HIC2

gene
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Also known as KIAA1020HRG22ZBTB30ZNF907

Summary

HIC2 (HIC ZBTB transcriptional repressor 2, HGNC:18595) is a protein-coding gene on chromosome 22q11.21, encoding Hypermethylated in cancer 2 protein (Q96JB3). Transcriptional repressor.

Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II; regulation of cytokine production; and regulation of immune system process. Located in nucleoplasm and plasma membrane.

Source: NCBI Gene 23119 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 113 total — 2 pathogenic
  • MANE Select transcript: NM_015094

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18595
Approved symbolHIC2
NameHIC ZBTB transcriptional repressor 2
Location22q11.21
Locus typegene with protein product
StatusApproved
AliasesKIAA1020, HRG22, ZBTB30, ZNF907
Ensembl geneENSG00000169635
Ensembl biotypeprotein_coding
OMIM607712
Entrez23119

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000407464, ENST00000407598, ENST00000443632, ENST00000927189, ENST00000927190

RefSeq mRNA: 1 — MANE Select: NM_015094 NM_015094

CCDS: CCDS13789

Canonical transcript exons

ENST00000407464 — 3 exons

ExonStartEnd
ENSE000013725612141737121417560
ENSE000013856602144275921442857
ENSE000015481172144492221451463

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 99.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5431 / max 107.5337, expressed in 1351 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1911844.35101320
2093990.192269

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.20gold quality
oocyteCL:000002398.65gold quality
amniotic fluidUBERON:000017390.45gold quality
endothelial cellCL:000011588.34gold quality
placentaUBERON:000198787.69gold quality
cervix squamous epitheliumUBERON:000692287.43silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.26gold quality
vena cavaUBERON:000408782.11silver quality
Brodmann (1909) area 23UBERON:001355481.61gold quality
parotid glandUBERON:000183181.18gold quality
CA1 field of hippocampusUBERON:000388181.16silver quality
gingival epitheliumUBERON:000194979.97silver quality
pancreatic ductal cellCL:000207979.93silver quality
squamous epitheliumUBERON:000691479.64gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.56gold quality
thymusUBERON:000237079.56silver quality
embryoUBERON:000092279.24gold quality
cerebellar vermisUBERON:000472079.10gold quality
spermCL:000001978.85silver quality
gingivaUBERON:000182878.82gold quality
triceps brachiiUBERON:000150978.49gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451178.44gold quality
male germ cellCL:000001577.96silver quality
oviduct epitheliumUBERON:000480477.24silver quality
esophagus squamous epitheliumUBERON:000692077.01gold quality
epithelium of esophagusUBERON:000197676.98gold quality
middle temporal gyrusUBERON:000277176.97silver quality
gluteal muscleUBERON:000200076.79gold quality
primary visual cortexUBERON:000243676.62gold quality
oral cavityUBERON:000016776.21gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-10018yes153.78
E-ANND-3no2.10

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA0738.1HIC2Factors with multiple dispersed zinc fingers
MA0738.2HIC2Factors with multiple dispersed zinc fingers

JASPAR matrix evidence (PMIDs): PMID:15231840

miRNA regulators (miRDB)

303 targeting HIC2, 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-8485100.0077.574731
HSA-MIR-4262100.0073.263931
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-513A-5P100.0069.772465
HSA-MIR-9-5P100.0072.282361
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4481100.0066.421669
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-450099.9972.722367
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787

Literature-anchored findings (GeneRIF, showing 6)

  • HIC1 and HRG22 define a subgroup of BTB/POZ domains unable to recruit repressing complexes containing a histone deacetylase activity. (PMID:11554746)
  • data suggest that HIC2 haploinsufficiency likely contributes to the cardiac defects seen in distal 22q11 deletion syndrome (PMID:24748541)
  • HIC2 is a pivotal transcriptional activator of SIRT1 (PMID:31127867)
  • HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription. (PMID:35941187)
  • Hypermethylation of HIC2 is a potential prognostic biomarker and tumor suppressor of glioma based on bioinformatics analysis and experiments. (PMID:36650953)
  • let-7 miRNAs repress HIC2 to regulate BCL11A transcription and hemoglobin switching. (PMID:38364109)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriohic2ENSDARG00000100497
mus_musculusHic2ENSMUSG00000050240
rattus_norvegicusHic2ENSRNOG00000051458

