CASP12

gene
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Summary

CASP12 (caspase 12 (gene/pseudogene), HGNC:19004) is a protein-coding gene on chromosome 11q22.3, encoding Inactive caspase-12 (Q6UXS9). May function as a negative regulator of inflammatory responses and innate immunity.

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.

Source: NCBI Gene 100506742 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 63 total
  • Druggable target: yes

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19004
Approved symbolCASP12
Namecaspase 12 (gene/pseudogene)
Location11q22.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000204403
Ensembl biotypeprotein_coding
OMIM608633
Entrez100506742

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding_LoF, 2 nonsense_mediated_decay

ENST00000375726, ENST00000417998, ENST00000433738, ENST00000441710, ENST00000446862, ENST00000447913, ENST00000448103, ENST00000458137, ENST00000494737, ENST00000508062, ENST00000613512, ENST00000703420

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000375726 — 7 exons

ExonStartEnd
ENSE00001468155104897217104897468
ENSE00001468157104898408104898670
ENSE00003530546104887196104887305
ENSE00003569524104890374104890523
ENSE00003582070104886690104886812
ENSE00003599230104891170104891404
ENSE00003672718104892331104892503

Expression profiles

Bgee: expression breadth ubiquitous, 154 present calls, max score 79.48.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1575 / max 97.5743, expressed in 46 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1220690.129139
1220700.02846

Top tissues by expression

242 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.48silver quality
right lungUBERON:000216778.41gold quality
left ovaryUBERON:000211976.32gold quality
mucosa of stomachUBERON:000119976.18gold quality
ascending aortaUBERON:000149675.83gold quality
thoracic aortaUBERON:000151575.83gold quality
aortaUBERON:000094774.99gold quality
descending thoracic aortaUBERON:000234574.90gold quality
popliteal arteryUBERON:000225074.68gold quality
tibial arteryUBERON:000761074.65gold quality
buccal mucosa cellCL:000233672.96gold quality
left coronary arteryUBERON:000162672.49gold quality
right ovaryUBERON:000211872.34gold quality
body of uterusUBERON:000985371.89gold quality
right coronary arteryUBERON:000162570.92gold quality
coronary arteryUBERON:000162170.62gold quality
ovaryUBERON:000099269.96gold quality
smooth muscle tissueUBERON:000113569.69gold quality
upper lobe of left lungUBERON:000895269.13gold quality
left uterine tubeUBERON:000130368.67gold quality
left lobe of thyroid glandUBERON:000112068.21gold quality
right lobe of thyroid glandUBERON:000111968.18gold quality
gall bladderUBERON:000211067.77gold quality
esophagogastric junction muscularis propriaUBERON:003584167.61gold quality
upper lobe of lungUBERON:000894867.34gold quality
thyroid glandUBERON:000204667.19gold quality
cerebellar hemisphereUBERON:000224566.91gold quality
secondary oocyteCL:000065566.78silver quality
cerebellar cortexUBERON:000212966.69gold quality
tibial nerveUBERON:000132366.64gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.25

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF4, ESR1

Literature-anchored findings (GeneRIF, showing 26)

