model Products

  • Taconic Biosciences Mouse Models for CAPN5

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for CAPN5 Gene

Localization for CAPN5 Gene

Subcellular locations from

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 CAPN5 gene
Compartment Confidence
extracellular 5
cytosol 4
nucleus 3

Gene Ontology (GO) - Cellular Components for CAPN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IBA --
GO:0005925 focal adhesion HDA 21423176
GO:0009986 cell surface IDA 23055945
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with CAPN5: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for CAPN5 Gene

Pathways & Interactions for CAPN5 Gene

genes like me logo Genes that share pathways with CAPN5: view

Pathways by source for CAPN5 Gene

1 Sino Biological pathway for CAPN5 Gene
1 BioSystems pathway for CAPN5 Gene

Gene Ontology (GO) - Biological Process for CAPN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA,IBA --
GO:0007165 signal transduction TAS 9339374
genes like me logo Genes that share ontologies with CAPN5: view

No data available for SIGNOR curated interactions for CAPN5 Gene

Drugs & Compounds for CAPN5 Gene

(2) Drugs for CAPN5 Gene - From: Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calpeptin Pharma Ca2+-dependent protease,calpain inhibitor, Calpain and cathepsin L inhibitor 0
MDL 28170 Pharma Calpain and cathepsin B inhibitor, selective, Potent, selective calpain and cathepsin B inhibitor 0

(2) Tocris Compounds for CAPN5 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
genes like me logo Genes that share compounds with CAPN5: view

Transcripts for CAPN5 Gene

mRNA/cDNA for CAPN5 Gene

Unigene Clusters for CAPN5 Gene

Calpain 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CAPN5 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b · 16c
SP1: - - -
SP2: - - -
SP3: - - - -
SP4: - -
SP5: - - - - - - -

Relevant External Links for CAPN5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CAPN5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CAPN5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CAPN5 Gene

This gene is overexpressed in Colon - Transverse (x7.0).

Protein differential expression in normal tissues from HIPED for CAPN5 Gene

This gene is overexpressed in Testis (18.5) and Spinal cord (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CAPN5 Gene

NURSA nuclear receptor signaling pathways regulating expression of CAPN5 Gene:


SOURCE GeneReport for Unigene cluster for CAPN5 Gene:


mRNA Expression by UniProt/SwissProt for CAPN5 Gene:

Tissue specificity: Expressed in many tissues. Strong expression in the photoreceptor cells of the retina, with a punctate pattern of labeling over the nuclei and inner segments with less expression along the other segments and outer plexiform layer.

Evidence on tissue expression from TISSUES for CAPN5 Gene

  • Nervous system(4.7)
  • Pancreas(4.1)
  • Eye(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CAPN5 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • cardiovascular
  • nervous
Head and neck:
  • cranial nerve
  • eye
  • head
  • blood
  • blood vessel
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CAPN5: view

No data available for Protein tissue co-expression partners for CAPN5 Gene

Orthologs for CAPN5 Gene

This gene was present in the common ancestor of animals.

Orthologs for CAPN5 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CAPN5 33
  • 97.86 (n)
(Bos Taurus)
Mammalia CAPN5 34 33
  • 91.04 (n)
(Canis familiaris)
Mammalia CAPN5 34 33
  • 89.53 (n)
(Mus musculus)
Mammalia Capn5 16 34 33
  • 87.92 (n)
(Rattus norvegicus)
Mammalia Capn5 33
  • 87.4 (n)
(Ornithorhynchus anatinus)
Mammalia CAPN5 34
  • 80 (a)
(Monodelphis domestica)
Mammalia CAPN5 34
  • 75 (a)
(Gallus gallus)
Aves CAPN5 34 33
  • 76.79 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia capn5 33
  • 73.12 (n)
African clawed frog
(Xenopus laevis)
Amphibia capn5-prov 33
(Danio rerio)
Actinopterygii capn5b 34 33
  • 70.68 (n)
capn5a 34
  • 69 (a)
(Caenorhabditis elegans)
Secernentea tra-3 34 35 33
  • 46.13 (n)
clp-7 35
  • 40 (a)
clp-6 35
  • 39 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3869 34
  • 29 (a)
Species where no ortholog for CAPN5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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 CAPN5 Gene

Gene Tree for CAPN5 (if available)
Gene Tree for CAPN5 (if available)
Evolutionary constrained regions (ECRs) for CAPN5: view image

