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CASP12 caspase 12 (gene/pseudogene) [ Homo sapiens (human) ]

Gene ID: 100506742, updated on 4-Jun-2020

Summary

Official Symbol
CASP12provided by HGNC
Official Full Name
caspase 12 (gene/pseudogene)provided by HGNC
Primary source
HGNC:HGNC:19004
See related
Ensembl:ENSG00000204403 MIM:608633
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
CASP-12; CASP12P1
Summary
Caspases are cysteine proteases that cleave C-terminal aspartic acid residues on their substrate molecules. This gene is most highly related to members of the ICE subfamily of caspases that process inflammatory cytokines. In rodents, the homolog of this gene mediates apoptosis in response to endoplasmic reticulum stress. However, in humans this gene contains a polymorphism for the presence or absence of a premature stop codon. The majority of human individuals have the premature stop codon and produce a truncated non-functional protein. The read-through codon occurs primarily in individuals of African descent and carriers have endotoxin hypo-responsiveness and an increased susceptibility to severe sepsis. Several alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Feb 2011]
Expression
Broad expression in ovary (RPKM 2.1), endometrium (RPKM 1.1) and 14 other tissues See more

Genomic context

See CASP12 in Genome Data Viewer
Location:
11q22.3
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (104885718..104898670, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (104756445..104769397, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2552 Neighboring gene uncharacterized LOC105369466 Neighboring gene uncharacterized LOC107984380 Neighboring gene caspase 4 like, pseudogene Neighboring gene caspase 4

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat induces endoplasmic reticulum (ER) stress response proteins CASP12 (Caspase 12), DDIT3 (CHOP), ROS1, ERN-1 (p-IRE1), EIF2AK3 (p-PERK), and ATF6 in human brain microvascular endothelial cells (HBMECs) PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Gene Ontology Provided by GOA

Process Evidence Code Pubs
NOT activation of cysteine-type endopeptidase activity involved in apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NOT apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
 
proteolysis IEA
Inferred from Electronic Annotation
more info
 
regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
AIM2 inflammasome complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
IPAF inflammasome complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NLRP3 inflammasome complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
inactive caspase-12
Names
caspase 12 pseudogene 1

NCBI Reference Sequences (RefSeq)

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_028201.2 RefSeqGene

    Range
    5001..17953
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001191016.2NP_001177945.2  inactive caspase-12

    See identical proteins and their annotated locations for NP_001177945.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the protein coding transcript, encoding Arg (CGA, aa 125) at the polymorphic site instead of the premature translation termination codon (TGA). The encoded protein (also known as Csp12-L) has no protease activity; however, it is thought to modulate inflammation and innate immune response to endotoxins, and is a risk factor for developing severe sepsis.
    Source sequence(s)
    AF464191, AY358222, BG183061
    UniProtKB/Swiss-Prot
    Q6UXS9
    Conserved Domains (2) summary
    smart00115
    Location:103339
    CASc; Caspase, interleukin-1 beta converting enzyme (ICE) homologues
    cd08325
    Location:688
    CARD_CASP1-like; Caspase activation and recruitment domain found in Caspase-1 and related proteins

RNA

  1. NR_034061.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes a translation termination codon (TGA) at the polymorphic site, resulting in a truncated protein product (known as Csp12-S), thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF464191, BG183061
    Related
    ENST00000613512.4
  2. NR_034063.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is missing an exon at the 3' end compared to variant 1, and encodes a translation termination codon (TGA) at the polymorphic site, resulting in a truncated protein product, thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF464192, BG183061
  3. NR_034064.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) is missing an exon at the 3' end and uses an alternate donor splice site at an internal exon compared to variant 1. It encodes a translation termination codon (TGA) at the polymorphic site, resulting in a truncated protein product, thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF464193, BG183061
  4. NR_034065.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) is missing an internal exon compared to variant 1, and encodes a translation termination codon (TGA) at the polymorphic site, resulting in a truncated protein product, thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF486846, BG183061
  5. NR_034066.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) is missing 2 internal exons compared to variant 1, and encodes a translation termination codon (TGA) at the polymorphic site, resulting in a truncated protein product, thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF486847, BG183061
  6. NR_034067.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) is missing 2 internal exons compared to variant 1, and encodes a translation termination codon (TGA) at the polymorphic site, resulting in a truncated protein product, thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF464194, BG183061
  7. NR_034068.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) is missing 3 internal exons compared to variant 1, and encodes a translation termination codon (TGA) at the polymorphic site, resulting in a truncated protein product, thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF464195, BG183061
  8. NR_034070.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) contains an additional internal exon compared to variant 1, resulting in a frame-shift and premature translation termination, thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF486844, AP002004, BG183061
  9. NR_034071.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) contains an additional internal exon and is missing another exon compared to variant 1, resulting in a frame-shift and premature translation termination, thus rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF486845, AP002004, BG183061

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    104885718..104898670 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_000035.2: Suppressed sequence

    Description
    NR_000035.2: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.
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