  • caspase 12 has acquired deleterious mutations (PMID:12054529)
  • Pathways involving this enzyme are involved in a neurodegenerative disease in vivo, and thus offer novel potential targets for the treatment of prion disorders. (PMID:14532116)
  • Na/Ca exchanger overexpression activates caspase-12 (PMID:15033764)
  • Csp12-L attenuates the inflammatory and innate immune response to endotoxins and in doing so may constitute a risk factor for developing sepsis (PMID:15129283)
  • The activation of caspase-9 and depolarization of mitochondrial membrane potential were induced by BIK, which were decreased concomitant with caspase-12 silenced. (PMID:17574210)
  • proteolytic activity of caspase-12 is confined to its own proenzyme (PMID:18332441)
  • hRPE cells express a high level of caspase-12S. The regulated expression of caspase-12S suggests that this caspase recruitment domain (CARD)-only protein may be an endogenous dominant negative regulator that modulates inflammatory responses in hRPE cells. (PMID:18791174)
  • estrogen-mediated inhibition of Csp-12L expression is a built-in mechanism that has evolved to protect females from Listeria monocytogenes infection. (PMID:19447924)
  • the NOD2/RIP2 pathway has a role in recognition of Yersinia, but caspase-12 does not modulate innate host defense against Y. pestis (PMID:19721713)
  • The calcium-calpain-caspase-12-caspase-3 cascade is altered in F508del-CFTR expressing cells. (PMID:20041182)
  • Reactive oxygen species promote caspase-12 expression and tubular apoptosis in diabetic nephropathy. (PMID:20299359)
  • Constitutively active forms of caspase-12 (rev-Deltapro1 and rev-Deltapro2) could induce cell death in cells transfected with the corresponding expression vectors. (PMID:20646990)
  • CASPASE-12 does not influence the susceptibility to Candida sepsis, nor has any effect on the serum cytokine concentrations in Candida sepsis patients during the course of infection. (PMID:21706251)
  • examines the role that CASP12 plays in down-regulating inflammation, we hypothesize that pathogens which exploit the inflammatory response are restrained by an active CASP12 gene product (PMID:21872999)
  • EtOH-induced activation of caspase-12 could be one of the underlying mechanisms of hepatocyte apoptosis. (PMID:24224909)
  • Distribution of CASP12 alleles (#rs497116) in African-Americans (AA) with rheumatoid arthritis (RA). There was no difference in the overall distribution of genotypes within AA with RA, but homozygous patients had lower baseline joint-narrowing scores. (PMID:24515649)
  • conclude that the functional CASP12L allele is not a marker for susceptibility and/or severity of CAP (PMID:24586588)
  • We found that RNA interference-induced Caspase-12 silencing increased NOD1, hBD1 and hBD2 expression (PMID:25503380)
  • Endoplasmic reticulum stress related factor ATF6 and caspase-12 trigger apoptosis in neonatal hypoxic-ischemic encephalopathy. (PMID:26261584)
  • Expression of caspase-12 was linked to decreased systemic and adipose tissue inflammation in a cohort of African American obese children. (PMID:26582949)
  • CASP12 genotype thus does not influence the phenotype of systemic lupus erythematosus in African-Americans (PMID:26973091)
  • Endoplasmic reticulum stress may be associated with apoptosis of LECs, resulting in cataract formation in diabetic patients. (PMID:27130368)
  • study indicated the potential effect of Casp12 was on the activation of NF-kappaB by the degradation of IkappaBalpha in NPC cells. (PMID:28380444)
  • The expression of three genes (STK26, KCNT2, CASP12) was correlated with the prognosis of skin cutaneous melanoma (SCM). STK26 and KCNT2 were significantly different between normal skin and SCM. These three hub genes have potential value as predictors for accurate diagnosis and prognosis of SCM in the future. (PMID:31557882)
  • Analysis of CASP12 diagnostic and prognostic values in cervical cancer based on TCGA database. (PMID:31804677)
  • Human Caspase 12 Enhances NF-kappaB Activity through Activation of IKK in Nasopharyngeal Carcinoma Cells. (PMID:33924755)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_reriocasp8ENSDARG00000058325
danio_reriocasp3lENSDARG00000086266
danio_rerioENSDARG00000112575
mus_musculusCasp12ENSMUSG00000025887
rattus_norvegicusCasp12ENSRNOG00000033434
drosophila_melanogasterDroncFBGN0026404
drosophila_melanogasterDecayFBGN0028381
caenorhabditis_elegansWBGENE00000417
caenorhabditis_elegansWBGENE00000819
caenorhabditis_elegansWBGENE00000820
caenorhabditis_eleganscsp-3WBGENE00000821

Paralogs (16): CASP10 (ENSG00000003400), CFLAR (ENSG00000003402), CASP8 (ENSG00000064012), PYCARD (ENSG00000103490), CASP14 (ENSG00000105141), CASP2 (ENSG00000106144), CASP9 (ENSG00000132906), CASP1 (ENSG00000137752), CASP5 (ENSG00000137757), CASP6 (ENSG00000138794), CASP3 (ENSG00000164305), CASP7 (ENSG00000165806), PYDC1 (ENSG00000169900), CASP4 (ENSG00000196954), CARD16 (ENSG00000204397), CARD18 (ENSG00000255501)

Protein

Protein identifiers

Inactive caspase-12Q6UXS9 (reviewed: Q6UXS9)

All UniProt accessions (1): Q6UXS9

UniProt curated annotations — full annotation on UniProt →

Function. May function as a negative regulator of inflammatory responses and innate immunity. May reduce cytokine release in response to bacterial lipopolysaccharide during infection. Reduces activation of NF-kappa-B in response to TNF. May lack protease activity.

