ZHX1

gene
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Summary

ZHX1 (zinc fingers and homeoboxes 1, HGNC:12871) is a protein-coding gene on chromosome 8q24.13, encoding Zinc fingers and homeoboxes protein 1 (Q9UKY1). Acts as a transcriptional repressor.

The members of the zinc fingers and homeoboxes gene family are nuclear homodimeric transcriptional repressors that interact with the A subunit of nuclear factor-Y (NF-YA) and contain two C2H2-type zinc fingers and five homeobox DNA-binding domains. This gene encodes member 1 of this gene family. In addition to forming homodimers, this protein heterodimerizes with members 2 and 3 of the zinc fingers and homeoboxes family. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream chromosome 8 open reading frame 76 (C8orf76) gene.

Source: NCBI Gene 11244 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 101 total
  • MANE Select transcript: NM_007222

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12871
Approved symbolZHX1
Namezinc fingers and homeoboxes 1
Location8q24.13
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000165156
Ensembl biotypeprotein_coding
OMIM604764
Entrez11244

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 22 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000297857, ENST00000395571, ENST00000480132, ENST00000517516, ENST00000522595, ENST00000522655, ENST00000524267, ENST00000602651, ENST00000863173, ENST00000863174, ENST00000863175, ENST00000863176, ENST00000863177, ENST00000863178, ENST00000863179, ENST00000863180, ENST00000863181, ENST00000863182, ENST00000863183, ENST00000863184, ENST00000863185, ENST00000956169, ENST00000956170, ENST00000956171, ENST00000956172, ENST00000956173

RefSeq mRNA: 2 — MANE Select: NM_007222 NM_001017926, NM_007222

CCDS: CCDS6342

Canonical transcript exons

ENST00000395571 — 4 exons

ExonStartEnd
ENSE00001090837123253322123256171
ENSE00001522127123274217123274286
ENSE00002138192123248456123250320
ENSE00002184971123267273123267386

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 96.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.4068 / max 61.1321, expressed in 1560 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
947118.97411665
947153.88271425
947130.9118522
947140.3855189
947120.226888

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
upper arm skinUBERON:000426396.18gold quality
secondary oocyteCL:000065596.17gold quality
oocyteCL:000002395.97gold quality
kidney epitheliumUBERON:000481995.85gold quality
calcaneal tendonUBERON:000370195.59gold quality
epithelium of mammary glandUBERON:000324495.56gold quality
mammary ductUBERON:000176595.55gold quality
substantia nigra pars reticulataUBERON:000196695.50gold quality
cerebellar vermisUBERON:000472095.41gold quality
medial globus pallidusUBERON:000247795.20gold quality
medulla oblongataUBERON:000189695.09gold quality
globus pallidusUBERON:000187595.05gold quality
superior vestibular nucleusUBERON:000722795.05gold quality
penisUBERON:000098995.00gold quality
lateral globus pallidusUBERON:000247694.98gold quality
corpus callosumUBERON:000233694.70gold quality
pigmented layer of retinaUBERON:000178294.56gold quality
retinaUBERON:000096694.53gold quality
substantia nigra pars compactaUBERON:000196594.40gold quality
dorsal plus ventral thalamusUBERON:000189794.39gold quality
subthalamic nucleusUBERON:000190694.32gold quality
parotid glandUBERON:000183194.31gold quality
pharyngeal mucosaUBERON:000035594.27gold quality
trigeminal ganglionUBERON:000167594.25gold quality
ganglionic eminenceUBERON:000402394.25gold quality
embryoUBERON:000092294.24gold quality
ventral tegmental areaUBERON:000269194.01gold quality
gingival epitheliumUBERON:000194993.72gold quality
Brodmann (1909) area 23UBERON:001355493.66gold quality
lateral nuclear group of thalamusUBERON:000273693.56gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.06
E-GEOD-106540no448.80
E-MTAB-7606no199.48

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
ZHX1

Upstream regulators (CollecTRI, top): ETV4, YY1, ZHX1

miRNA regulators (miRDB)

185 targeting ZHX1, 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-513A-5P100.0069.772465
HSA-MIR-3163100.0077.238605
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-5692A100.0074.406850
HSA-MIR-574-5P100.0066.01989
HSA-MIR-428299.9975.366408
HSA-MIR-186-5P99.9970.833707
HSA-MIR-318599.9968.121959
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-1213699.9872.815713
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-60799.9773.625593
HSA-MIR-9-3P99.9670.882068
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-365899.9673.874379
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-96-5P99.9572.802140
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505