Paralogs for CAPN5 Gene

Paralogs for CAPN5 Gene

(7) SIMAP similar genes for CAPN5 Gene using alignment to 4 proteins:

  • E7EV01_HUMAN
  • E9PS73_HUMAN
  • K7EP62_HUMAN
genes like me logo Genes that share paralogs with CAPN5: view

Variants for CAPN5 Gene

Sequence variations from dbSNP and Humsavar for CAPN5 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs397514601 pathogenic, Vitreoretinopathy, neovascular inflammatory, Vitreoretinopathy, neovascular inflammatory (VRNI) [MIM:193235] 77,115,423(+) G/A/T coding_sequence_variant, missense_variant
rs397514602 pathogenic, Vitreoretinopathy, neovascular inflammatory, Vitreoretinopathy, neovascular inflammatory (VRNI) [MIM:193235] 77,115,426(+) T/C coding_sequence_variant, missense_variant
rs886041303 pathogenic, not provided 77,115,560(+) C/T coding_sequence_variant, missense_variant
rs1064797159 uncertain-significance, not provided 77,120,821(+) C/T coding_sequence_variant, missense_variant
rs11604536 benign, not specified 77,116,314(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CAPN5 Gene

Variant ID Type Subtype PubMed ID
dgv1230n100 CNV gain 25217958
dgv1231n100 CNV gain 25217958
dgv1232n100 CNV gain 25217958
dgv1233n100 CNV gain 25217958
esv1254554 CNV deletion 17803354
esv2744802 CNV deletion 23290073
nsv1040996 CNV gain 25217958
nsv1044491 CNV gain 25217958
nsv1047361 CNV gain 25217958
nsv509434 CNV insertion 20534489
nsv555450 CNV loss 21841781
nsv555451 CNV loss 21841781
nsv825998 CNV gain 20364138
nsv825999 CNV gain 20364138
nsv951045 CNV deletion 24416366

Variation tolerance for CAPN5 Gene

Residual Variation Intolerance Score: 78.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.25; 62.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CAPN5 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CAPN5 Gene

Disorders for CAPN5 Gene

MalaCards: The human disease database

(9) MalaCards diseases for CAPN5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CAPN5 in MalaCards View complete list of genes associated with diseases


  • Vitreoretinopathy, neovascular inflammatory (VRNI) [MIM:193235]: An autoimmune condition of the eye that sequentially mimics uveitis, retinitis pigmentosa, and proliferative diabetic retinopathy as it progresses to complete blindness. Patients present during the second or third decade of life with posterior uveitis and reduction of the electroretinogram b-wave. They become more symptomatic when cataracts, cystoid macular edema, and disk edema diminish visual acuity during the second stage. Severe vision loss begins during the third stage when proliferative retinal neovascularization and epiretinal membranes appear. There is an ongoing pigmentary retinal degeneration and peripheral visual field loss during all stages. In the fourth stage, proliferative vitreoretinopathy causes tractional retinal detachments at the macula and vitreous base. The fifth or end-stage disease is marked by phthisis. {ECO:0000269 PubMed:23055945}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CAPN5

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CAPN5: view

No data available for Genatlas for CAPN5 Gene

Publications for CAPN5 Gene

  1. Identification of a novel, tissue-specific calpain htra-3; a human homologue of the Caenorhabditis elegans sex determination gene. (PMID: 9367857) Mugita N … Nakao M (Biochemical and biophysical research communications 1997) 2 3 4 22 58
  2. Calpain-5 mutations cause autoimmune uveitis, retinal neovascularization, and photoreceptor degeneration. (PMID: 23055945) Mahajan VB … Stone EM (PLoS genetics 2012) 2 3 4 58
  3. Interaction between Calpain 5, Peroxisome proliferator-activated receptor-gamma and Peroxisome proliferator-activated receptor-delta genes: a polygenic approach to obesity. (PMID: 18657264) Sáez ME … Serrano-Ríos M (Cardiovascular diabetology 2008) 3 22 44 58
  4. Calpain-5 gene variants are associated with diastolic blood pressure and cholesterol levels. (PMID: 17227582) Sáez ME … Serrano-Ríos M (BMC medical genetics 2007) 3 22 44 58
  5. Specific haplotypes of the CALPAIN-5 gene are associated with polycystic ovary syndrome. (PMID: 16396936) González A … Ramírez-Lorca R (Human reproduction (Oxford, England) 2006) 3 22 44 58

Products for CAPN5 Gene

Sources for CAPN5 Gene

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