Tissue specificity. Widely expressed, with highest levels in lung.

Polymorphism. The sequence shown in this entry differs from the translation of the reference genome assembly (GRCh38/hg38) due to a nonsense variant creating stop codon at position 125 in the reference genome, giving rise to a truncated protein (Csp12-S). The sequence shown in this entry is that of variant p.Ter125Arg. This variant gives rise to a full length protein (Csp12-L). It occurs in the human population at a frequence of about 4% according to the Genome Aggregation Database (gnomAD v3.1.2), with highest frequency observed in people of African descent (up to 60% in certain sub-Saharan populations). Csp12-L expression may increase the susceptibility to severe sepsis, and may result in higher mortality rates (up to 3-fold) once severe sepsis develop.

Similarity. Belongs to the peptidase C14A family.

Isoforms (8)

UniProt IDNamesCanonical?
Q6UXS9-11, Epsilon, Gammayes
Q6UXS9-22, Alpha, Beta
Q6UXS9-33, Iota
Q6UXS9-44, Zeta, Epsilon
Q6UXS9-55, Eta, Delta
Q6UXS9-66, Gamma, Zeta
Q6UXS9-77, Theta, Eta
Q6UXS9-88, Delta, Theta

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001309Pept_C14_p20Domain
IPR001315CARDDomain
IPR002138Pept_C14_p10Domain
IPR002398Pept_C14Family
IPR011029DEATH-like_dom_sfHomologous_superfamily
IPR011600Pept_C14_caspaseDomain
IPR015917Pept_C14ADomain
IPR029030Caspase-like_dom_sfHomologous_superfamily
IPR033139Caspase_cys_ASActive_site

Pfam: PF00619, PF00656

Enzyme classification (BRENDA):

  • EC 3.4.22.B66 — (BRENDA: organisms, substrates, inhibitors, Km, kcat entries)

UniProt features (17 total): splice variant 7, sequence variant 3, active site 2, modified residue 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6UXS9-F177.130.31

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 172; 220

Post-translational modifications (2): 85, 90

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 87 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, GOBP_INFLAMMATORY_RESPONSE, chr11q22, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, FOSTER_TOLERANT_MACROPHAGE_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, GOMF_CYSTEINE_TYPE_PEPTIDASE_ACTIVITY, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, GOBP_NEURON_APOPTOTIC_PROCESS, GOBP_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_REGULATION_OF_INFLAMMATORY_RESPONSE, GOBP_REGULATION_OF_DEFENSE_RESPONSE, GOBP_POSITIVE_REGULATION_OF_INFLAMMATORY_RESPONSE, GOBP_POSITIVE_REGULATION_OF_NEURON_APOPTOTIC_PROCESS

GO Biological Process (4): proteolysis (GO:0006508), positive regulation of neuron apoptotic process (GO:0043525), positive regulation of inflammatory response (GO:0050729), regulation of apoptotic process (GO:0042981)

GO Molecular Function (1): cysteine-type peptidase activity (GO:0008234)

GO Cellular Component (4): cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), NLRP1 inflammasome complex (GO:0072558)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cytoplasm2
protein metabolic process1
positive regulation of apoptotic process1
regulation of neuron apoptotic process1
neuron apoptotic process1
inflammatory response1
positive regulation of defense response1
positive regulation of response to external stimulus1
regulation of inflammatory response1
apoptotic process1
regulation of programmed cell death1
peptidase activity1
intracellular anatomical structure1
endomembrane system1
intracellular membrane-bounded organelle1
canonical inflammasome complex1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

8 interactions, top by confidence:

ABTypeScore
MYCMAXpsi-mi:“MI:0914”(association)0.980
STAT1STAT3psi-mi:“MI:0914”(association)0.910
CFTRCNOT1psi-mi:“MI:0914”(association)0.480
MYOD1TCF4psi-mi:“MI:0914”(association)0.420
NEK10psi-mi:“MI:0914”(association)0.350
ATG16L1psi-mi:“MI:0914”(association)0.350
HSPA5CASP7psi-mi:“MI:0914”(association)0.350

BioGRID (21): CASP12 (Biochemical Activity), CASP9 (Biochemical Activity), MAGEA3 (Two-hybrid), MAGEA3 (Affinity Capture-Western), CASP12 (Affinity Capture-Western), CASP12 (Affinity Capture-Western), CASP12 (Affinity Capture-Western), CASP12 (Affinity Capture-Western), CASP12 (Affinity Capture-MS), CASP12 (Affinity Capture-MS), CASP12 (Affinity Capture-MS), CASP12 (Affinity Capture-MS), CASP12 (Proximity Label-MS), CASP12 (Affinity Capture-MS), CASP12 (Affinity Capture-MS)

ESM2 similar proteins: A0A140LIF8, B1ARD6, B1ARD8, G1SRW8, O08736, O14862, O35368, O89110, P0C7P3, P0DOV1, P13504, P29452, P41218, P43527, P51878, P55865, P55867, P70343, Q02955, Q075B4, Q08AF3, Q153Z0, Q16666, Q3UX83, Q4R7Q1, Q504J1, Q504N7, Q5RCZ8, Q5U311, Q60766, Q62929, Q6AYC2, Q6IEE8, Q6UXS9, Q7Z7L1, Q8BV49, Q8CGE8, Q8IXQ6, Q8IYM2, Q8SPH9

Diamond homologs: O08736, O35397, O75601, P29452, P29466, P42574, P43527, P49662, P51878, P55212, P55213, P55865, P55867, P70343, P70677, Q075B4, Q08DY9, Q153Z0, Q2PFV2, Q504J1, Q5E9C1, Q5IS54, Q5IS99, Q60431, Q6UXS9, Q8MJC3, Q8MJU1, Q8MKI5, Q920D5, Q95ND5, Q9I9L7, Q9MZV6, Q9MZV7, Q9N2I1, Q9TV13, A0A1D5PPP7, F1NV61, G5ECW5, O01382, O02002

SIGNOR signaling

1 interactions.

AEffectBMechanism
CASP12up-regulatesCASP9cleavage

Disease & clinical

Clinical variants and AI predictions

ClinVar

63 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance42
Likely benign8
Benign6

Top pathogenic / likely-pathogenic (0)

SpliceAI

1122 predictions. Top by Δscore:

VariantEffectΔscore
11:104887190:CCCTA:Cdonor_loss1.0000
11:104887191:CCTA:Cdonor_loss1.0000
11:104887192:CTACC:Cdonor_loss1.0000
11:104887193:TACCT:Tdonor_loss1.0000
11:104887195:C:CAdonor_loss1.0000
11:104887302:TTAT:Tacceptor_gain1.0000
11:104887303:TAT:Tacceptor_gain1.0000
11:104887303:TATC:Tacceptor_loss1.0000
11:104887304:ATCT:Aacceptor_loss1.0000
11:104887305:TCT:Tacceptor_loss1.0000
11:104887306:C:CCacceptor_gain1.0000
11:104887307:T:Aacceptor_loss1.0000
11:104890373:T:Cdonor_gain1.0000
11:104891168:A:ACdonor_gain1.0000
11:104891168:ACTG:Adonor_gain1.0000
11:104891169:C:CCdonor_gain1.0000
11:104891169:CTGC:Cdonor_gain1.0000
11:104886811:ACCTA:Aacceptor_loss0.9900
11:104886814:T:Gacceptor_loss0.9900
11:104887301:ATTAT:Aacceptor_gain0.9900
11:104887312:A:ACacceptor_gain0.9900
11:104887312:A:Cacceptor_gain0.9900
11:104890372:A:ACdonor_gain0.9900
11:104890520:CCAT:Cacceptor_gain0.9900
11:104890521:CATC:Cacceptor_gain0.9900
11:104891147:CAG:Cdonor_gain0.9900
11:104891168:ACTGC:Adonor_gain0.9900
11:104891169:CTG:Cdonor_gain0.9900
11:104891169:CTGCC:Cdonor_gain0.9900
11:104891171:G:GAdonor_gain0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000133900 (11:104893817 T>C), RS1000414834 (11:104896191 A>T), RS1000742290 (11:104895088 A>G), RS1000749196 (11:104889774 G>A), RS1000799111 (11:104896485 T>C), RS1000818106 (11:104891303 G>T), RS1001153477 (11:104894780 C>A,G), RS1001191635 (11:104899365 A>G), RS1001855705 (11:104897738 A>G), RS1001864031 (11:104892424 A>G,T), RS1002247185 (11:104891788 A>T), RS1002253553 (11:104886706 T>A,G), RS1002435537 (11:104885818 G>T), RS1002926528 (11:104889479 C>T), RS1003250601 (11:104893377 T>C)

