THAP12

gene
On this page

Also known as P52rIPKDAP4THAP0

Summary

THAP12 (THAP domain containing 12, HGNC:9440) is a protein-coding gene on chromosome 11q13.5, encoding 52 kDa repressor of the inhibitor of the protein kinase (O43422). Upstream regulator of interferon-induced serine/threonine protein kinase R (PKR). It is a selective cancer dependency (DepMap: 36.8% of cell lines).

Predicted to enable several functions, including DNA binding activity; protein dimerization activity; and zinc ion binding activity. Predicted to be involved in negative regulation of cell population proliferation and signal transduction. Predicted to be located in nucleus.

Source: NCBI Gene 5612 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): syndromic complex neurodevelopmental disorder (Limited, GenCC)
  • GWAS associations: 14
  • Clinical variants (ClinVar): 11 total
  • Cancer dependency (DepMap): dependent in 36.8% of screened cell lines
  • MANE Select transcript: NM_004705

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9440
Approved symbolTHAP12
NameTHAP domain containing 12
Location11q13.5
Locus typegene with protein product
StatusApproved
AliasesP52rIPK, DAP4, THAP0
Ensembl geneENSG00000137492
Ensembl biotypeprotein_coding
OMIM607374
Entrez5612

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 nonsense_mediated_decay, 3 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000260045, ENST00000525277, ENST00000528993, ENST00000529901, ENST00000531878, ENST00000682046, ENST00000682527, ENST00000682978, ENST00000683600, ENST00000684059, ENST00000684702, ENST00000937942

RefSeq mRNA: 1 — MANE Select: NM_004705 NM_004705

CCDS: CCDS8243

Canonical transcript exons

ENST00000260045 — 5 exons

ExonStartEnd
ENSE000009276497638074876381132
ENSE000035693977634995676352794
ENSE000036089587635561876355654
ENSE000036324987636095676361063
ENSE000036677267636585276365972

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 96.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.0468 / max 61.1785, expressed in 1725 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1213876.84061719
1213860.206270

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370196.57gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450294.59gold quality
corpus epididymisUBERON:000435994.58gold quality
mucosa of sigmoid colonUBERON:000499394.18gold quality
biceps brachiiUBERON:000150794.00gold quality
trabecular bone tissueUBERON:000248393.97gold quality
caput epididymisUBERON:000435893.95gold quality
colonic mucosaUBERON:000031793.92gold quality
secondary oocyteCL:000065593.83gold quality
pigmented layer of retinaUBERON:000178293.83gold quality
retinaUBERON:000096693.81gold quality
ventricular zoneUBERON:000305393.67gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451193.66gold quality
ganglionic eminenceUBERON:000402393.64gold quality
body of pancreasUBERON:000115093.53gold quality
cauda epididymisUBERON:000436093.52gold quality
adrenal tissueUBERON:001830393.39gold quality
oocyteCL:000002393.22gold quality
mammary ductUBERON:000176593.14gold quality
epithelium of nasopharynxUBERON:000195193.06gold quality
tendonUBERON:000004392.94gold quality
superficial temporal arteryUBERON:000161492.91gold quality
pancreasUBERON:000126492.89gold quality
rectumUBERON:000105292.81gold quality
skin of hipUBERON:000155492.80gold quality
leukocyteCL:000073892.78gold quality
mononuclear cellCL:000084292.72gold quality
monocyteCL:000057692.68gold quality
embryoUBERON:000092292.64gold quality
germinal epithelium of ovaryUBERON:000130492.59gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.56

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

TargetRegulation
IFNA1
TPM1

miRNA regulators (miRDB)

81 targeting THAP12, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3163100.0077.238605
HSA-MIR-340-5P100.0072.504437
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-366299.9973.825684
HSA-MIR-607799.9968.042299
HSA-MIR-1213699.9872.815713
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-61399.9171.501710
HSA-MIR-806399.9169.763146
HSA-MIR-367199.9073.043897
HSA-MIR-806299.8868.43995
HSA-MIR-391999.8769.452489

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 36.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • role in promoting MST1-induced apoptosis by enabling colocalization of MST with p53 (PMID:12384512)
  • PRKRIR provides a novel positive regulator controlling the RIG-I-IFN production system through protein stability control. (PMID:21910972)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriothap12bENSDARG00000020964
danio_reriothap12aENSDARG00000042489
mus_musculusThap12ENSMUSG00000030753
rattus_norvegicusThap12ENSRNOG00000053923

