INTS12

gene
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Also known as SBBI22INT12

Summary

INTS12 (integrator complex subunit 12, HGNC:25067) is a protein-coding gene on chromosome 4q24, encoding Integrator complex subunit 12 (Q96CB8). Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes. It is a selective cancer dependency (DepMap: 43.4% of cell lines).

INTS12 is a subunit of the Integrator complex, which associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690) (Baillat et al., 2005 [PubMed 16239144]).

Source: NCBI Gene 57117 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 53 total
  • Cancer dependency (DepMap): dependent in 43.4% of screened cell lines
  • MANE Select transcript: NM_020395

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25067
Approved symbolINTS12
Nameintegrator complex subunit 12
Location4q24
Locus typegene with protein product
StatusApproved
AliasesSBBI22, INT12
Ensembl geneENSG00000138785
Ensembl biotypeprotein_coding
OMIM611355
Entrez57117

Gene structure

Transcript identifiers

Ensembl transcripts: 41 — 40 protein_coding, 1 retained_intron

ENST00000340139, ENST00000394735, ENST00000416543, ENST00000420368, ENST00000433009, ENST00000451321, ENST00000493425, ENST00000503746, ENST00000510876, ENST00000515819, ENST00000891042, ENST00000891043, ENST00000891044, ENST00000891045, ENST00000891046, ENST00000891047, ENST00000891048, ENST00000891049, ENST00000891050, ENST00000891051, ENST00000891052, ENST00000891053, ENST00000891054, ENST00000891055, ENST00000891056, ENST00000891057, ENST00000891058, ENST00000891059, ENST00000891060, ENST00000891061, ENST00000891062, ENST00000925833, ENST00000925834, ENST00000925835, ENST00000925836, ENST00000925837, ENST00000925838, ENST00000925839, ENST00000947226, ENST00000947227, ENST00000947228

RefSeq mRNA: 2 — MANE Select: NM_020395 NM_001142471, NM_020395

CCDS: CCDS3671

Canonical transcript exons

ENST00000340139 — 8 exons

ExonStartEnd
ENSE00000735874105695516105695668
ENSE00000735877105693299105693486
ENSE00000735885105691976105692135
ENSE00000735915105686692105686838
ENSE00001387082105699850105700014
ENSE00001519403105682627105683317
ENSE00001519414105703648105703809
ENSE00002075774105708638105708689

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 91.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.1477 / max 88.6392, expressed in 1771 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
534747.99211771
534760.155693

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047391.98gold quality
oocyteCL:000002391.35gold quality
cortical plateUBERON:000534391.14gold quality
secondary oocyteCL:000065591.12gold quality
heart right ventricleUBERON:000208090.15gold quality
islet of LangerhansUBERON:000000689.80gold quality
gastrocnemiusUBERON:000138889.07gold quality
jejunal mucosaUBERON:000039988.96gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.88gold quality
muscle of legUBERON:000138388.79gold quality
triceps brachiiUBERON:000150988.79gold quality
ganglionic eminenceUBERON:000402388.77gold quality
hindlimb stylopod muscleUBERON:000425288.73gold quality
biceps brachiiUBERON:000150788.62gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450288.58gold quality
muscle organUBERON:000163088.10gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451188.02gold quality
calcaneal tendonUBERON:000370187.68gold quality
rectumUBERON:000105287.48gold quality
heart left ventricleUBERON:000208487.40gold quality
jejunumUBERON:000211587.40gold quality
cardiac ventricleUBERON:000208287.36gold quality
myocardiumUBERON:000234987.36gold quality
thoracic aortaUBERON:000151587.32gold quality
left lobe of thyroid glandUBERON:000112087.30gold quality
ascending aortaUBERON:000149687.23gold quality
right lobe of thyroid glandUBERON:000111987.15gold quality
aortaUBERON:000094787.08gold quality
pancreasUBERON:000126487.07gold quality
descending thoracic aortaUBERON:000234587.07gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-119yes26.89
E-ANND-3yes8.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting INTS12, 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-MIR-808799.9069.551351
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-451799.7669.191867
HSA-MIR-154-3P99.5070.05831
HSA-MIR-487A-3P99.5069.95840
HSA-MIR-608399.4768.732393
HSA-MIR-568399.3668.592083
HSA-MIR-223-5P99.2468.821206
HSA-MIR-10399-5P99.1769.872610
HSA-MIR-6504-3P99.1769.312891
HSA-MIR-4477A98.8369.752952
HSA-MIR-1211697.9468.91595