Literature-anchored findings (GeneRIF, showing 12)

  • This study characterized features of ZHX-1 involved in nuclear localization, dimerization, and transcriptional activity, and mapped these domains. (PMID:12237128)
  • a search of ZHX1-interacting proteins using a yeast two-hybrid system (PMID:12659632)
  • ZHX proteins 1, 2 and 3 are major transcriptional mediators of podocyte disease (PMID:17056598)
  • ZHX1 enhanced the transcriptional repression mediated by DNMT3B when DNMT3B is directly targeted to DNA. These results showed for the first the direct linkage between DNMT and zinc-fingers homeoboxes protein, leading to enhanced gene silencing by DNMT3B (PMID:17303076)
  • structure of the tandem zinc-finger region of human ZHX1 (PMID:19348505)
  • Study showed that ZHX1 is SUMOylated by Ubc9 with SUMO1 at the sites K159, K454, and K626 and that the SUMOylation of ZHX1 regulated the stability, ubiquitination and transcriptional activity of ZHX1. (PMID:23686912)
  • Low expression of ZHX1 may be responsible for hepatocarcinogenesis. (PMID:24064680)
  • High-quality solution NMR structures of three homeodomains from human proteins ALX4, ZHX1 and CASP8AP2 were solved. (PMID:24941917)
  • miR-199a-3p may function as a novel tumor promoter in gastric cancer and its oncogenic activity may involve the direct targeting and inhibition of ZHX1 (PMID:25448600)
  • ZHX1 was found to play essential roles in the proliferation, migration, and invasion of cholangiocarcinoma cells, and its effect on the proliferation was mediated partially through EGR1. (PMID:27835650)
  • ZHX1 expression is correlated with renal cell carcinoma progression and poor survival. (PMID:28152006)
  • together, this study demonstrates that ZHX1 plays crucial roles in the progression of glioblastoma, and its findings suggest that ZHX1 be viewed as a potential prognostic maker and therapeutic target of glioblastoma. (PMID:28351300)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZhx1ENSMUSG00000022361
rattus_norvegicusZhx1ENSRNOG00000006412

Paralogs (3): ZHX3 (ENSG00000174306), ZHX2 (ENSG00000178764), HOMEZ (ENSG00000290292)

Protein

Protein identifiers

Zinc fingers and homeoboxes protein 1Q9UKY1 (reviewed: Q9UKY1)

All UniProt accessions (2): Q9UKY1, U3KPX4

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a transcriptional repressor. Increases DNMT3B-mediated repressive transcriptional activity when DNMT3B is tethered to DNA. May link molecule between DNMT3B and other co-repressor proteins.

Subunit / interactions. Forms homodimers. Heterodimer (via HD1 domain) with ZHX2 (via HD1 domain). Also forms a heterodimer with ZHX3 which is a prerequisite for repressor activity. Interacts with ATF7IP and NFYA. Interacts (via homeobox domains) with DNMT3B (via PWWP domain).

Subcellular location. Nucleus.

Tissue specificity. Ubiquitously expressed. Expressed in podocytes.

Similarity. Belongs to the ZHX family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9UKY1-11yes
Q96EF9-12, ZHX1-C8orf76

RefSeq proteins (2): NP_001017926, NP_009153* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR013087Znf_C2H2_typeDomain
IPR024578Homez_homeobox_domDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR041057ZHX_Znf_C2H2Domain

Pfam: PF00046, PF11569, PF18387

UniProt features (60 total): helix 13, region of interest 9, modified residue 7, strand 7, compositionally biased region 5, cross-link 5, DNA-binding region 5, turn 4, zinc finger region 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
3NARX-RAY DIFFRACTION2.6
2ECBSOLUTION NMR
2GHFSOLUTION NMR
2LY9SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UKY1-F162.100.24

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 (12): 36, 45, 47, 48, 202, 648, 774, 159, 441, 454, 485, 629

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 145 (showing top): TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GCM_ZNF198, GCM_PPM1D, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, ATTCTTT_MIR186, TAATGTG_MIR323, CUI_TCF21_TARGETS_2_DN, HOXA4_Q2, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, GOMF_PROTEIN_HETERODIMERIZATION_ACTIVITY, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, HAMAI_APOPTOSIS_VIA_TRAIL_UP, GCTCTTG_MIR335