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), ZMYM5 (ENSG00000132950), ZMYM4 (ENSG00000146463), ZMYM3 (ENSG00000147130), ZMYM6 (ENSG00000163867), KIAA1958 (ENSG00000165185), GTF2IRD2B (ENSG00000174428), EPM2AIP1 (ENSG00000178567), GTF2IRD2 (ENSG00000196275), ZMYM1 (ENSG00000197056), QRICH1 (ENSG00000198218), FAM200C (ENSG00000221886), FAM200A (ENSG00000221909), SCAND3 (ENSG00000232040), ZBED5 (ENSG00000236287), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Protein

Protein identifiers

52 kDa repressor of the inhibitor of the protein kinaseO43422 (reviewed: O43422)

Alternative names: 58 kDa interferon-induced protein kinase-interacting protein, Death-associated protein 4, THAP domain-containing protein 0, THAP domain-containing protein 12

All UniProt accessions (8): O43422, A0A140VJQ7, A0A804HKN8, A0A804HKR8, A0A804HKT7, A0A804HKY5, A0A804HL83, E9PSI2

UniProt curated annotations — full annotation on UniProt →

Function. Upstream regulator of interferon-induced serine/threonine protein kinase R (PKR). May block the PKR-inhibitory function of DNAJC3, resulting in restoration of kinase activity and suppression of cell growth.

Subunit / interactions. Interacts with DNAJC3, probably sequestring it.

Isoforms (2)

UniProt IDNamesCanonical?
O43422-1Longyes
O43422-2Short

RefSeq proteins (1): NP_004696* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006612THAP_ZnfDomain
IPR008906HATC_C_domDomain
IPR012337RNaseH-like_sfHomologous_superfamily
IPR025398RNase-like_ZMYM1Domain
IPR052958IFN-induced_PKR_regulatorFamily

Pfam: PF05485, PF05699, PF14291

UniProt features (10 total): sequence conflict 3, splice variant 2, chain 1, zinc finger region 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O43422-F183.910.59

Functional residue map

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

Post-translational modifications (1): 566

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 166 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, TGCGCANK_UNKNOWN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, BROWNE_HCMV_INFECTION_16HR_UP, MEF2_02, chr11q13, PUJANA_CHEK2_PCC_NETWORK, TCF4_Q5, OCT1_06, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, FISCHER_DREAM_TARGETS, NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON, DANG_BOUND_BY_MYC, BENPORATH_MYC_MAX_TARGETS

GO Biological Process (2): signal transduction (GO:0007165), negative regulation of cell population proliferation (GO:0008285)

GO Molecular Function (5): DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein dimerization activity (GO:0046983), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
cell population proliferation1
regulation of cell population proliferation1
negative regulation of cellular process1
nucleic acid binding1
transition metal ion binding1
protein binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

826 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
THAP12THAP7Q9BT49912
THAP12THAP4Q8WY91904
THAP12THAP11Q96EK4899
THAP12THAP1Q9NVV9891
THAP12THAP3Q8WTV1882
THAP12DNAJC3Q13217874
THAP12THAP5Q7Z6K1644
THAP12EIF2AK2P19525627
THAP12THAP9Q9H5L6607
THAP12THAP10Q9P2Z0592
THAP12THAP8Q8NA92583
THAP12THAP6Q8TBB0473
THAP12HSP90AB1P08238455
THAP12SPATA31D3P0C874447
THAP12A0A3B3IRQ3A0A3B3IRQ3445

IntAct

131 interactions, top by confidence:

ABTypeScore
THAP12ZNF526psi-mi:“MI:0915”(physical association)0.670
GPR156PLD2psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
THAP12ZNF574psi-mi:“MI:0915”(physical association)0.620
ZNF574THAP12psi-mi:“MI:0914”(association)0.620
THAP12TACC1psi-mi:“MI:0915”(physical association)0.560
TACC1THAP12psi-mi:“MI:0915”(physical association)0.560
SELENBP1THAP12psi-mi:“MI:0915”(physical association)0.560
THAP12SELENBP1psi-mi:“MI:0915”(physical association)0.560
THAP12KIAA1958psi-mi:“MI:0915”(physical association)0.560
RPS14MAGEB2psi-mi:“MI:0914”(association)0.560
CACNG5ZNF316psi-mi:“MI:0914”(association)0.530
XAGE1ATHAP12psi-mi:“MI:0914”(association)0.530
IGHMBP2THAP12psi-mi:“MI:0914”(association)0.530
FADDTHAP12psi-mi:“MI:0914”(association)0.530
TMEM171THAP12psi-mi:“MI:0914”(association)0.530
LHX4THAP12psi-mi:“MI:0914”(association)0.530
H2AC20PPM1Gpsi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
KRR1MPHOSPH10psi-mi:“MI:0914”(association)0.530