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 43.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • In fixed sections of human lung tissue, GSTCD protein expression was ubiquitous, whereas INTS12 expression was predominantly in epithelial cells and pneumocytes. (PMID:24058608)
  • INTS12 activities on a genome-wide scale (PMID:28335732)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioints12ENSDARG00000091678
mus_musculusInts12ENSMUSG00000028016
rattus_norvegicusInts12ENSRNOG00000011844
drosophila_melanogasterIntS12FBGN0039459
caenorhabditis_elegansWBGENE00018778
caenorhabditis_elegansWBGENE00020716

Protein

Protein identifiers

Integrator complex subunit 12Q96CB8 (reviewed: Q96CB8)

Alternative names: PHD finger protein 22

All UniProt accessions (7): Q96CB8, A0A1B0GX90, C9J0M6, C9JDP3, D6R9W3, D6R9Y5, E9PGI3

UniProt curated annotations — full annotation on UniProt →

Function. Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes. The integrator complex provides a quality checkpoint during transcription elongation by driving premature transcription termination of transcripts that are unfavorably configured for transcriptional elongation: the complex terminates transcription by (1) catalyzing dephosphorylation of the C-terminal domain (CTD) of Pol II subunit POLR2A/RPB1 and SUPT5H/SPT5, (2) degrading the exiting nascent RNA transcript via endonuclease activity and (3) promoting the release of Pol II from bound DNA. The integrator complex is also involved in terminating the synthesis of non-coding Pol II transcripts, such as enhancer RNAs (eRNAs), small nuclear RNAs (snRNAs), telomerase RNAs and long non-coding RNAs (lncRNAs). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the integrator complex.

Subunit / interactions. Component of the Integrator complex, composed of core subunits INTS1, INTS2, INTS3, INTS4, INTS5, INTS6, INTS7, INTS8, INTS9/RC74, INTS10, INTS11/CPSF3L, INTS12, INTS13, INTS14 and INTS15. The core complex associates with protein phosphatase 2A subunits PPP2CA and PPP2R1A, to form the Integrator-PP2A (INTAC) complex.

Subcellular location. Nucleus.

Post-translational modifications. Dephosphorylated at Ser-128 by the PNUTS-PP1 complex, promoting RNA polymerase II transcription pause-release.

Similarity. Belongs to the Integrator subunit 12 family.

RefSeq proteins (2): NP_001135943, NP_065128* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001965Znf_PHDDomain
IPR011011Znf_FYVE_PHDHomologous_superfamily
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR019786Zinc_finger_PHD-type_CSConserved_site
IPR019787Znf_PHD-fingerDomain
IPR039054Int12_PHDDomain
IPR051776Integrator_subunit_12Family

Pfam: PF00628

UniProt features (14 total): compositionally biased region 6, cross-link 2, region of interest 2, chain 1, zinc finger region 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96CB8-F158.950.14

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 (3): 128, 68, 254

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-6807505RNA polymerase II transcribes snRNA genes
R-HSA-73857RNA Polymerase II Transcription
R-HSA-74160Gene expression (Transcription)

MSigDB gene sets: 199 (showing top): chr4q24, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP, MARTINEZ_RB1_TARGETS_UP, GOBP_RNA_SURVEILLANCE, BRN2_01, E4F1_Q6, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_TRANSCRIPTION_INITIATION_AT_RNA_POLYMERASE_II_PROMOTER, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_SNRNA_PROCESSING, MARTINEZ_RB1_AND_TP53_TARGETS_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, TAANNYSGCG_UNKNOWN, GOBP_REGULATION_OF_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION

GO Biological Process (4): snRNA processing (GO:0016180), regulation of transcription elongation by RNA polymerase II (GO:0034243), snRNA 3’-end processing (GO:0034472), RNA polymerase II transcription initiation surveillance (GO:0160240)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), integrator complex (GO:0032039), INTAC complex (GO:0160232)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
RNA Polymerase II Transcription1
Gene expression (Transcription)1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nuclear protein-containing complex2
RNA processing1
snRNA metabolic process1
transcription elongation by RNA polymerase II1
regulation of DNA-templated transcription elongation1
snRNA processing1
RNA 3’-end processing1
transcription initiation at RNA polymerase II promoter1
nuclear RNA surveillance1
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
integrator complex1

Protein interactions and networks

STRING

1244 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
INTS12INTS11Q5TA45976
INTS12INTS1Q8N201884
INTS12INTS7Q9NVH2879
INTS12INTS9Q9NV88852
INTS12INTS5Q6P9B9811
INTS12INTS10Q9NVR2811
INTS12INTS4Q96HW7810
INTS12GSTCDQ8NEC7766
INTS12INTS8Q75QN2755
INTS12POLR2AP24928713
INTS12INTS6Q9UL03694
INTS12INTS3Q68E01667
INTS12INTS14Q96SY0667
INTS12INTS2Q9H0H0665
INTS12INTS13Q9NVM9616