Paralogs (36): ZBTB32 (ENSG00000011590), SNAI2 (ENSG00000019549), PRDM1 (ENSG00000057657), PRDM6 (ENSG00000061455), ZNF76 (ENSG00000065029), PATZ1 (ENSG00000100105), MAZ (ENSG00000103495), ZBTB16 (ENSG00000109906), ZNF451 (ENSG00000112200), ZBTB45 (ENSG00000119574), ZNF410 (ENSG00000119725), SNAI1 (ENSG00000124216), ZNF384 (ENSG00000126746), ZBTB1 (ENSG00000126804), VEZF1 (ENSG00000136451), PRDM14 (ENSG00000147596), ZNF276 (ENSG00000158805), ZNF362 (ENSG00000160094), ZNF653 (ENSG00000161914), ZNF281 (ENSG00000162702), ZNF148 (ENSG00000163848), ZNF143 (ENSG00000166478), PRDM10 (ENSG00000170325), ZNF296 (ENSG00000170684), ZNF692 (ENSG00000171163), ZNF575 (ENSG00000176472), HIC1 (ENSG00000177374), ZBTB18 (ENSG00000179456), ZBTB42 (ENSG00000179627), ZBTB20 (ENSG00000181722), ZBTB7C (ENSG00000184828), SNAI3 (ENSG00000185669), ZFP91 (ENSG00000186660), MTF1 (ENSG00000188786), SCRT2 (ENSG00000215397), SCRT1 (ENSG00000261678)

Protein

Protein identifiers

Hypermethylated in cancer 2 proteinQ96JB3 (reviewed: Q96JB3)

Alternative names: HIC1-related gene on chromosome 22 protein, Hic-3, Zinc finger and BTB domain-containing protein 30

All UniProt accessions (1): Q96JB3

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor.

Subunit / interactions. Self-associates. Interacts with HIC1.

Subcellular location. Nucleus.

Tissue specificity. Highest levels in cerebellum.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family. Hic subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q96JB3-11yes
Q96JB3-22

RefSeq proteins (1): NP_055909* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000210BTB/POZ_domDomain
IPR011333SKP1/BTB/POZ_sfHomologous_superfamily
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096, PF00651

UniProt features (35 total): strand 7, modified residue 5, zinc finger region 5, helix 5, region of interest 4, compositionally biased region 3, sequence conflict 2, chain 1, domain 1, splice variant 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
7TXCX-RAY DIFFRACTION3.04

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96JB3-F150.390.03

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 (5): 166, 169, 197, 348, 412

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 260 (showing top): GGGACCA_MIR133A_MIR133B, MORF_MSH3, PEREZ_TP63_TARGETS, ATACCTC_MIR202, MORF_BRCA1, NAGASHIMA_NRG1_SIGNALING_UP, AAAYRNCTG_UNKNOWN, YY1_Q6, AGTCTTA_MIR499, YY1_02, KMCATNNWGGA_UNKNOWN, GOBP_CYTOKINE_PRODUCTION, E4F1_Q6, ACATTCC_MIR1_MIR206, AGGAGTG_MIR483

GO Biological Process (4): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of cytokine production (GO:0001817), regulation of immune system process (GO:0002682), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), plasma membrane (GO:0005886)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
cytokine production1
regulation of gene expression1
regulation of multicellular organismal process1
immune system process1
regulation of biological process1
DNA-templated transcription1
regulation of DNA-templated transcription1
negative regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
nucleic acid binding1
transition metal ion binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
membrane1
cell periphery1

Protein interactions and networks

STRING

606 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HIC2CTBP2P56545649
HIC2CTBP1Q13363625
HIC2CCDC61Q9Y6R9542
HIC2FNDC4Q9H6D8462
HIC2PNPOQ9NVS9434
HIC2PALS1Q8N3R9393
HIC2VSX2P58304383
HIC2AKAP12Q02952375
HIC2MDFICQ9P1T7363
HIC2FOXD4L4Q8WXT5359
HIC2DUSP5Q16690306
HIC2CD200P41217280
HIC2ASXL3Q9C0F0278
HIC2EGR1P18146272
HIC2ZNF862O60290269
HIC2C2CD4CQ8TF44269

IntAct

68 interactions, top by confidence:

ABTypeScore
CTBP1ZEB2psi-mi:“MI:0914”(association)0.800
CTBP1CBX4psi-mi:“MI:0914”(association)0.700
ZBTB8AHIC2psi-mi:“MI:0915”(physical association)0.630
HIC2ZBTB8Apsi-mi:“MI:0915”(physical association)0.630
HIC2EHMT2psi-mi:“MI:0915”(physical association)0.560
CEP70HIC2psi-mi:“MI:0915”(physical association)0.560
ZNF169ZNF316psi-mi:“MI:0914”(association)0.530
E4F1ZBTB24psi-mi:“MI:0914”(association)0.530
PRICKLE3SIAH2psi-mi:“MI:0914”(association)0.530
ZNF460ZNF324psi-mi:“MI:0914”(association)0.530
HIC2MFHAS1psi-mi:“MI:0407”(direct interaction)0.440
CALUHIC2psi-mi:“MI:0915”(physical association)0.400
HIC2psi-mi:“MI:0915”(physical association)0.370
HIC2HIC1psi-mi:“MI:0915”(physical association)0.370
HIC2HIC2psi-mi:“MI:0915”(physical association)0.370
CHIC2psi-mi:“MI:0915”(physical association)0.370
FOXA3DDX39Apsi-mi:“MI:0914”(association)0.350
FOXB1DDX39Apsi-mi:“MI:0914”(association)0.350
FOXJ2TCERG1psi-mi:“MI:0914”(association)0.350
FOXQ1DDX39Apsi-mi:“MI:0914”(association)0.350
JUNpsi-mi:“MI:0914”(association)0.350
JUNTPM3psi-mi:“MI:0914”(association)0.350
NUDCD1TUBAL3psi-mi:“MI:0914”(association)0.350
KLF8psi-mi:“MI:0914”(association)0.350
CUL4ADDX39Apsi-mi:“MI:0914”(association)0.350
CTBP2ZEB2psi-mi:“MI:0914”(association)0.350
MIFBLTP3Bpsi-mi:“MI:0914”(association)0.350
S100BPLEKHG3psi-mi:“MI:0914”(association)0.350
FBLN5ZNF320psi-mi:“MI:0914”(association)0.350

BioGRID (91): HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS), HIC2 (Affinity Capture-MS)

ESM2 similar proteins: A3KNX5, A6NI15, A7YWL5, B0BN13, D3ZLB7, E9Q9M8, O02761, O35906, O70240, O94983, O97930, P01102, P11939, P13346, P23050, P53539, P70298, P70595, P70660, P97303, Q15742, Q28C89, Q3U1J1, Q5EBA3, Q61122, Q61127, Q62722, Q62912, Q62985, Q6NW59, Q80Y50, Q86UZ6, Q8CD60, Q8HZP6, Q90ZL1, Q91ZM2, Q92886, Q96JB3, Q99NA2, Q9BE45

Diamond homologs: A0A1B8YAB1, A1YPR0, B0WWP2, B1H285, B3M9V8, B3NDN0, B4GRJ2, B4HIK1, B4J045, B4L0G9, B4LIG6, B4MXW3, B4PD06, B4QLQ2, C9JR72, D3Z8N4, E0CZ16, G3X9X1, O15062, O88939, O93567, O95365, P28575, P41182, P41183, Q08CL3, Q08DK3, Q13105, Q16RL8, Q2M0J9, Q3UQV5, Q52KB5, Q5EXX3, Q5R7B8, Q5RDY3, Q5TC79, Q5ZI33, Q5ZKD9, Q5ZM39, Q60821

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 84 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
mRNA Splicing612.4×7e-04
Processing of Capped Intron-Containing Pre-mRNA812.4×4e-05
mRNA Polyadenylation711.6×2e-04
mRNA Splicing - Major Pathway1010.3×1e-05
Dengue Virus-Host Interactions86.9×1e-03

GO biological processes:

GO termPartnersFoldFDR
mRNA splicing, via spliceosome78.2×4e-03
RNA splicing77.9×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance99
Likely benign6
Benign1

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
1807715GRCh37/hg19 22q11.21(chr22:20728957-21798907)x1Pathogenic
548980GRCh37/hg19 22q11.21(chr22:18886915-21811991)x1Pathogenic

SpliceAI

1109 predictions. Top by Δscore:

VariantEffectΔscore
22:21417558:GAG:Gdonor_gain1.0000
22:21417561:GTGAG:Gdonor_loss1.0000
22:21417562:T:Gdonor_loss1.0000
22:21417561:G:GGdonor_gain0.9900
22:21444916:CCACA:Cacceptor_loss0.9900
22:21444917:CACA:Cacceptor_loss0.9900
22:21444919:CA:Cacceptor_loss0.9900
22:21444920:AGGT:Aacceptor_gain0.9900
22:21444921:G:GTacceptor_loss0.9900
22:21444921:GGTG:Gacceptor_gain0.9900
22:21417557:CGAG:Cdonor_gain0.9800
22:21417558:GAGG:Gdonor_gain0.9800
22:21434586:T:TAdonor_gain0.9800
22:21434587:A:AAdonor_gain0.9800
22:21444913:T:TAacceptor_gain0.9800
22:21444920:A:AGacceptor_gain0.9800
22:21444921:G:GGacceptor_gain0.9800
22:21417556:ACGAG:Adonor_gain0.9700
22:21433124:G:GTdonor_gain0.9700
22:21444920:AG:Aacceptor_gain0.9700
22:21444920:AGGTG:Aacceptor_gain0.9700
22:21444921:GG:Gacceptor_gain0.9700
22:21444921:GGT:Gacceptor_gain0.9700
22:21444921:GGTGG:Gacceptor_gain0.9700
22:21417559:AG:Adonor_gain0.9600
22:21417560:GG:Gdonor_gain0.9600
22:21418197:G:GTdonor_gain0.9600
22:21433178:A:Gdonor_gain0.9500
22:21442785:G:GTdonor_gain0.9400
22:21417561:GTGA:Gdonor_gain0.9200

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000212880 (22:21420174 T>C), RS1000282375 (22:21444849 C>T), RS1000414449 (22:21420585 G>A), RS1000443024 (22:21444587 G>A,C), RS1000553688 (22:21425492 C>T), RS1000750928 (22:21426583 C>G,T), RS1001080868 (22:21443248 G>T), RS1001188176 (22:21446807 G>A,C), RS1001491009 (22:21443509 T>G), RS1001514882 (22:21450051 C>T), RS1001711176 (22:21451088 G>T), RS1002049132 (22:21446835 C>G), RS1002068018 (22:21450974 G>A), RS1002100528 (22:21450467 G>A), RS1002206269 (22:21437980 C>G,T)

Disease associations

OMIM: gene MIM:607712 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): megacolon (MONDO:0001273)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST000507_6Systemic lupus erythematosus1.000000e-16
GCST000585_2Mean corpuscular volume1.000000e-08

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008531MegacolonC06.405.469.158.701

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
methacrylaldehydeaffects cotreatment, increases expression, increases abundance2
Acetaminophenincreases expression2
Acroleinaffects cotreatment, increases expression, increases abundance2
Benzo(a)pyreneincreases methylation, affects methylation2
Ozoneaffects cotreatment, increases expression, increases abundance2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
dicrotophosincreases expression1
methylmercuric chlorideincreases expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
pirinixic acidaffects binding, increases activity, increases expression1
sulforaphaneincreases expression1
sodium arsenitedecreases expression1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediaminedecreases expression1
CGP 52608affects binding, increases reaction1
licochalcone Bincreases expression1
jinfukangaffects cotreatment, increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Sunitinibincreases expression1
Vorinostatdecreases expression1
Air Pollutantsaffects cotreatment, increases abundance, increases expression1
Arsenicaffects methylation1
Atrazinedecreases expression1
Cadmiumincreases abundance, increases expression1
Caffeineincreases phosphorylation1
Cisplatinaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Fluorouracilaffects response to substance1
Formaldehydedecreases expression1
Tobacco Smoke Pollutionincreases expression1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

CellosaurusNameCategorySex
CVCL_A2Q5SEES3-1V human HIC2, clone1Embryonic stem cellMale
CVCL_A2Q6SEES3-1V human HIC2, clone2Embryonic stem cellMale
CVCL_A2Q7SEES3-1V human HIC2, clone3Embryonic stem cellMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04340856Not specifiedCOMPLETEDRetrospective, Uncontrolled Cohort Study on the Therapy of Chronic Megalon
NCT07470892Not specifiedNOT_YET_RECRUITINGPreoperative Fish Oil PN and Prognosis After Constipation Surgery
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): megacolon