BioGRID (133): TACC1 (Two-hybrid), PRKRIR (Affinity Capture-MS), PRKRIR (Affinity Capture-MS), PRKRIR (Affinity Capture-MS), PRKRIR (Affinity Capture-MS), PRKRIR (Affinity Capture-MS), PRKRIR (Affinity Capture-MS), PRKRIR (Affinity Capture-MS), PRKRIR (Affinity Capture-MS), MAPKAPK3 (Two-hybrid), MAPKAPK3 (Affinity Capture-Western), MAPKAPK2 (Affinity Capture-Western), EIF2AK2 (Affinity Capture-Western), PRKRIR (Affinity Capture-MS), PRKRIR (Affinity Capture-MS)

ESM2 similar proteins: A3KMX0, A4IFA3, A4IGY9, A4Z943, A4Z944, B8QB46, D2EAC2, E1C2V1, O43422, O60290, P10911, P35125, P86452, Q13075, Q2NKX8, Q3UPF5, Q49AG3, Q5FWF4, Q5SVZ6, Q5T890, Q5TKR9, Q6DJS0, Q6EKJ0, Q6R2W3, Q6YI93, Q7Z2W4, Q80WE4, Q86UP8, Q86VD1, Q8BZ21, Q8N8K9, Q8QMP8, Q8TDB6, Q8WML3, Q92794, Q96JM7, Q96JS3, Q99388, Q99NI3, Q9CUX1

Diamond homologs: O43422, Q9CUX1, A4IGQ8, A5PKF5, Q6IR68, Q6TGZ4, Q96EK4, Q9JJD0

SIGNOR signaling

1 interactions.

AEffectBMechanism
THAP12unknownEIF2S1phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 116 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
SARS-CoV-1 modulates host translation machinery832.9×1e-09
Eukaryotic Translation Initiation728.8×5e-08
Cap-dependent Translation Initiation728.8×5e-08
Eukaryotic Translation Elongation726.0×9e-08
Peptide chain elongation1525.4×2e-15
Viral mRNA Translation1525.4×2e-15
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S725.4×9e-08
Transport of Mature Transcript to Cytoplasm525.4×9e-06

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1629.1×9e-17
translation1818.1×1e-15
ribosomal small subunit biogenesis715.6×4e-05
mitochondrial translation915.3×1e-06
regulation of alternative mRNA splicing, via spliceosome614.4×3e-04
mRNA transport512.9×3e-03
negative regulation of translation59.6×1e-02
rRNA processing68.3×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance4
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

999 predictions. Top by Δscore:

VariantEffectΔscore
11:76352790:ATCAA:Aacceptor_gain1.0000
11:76352791:TCAA:Tacceptor_gain1.0000
11:76352792:CAA:Cacceptor_gain1.0000
11:76352792:CAAC:Cacceptor_gain1.0000
11:76352793:AA:Aacceptor_gain1.0000
11:76352793:AACT:Aacceptor_loss1.0000
11:76352795:C:CCacceptor_gain1.0000
11:76355616:A:ACdonor_gain1.0000
11:76355617:C:CCdonor_gain1.0000
11:76355663:C:CTacceptor_gain1.0000
11:76355664:A:Tacceptor_gain1.0000
11:76361062:CT:Cacceptor_gain1.0000
11:76361064:C:CCacceptor_gain1.0000
11:76361064:CT:Cacceptor_loss1.0000
11:76365850:A:ACdonor_gain1.0000
11:76365851:C:CCdonor_gain1.0000
11:76365851:CAGTT:Cdonor_gain1.0000
11:76365911:G:Cdonor_gain1.0000
11:76380746:ACC:Adonor_loss1.0000
11:76352793:A:Tacceptor_gain0.9900
11:76352803:C:CTacceptor_gain0.9900
11:76352804:A:Tacceptor_gain0.9900
11:76355611:CACTT:Cdonor_loss0.9900
11:76355612:ACTT:Adonor_loss0.9900
11:76355613:CT:Cdonor_loss0.9900
11:76355614:T:TAdonor_loss0.9900
11:76355615:TACTT:Tdonor_loss0.9900
11:76355616:AC:Adonor_loss0.9900
11:76355617:C:Tdonor_loss0.9900
11:76355617:CT:Cdonor_gain0.9900