IntAct

173 interactions, top by confidence:

ABTypeScore
PPP2R1ASTRNpsi-mi:“MI:0914”(association)0.880
GATAD2ACDK2AP1psi-mi:“MI:0914”(association)0.730
INTS12INTS1psi-mi:“MI:0915”(physical association)0.690
POLR2CSUPT5Hpsi-mi:“MI:0914”(association)0.640
ILVBLCOG7psi-mi:“MI:0914”(association)0.640
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
HAPSTR1INTS12psi-mi:“MI:0915”(physical association)0.560
FAM9AINTS12psi-mi:“MI:0915”(physical association)0.560
MAS1POTEFpsi-mi:“MI:0914”(association)0.530
ST8SIA1POTEFpsi-mi:“MI:0914”(association)0.530
APLNRMETTL15psi-mi:“MI:0914”(association)0.530
IL13RA2METTL15psi-mi:“MI:0914”(association)0.530
FZD10NRP1psi-mi:“MI:0914”(association)0.530
POLR2ISUPT5Hpsi-mi:“MI:0914”(association)0.530
POLR2JSUPT5Hpsi-mi:“MI:0914”(association)0.530
SUPT5HPOLR2Dpsi-mi:“MI:0914”(association)0.530
CXCR4TMEM120Bpsi-mi:“MI:0914”(association)0.530
ILVBLSLC33A1psi-mi:“MI:0914”(association)0.530
INTS12GTF2IRD1psi-mi:“MI:0915”(physical association)0.510
GTF2IRD1INTS12psi-mi:“MI:0915”(physical association)0.510
TAS2R7ATP2B4psi-mi:“MI:0914”(association)0.500
PPP2CASMCO3psi-mi:“MI:0914”(association)0.420
INTS12CALUpsi-mi:“MI:0915”(physical association)0.400
ECE1INTS12psi-mi:“MI:0915”(physical association)0.370
Ppp2r1aCCHCR1psi-mi:“MI:0914”(association)0.350

BioGRID (156): INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS1 (Co-fractionation), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), INTS12 (Affinity Capture-MS)

ESM2 similar proteins: A1Z9E2, B0R0I6, B5DE69, G5ED89, O94842, P25425, P32519, P34333, P34447, Q02086, Q08CM4, Q09XV5, Q0IHV2, Q0P5K4, Q0V9U1, Q15723, Q28BL7, Q3TUF7, Q571G4, Q5E9U0, Q5F3U0, Q5R6A9, Q5RBN8, Q5RCV7, Q60775, Q641Z1, Q6DJM6, Q6IQU7, Q6MZP7, Q7Z589, Q7ZUV7, Q7ZX03, Q86NP2, Q8AYC1, Q8BIH0, Q8BMB0, Q8BU11, Q8CHI8, Q8IRW8, Q8WNV2

Diamond homologs: O43189, Q02395, Q0V9U1, Q24459, Q32LL5, Q5R7T9, Q5RCV7, Q5T6S3, Q68FR3, Q6DJM6, Q6IQU7, Q8WNV2, Q96CB8, Q9CXG9, Q9D168, Q9VBB3, Q9Y483, Q9Z1B8

SIGNOR signaling

1 interactions.

AEffectBMechanism
INTS12“form complex”“Integrator complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 212 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
FGFR2 mutant receptor activation841.1×3e-10
Abortive elongation of HIV-1 transcript in the absence of Tat1033.5×3e-11
Signaling by FGFR2 IIIa TM832.5×2e-09
MicroRNA (miRNA) biogenesis927.8×6e-10
Signaling by FGFR21027.6×1e-10
Pausing and recovery of Tat-mediated HIV elongation1127.4×3e-11
Tat-mediated HIV elongation arrest and recovery1127.4×3e-11
Activation of HOX genes during differentiation926.7×9e-10

GO biological processes:

GO termPartnersFoldFDR
RNA polymerase II transcription initiation surveillance522.6×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3464 predictions. Top by Δscore:

VariantEffectΔscore
4:105686687:TATAC:Tdonor_loss1.0000
4:105686688:ATACC:Adonor_loss1.0000
4:105686689:TACC:Tdonor_loss1.0000
4:105686690:ACCTT:Adonor_loss1.0000
4:105686837:GCCT:Gacceptor_loss1.0000
4:105686850:A:Tacceptor_gain1.0000
4:105691975:CCATT:Cdonor_gain1.0000
4:105693294:CTTA:Cdonor_loss1.0000
4:105693295:TTA:Tdonor_loss1.0000
4:105693297:A:ACdonor_gain1.0000
4:105693297:A:Cdonor_loss1.0000
4:105693297:AC:Adonor_gain1.0000
4:105693298:C:CCdonor_gain1.0000
4:105693298:CC:Cdonor_gain1.0000
4:105693298:CCT:Cdonor_gain1.0000
4:105693298:CCTA:Cdonor_gain1.0000
4:105693482:TTCAT:Tacceptor_gain1.0000
4:105693483:TCAT:Tacceptor_gain1.0000
4:105693484:CAT:Cacceptor_gain1.0000
4:105693484:CATC:Cacceptor_gain1.0000
4:105693485:AT:Aacceptor_gain1.0000
4:105693487:C:CCacceptor_gain1.0000
4:105693488:T:Gacceptor_loss1.0000
4:105693489:A:Cacceptor_gain1.0000
4:105693504:C:CTacceptor_gain1.0000
4:105693505:A:Tacceptor_gain1.0000
4:105695510:TCTTA:Tdonor_loss1.0000
4:105695512:TTA:Tdonor_loss1.0000
4:105695514:A:ACdonor_gain1.0000
4:105695515:C:CGdonor_gain1.0000

AlphaMissense

2996 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:105682779:A:GL448S0.998
4:105691998:C:GC212S0.998
4:105691999:A:GC212R0.998
4:105691999:A:TC212S0.998
4:105692007:C:TC209Y0.998
4:105692008:A:GC209R0.998
4:105699905:A:GL34P0.998
4:105699914:A:GL31P0.998
4:105699968:A:GF13S0.998
4:105692006:A:CC209W0.997
4:105692007:C:GC209S0.997
4:105692008:A:TC209S0.997
4:105692014:A:GW207R0.997
4:105692014:A:TW207R0.997
4:105692089:A:GC182R0.997
4:105692098:A:GC179R0.997
4:105693312:A:GC162R0.997
4:105699956:A:GL17P0.997
4:105691997:A:CC212W0.996
4:105692074:G:CH187D0.996
4:105692088:C:GC182S0.996
4:105692089:A:TC182S0.996
4:105692097:C:GC179S0.996
4:105692098:A:TC179S0.996
4:105693303:A:GC165R0.996
4:105693310:G:CC162W0.996
4:105693311:C:TC162Y0.996
4:105699959:G:TA16E0.996
4:105682766:C:AK452N0.995
4:105682766:C:GK452N0.995

dbSNP variants (sampled 300 via entrez): RS1000025192 (4:105701632 A>G), RS1000169514 (4:105694973 G>A), RS1000263456 (4:105709236 T>C), RS1000296049 (4:105708970 C>G), RS1000304162 (4:105708087 T>G), RS1000340908 (4:105687537 T>C), RS1000494007 (4:105703180 C>A,T), RS1000509394 (4:105683598 A>C), RS1000539314 (4:105703488 T>C), RS1000692093 (4:105691366 A>C), RS10008158 (4:105683066 G>A), RS1000820461 (4:105697902 T>C), RS1000844087 (4:105682353 A>G), RS1000873081 (4:105698118 A>G), RS1001506339 (4:105688050 C>G)

Disease associations

OMIM: gene MIM:611355 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST000542_6Pulmonary function5.000000e-17
GCST001784_49Pulmonary function (smoking interaction)1.000000e-16
GCST002165_9Lung function (FEV1)1.000000e-07
GCST003262_462Post bronchodilator FEV15.000000e-06
GCST003262_463Post bronchodilator FEV14.000000e-06
GCST003262_888Post bronchodilator FEV15.000000e-06
GCST003542_180Night sleep phenotypes4.000000e-06
GCST004554_1Weight3.000000e-08
GCST007692_16Chronic obstructive pulmonary disease5.000000e-15
GCST009798_66Asthma4.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0003892pulmonary function measurement
EFO:0004314forced expiratory volume
EFO:0004338body weight

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
FR900359affects phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
coumarinincreases phosphorylation1
CGP 52608increases reaction, affects binding1
abrineincreases expression1
Air Pollutantsincreases abundance, increases expression1
Benzo(a)pyreneaffects methylation1
Caffeineincreases phosphorylation1
Phenobarbitalaffects expression1
Tetrachlorodibenzodioxindecreases expression1
Tretinoindecreases expression1
Cyclosporineincreases expression1
Aflatoxin B1increases expression1
Particulate Matterincreases expression, increases abundance1

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.