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    CAPN5 calpain 5 [ Homo sapiens (human) ]

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

    Summary

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    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
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    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

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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
    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

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    • 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

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    Preferred Names
    calpain-5
    Names
    calpain htra-3
    new calpain 3
    testis tissue sperm-binding protein Li 91mP

    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

    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.

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