AlphaMissense

5067 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:76351128:A:CF674L1.000
11:76351128:A:TF674L1.000
11:76351130:A:GF674L1.000
11:76351203:C:AW649C1.000
11:76351203:C:GW649C1.000
11:76351204:C:GW649S1.000
11:76351205:A:GW649R1.000
11:76351205:A:TW649R1.000
11:76351215:C:AW645C1.000
11:76351215:C:GW645C1.000
11:76351216:C:GW645S1.000
11:76351217:A:GW645R1.000
11:76351217:A:TW645R1.000
11:76351218:A:CC644W1.000
11:76351220:A:GC644R1.000
11:76351225:A:GL642P1.000
11:76351324:G:CP609R1.000
11:76351324:G:TP609H1.000
11:76351325:G:AP609S1.000
11:76351325:G:TP609T1.000
11:76361016:A:CF86L1.000
11:76361016:A:TF86L1.000
11:76361018:A:GF86L1.000
11:76361026:G:CP83R1.000
11:76361026:G:TP83Q1.000
11:76361027:G:AP83S1.000
11:76361027:G:TP83T1.000
11:76361044:A:GL77P1.000
11:76361044:A:TL77H1.000
11:76365876:A:CF62L1.000

dbSNP variants (sampled 300 via entrez): RS1000136620 (11:76380004 T>C), RS1000180032 (11:76363034 T>C), RS1000383682 (11:76357014 C>G), RS1000402271 (11:76379750 G>A), RS1000422203 (11:76372222 G>A,C), RS1000485640 (11:76374689 G>A,T), RS1000597187 (11:76368511 G>A), RS1000682748 (11:76360531 C>A,G,T), RS1000865162 (11:76354904 T>C), RS1001009047 (11:76381104 G>C), RS1001099447 (11:76368753 A>G), RS1001177565 (11:76382926 C>T), RS1001184230 (11:76364318 T>A,G), RS1001276182 (11:76354553 T>C), RS1001290079 (11:76377258 T>A,C)

Disease associations

OMIM: gene MIM:607374 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
syndromic complex neurodevelopmental disorderLimitedAutosomal recessive

Mondo (1): syndromic complex neurodevelopmental disorder (MONDO:0800439)

Orphanet (0):

HPO phenotypes

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

GWAS associations

14 associations (top):

StudyTraitp-value
GCST007095_2Systolic blood pressure4.000000e-08
GCST007095_3Systolic blood pressure2.000000e-07
GCST007096_56Pulse pressure3.000000e-08
GCST007097_104Pulse pressure2.000000e-10
GCST007097_105Pulse pressure7.000000e-11
GCST007099_14Systolic blood pressure4.000000e-09
GCST007564_15Asthma or allergic disease (pleiotropy)3.000000e-28
GCST007994_26Asthma (age of onset)4.000000e-15
GCST007995_34Asthma (childhood onset)2.000000e-39
GCST008916_101Asthma1.000000e-48
GCST008916_84Asthma8.000000e-29
GCST009798_77Asthma4.000000e-35
GCST012298_9Schizophrenia, bipolar disorder or major depressive disorder x sex interaction5.000000e-06
GCST012301_11Schizophrenia, bipolar disorder or major depressive disorder x sex interaction8.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0006335systolic blood pressure
EFO:0005763pulse pressure measurement
EFO:0008343sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression2
Particulate Matteraffects cotreatment, decreases expression, increases abundance2
aristolochic acid Idecreases expression, increases expression1
FR900359increases phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
glycidyl methacrylatedecreases expression1
sodium arsenitedecreases expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
jinfukangdecreases expression1
Sunitinibincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Ethanoldecreases expression, increases abundance, affects cotreatment1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation1
Doxorubicindecreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Methyl Methanesulfonatedecreases expression1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, decreases expression, increases abundance1
Tobacco Smoke Pollutionincreases expression1
Tretinoindecreases expression1
Antirheumatic Agentsincreases expression1
Cadmium Chloridedecreases expression1

Cellosaurus cell lines

12 cell lines: 4 transformed cell line, 4 finite cell line, 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C7LLGM27988Transformed cell lineFemale
CVCL_C7LMGM27990Finite cell lineFemale
CVCL_C7LNGM27991Transformed cell lineFemale
CVCL_C7LPGM27993Finite cell lineFemale
CVCL_C7LQGM27994Transformed cell lineFemale
CVCL_C7LRGM27995Finite cell lineFemale
CVCL_C7LSGM27996Transformed cell lineMale
CVCL_C7LTGM27997Finite cell lineMale
CVCL_D8CEUbigene A-549 THAP12 KOCancer cell lineMale
CVCL_E2HWHAP1 PRKRIR (-) 1Cancer cell lineMale

Clinical trials (associated diseases)

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