Disease associations

OMIM: gene MIM:608633 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

StudyTraitp-value
GCST006461_1Self-reported risk-taking behaviour4.000000e-08
GCST007325_4General risk tolerance (MTAG)5.000000e-09
GCST011768_8Schizophrenia1.000000e-08
GCST011769_21Schizophrenia3.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008579risk-taking behaviour

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3831289 (PROTEIN FAMILY)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

1 potent at pChembl≥5 of 1 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.80EC5016nMCHEMBL1091826

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
N-(4-methoxyphenyl)-N-methyl-1,2,3-benzotriazin-4-amine1393168: Activation of caspase cascade in human T47D cells using N-(Ac-DEVD)-N’-ethoxycarbonyl-R110 fluorogenic substrate incubated for 48 hrs by fluorescent plate reader based assayec500.0160uM

CTD chemical–gene interactions

77 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Arsenic Trioxideincreases activity, increases expression, decreases reaction, increases cleavage, increases reaction4
4-phenylbutyric acidincreases expression, decreases cleavage, decreases reaction, increases cleavage3
7-methyl-5-(1-((3-(trifluoromethyl)phenyl)acetyl)-2,3-dihydro-1H-indol-5-yl)-7H-pyrrolo(2,3-d)pyrimidin-4-amineincreases cleavage, increases expression, decreases cleavage, decreases expression, affects cotreatment (+4 more)3
Thapsigargindecreases reaction, increases expression, increases activity, increases cleavage3
Resveratrolincreases activity, increases expression, decreases reaction, increases cleavage2
Acetylcysteinedecreases reaction, increases abundance, increases cleavage, increases reaction2
Cadmiumincreases cleavage, increases abundance, decreases reaction, increases activity2
Cisplatinaffects cotreatment, increases activity, increases reaction2
Methamphetamineincreases expression, decreases expression, decreases reaction, affects reaction2
Tunicamycinaffects cotreatment, increases activity, increases reaction, decreases reaction2
1-Methyl-4-phenylpyridiniumdecreases reaction, increases cleavage, increases expression2
Paclitaxeldecreases expression, increases expression, affects cotreatment2
SC-66 compounddecreases expression1
CB-5083affects cotreatment, increases cleavage1
methylgerambullinincreases cleavage1
ML385decreases reaction, increases cleavage1
thymoquinonedecreases expression1
bufotalindecreases reaction, increases activity, increases cleavage1
naringinincreases expression1
methylselenic aciddecreases reaction, increases cleavage1
tetrandrineincreases cleavage1
antibiotic G 418increases cleavage1
2,4,5,2’,4’,5’-hexachlorobiphenylincreases reaction, increases expression1
arseniteincreases expression1
zinc chlorideincreases activity, affects cotreatment1
fisetindecreases reaction, increases expression1
sodium arseniteaffects reaction, increases cleavage1
manganese chlorideincreases activity, increases cleavage, increases reaction1
1,2-bis(2-aminophenoxy)ethane-N,N,N’,N’-tetraacetic aciddecreases reaction, increases expression1
benzo(e)pyreneincreases activity1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4199992BindingActivation of caspase (unknown origin)MK-8353: Discovery of an Orally Bioavailable Dual Mechanism ERK Inhibitor for Oncology. — ACS Med Chem Lett

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.