GO Biological Process (4): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), cell differentiation (GO:0030154), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (7): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), protein heterodimerization activity (GO:0046982), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription3
regulation of transcription by RNA polymerase II2
transcription by RNA polymerase II2
cellular anatomical structure2
negative regulation of DNA-templated transcription1
cellular developmental process1
DNA-templated transcription1
negative regulation of RNA biosynthetic process1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
nucleic acid binding1
transcription cis-regulatory region binding1
transcription regulator activity1
transition metal ion binding1
protein dimerization activity1
binding1
cation binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1

Protein interactions and networks

STRING

644 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZHX1NFYAP23511938
ZHX1DNMT3BQ9UBC3721
ZHX1NFYCQ13952713
ZHX1NFYBP25208614
ZHX1ZMYND11Q15326577
ZHX1HOXC8P31273568
ZHX1CDC25CP30307488
ZHX1MYCP01106473
ZHX1MED21Q13503450
ZHX1USF2Q15853439
ZHX1CREB1P16220393
ZHX1KPNA2P52292390
ZHX1HOMEZQ8IX15377
ZHX1ATF6BQ99941375
ZHX1DHX35Q9H5Z1354

IntAct

119 interactions, top by confidence:

ABTypeScore
RIOK1PRMT5psi-mi:“MI:0914”(association)0.710
ATXN1ZHX1psi-mi:“MI:0915”(physical association)0.700
NFICNFIBpsi-mi:“MI:2364”(proximity)0.690
ZHX1DNMT3Bpsi-mi:“MI:0915”(physical association)0.610
ZHX1DNMT3Bpsi-mi:“MI:0403”(colocalization)0.610
DNMT3BZHX1psi-mi:“MI:0407”(direct interaction)0.610
ZHX1DNMT3Bpsi-mi:“MI:0407”(direct interaction)0.610
ZHX1ZHX2psi-mi:“MI:0915”(physical association)0.590
ZMYND11ZHX1psi-mi:“MI:0407”(direct interaction)0.590
ZHX1ZMYND11psi-mi:“MI:0915”(physical association)0.590
YY1YY2psi-mi:“MI:0914”(association)0.570
HTTZHX1psi-mi:“MI:0915”(physical association)0.560
WDR83SH2B2psi-mi:“MI:0914”(association)0.530
UBE2IZHX1psi-mi:“MI:0915”(physical association)0.370

BioGRID (134): UBE2I (Two-hybrid), ZHX1 (Affinity Capture-Western), UBE2I (Affinity Capture-Western), ZHX1 (Affinity Capture-MS), ZHX1 (Affinity Capture-MS), ZHX2 (Affinity Capture-MS), ZHX1 (Affinity Capture-MS), ZHX1 (Affinity Capture-MS), ZHX1 (Proximity Label-MS), ZHX1 (Two-hybrid), ZMYND11 (Two-hybrid), ATXN1 (Two-hybrid), EFNA2 (Two-hybrid), ELL (Two-hybrid), ZHX1 (Two-hybrid)

ESM2 similar proteins: A1YF22, A1YG99, A2T771, A2T7S4, B3DJM5, D3ZKB9, H2L008, O42410, O73590, P34303, P70121, Q03112, Q15652, Q15723, Q19418, Q21502, Q24478, Q2HNT1, Q2HNT2, Q2TB10, Q3UG20, Q58F21, Q5DTH5, Q5R7F2, Q5RCU4, Q61SK8, Q63HK5, Q66J63, Q69ZW3, Q6GN21, Q6P2L6, Q6ZSZ6, Q80VX4, Q86MI0, Q86T24, Q86UP3, Q8BN78, Q8C0C0, Q8CGV9, Q8IZD2

Diamond homologs: A1YF22, A1YG99, A2T771, A2T7S4, P70121, Q5R7F2, Q80VX4, Q80Z36, Q8C0C0, Q8C0Q2, Q8IX15, Q8R515, Q9H4I2, Q9UKY1, Q9Y6X8, Q80W88, Q8K3E9, Q61321, Q9UIU6

SIGNOR signaling

4 interactions.

AEffectBMechanism
ZHX1“down-regulates activity”ZMYND11binding
UBE2I“up-regulates quantity by stabilization”ZHX1sumoylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 100 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
Regulation of TP53 Activity through Acetylation530.4×3e-04
KEAP1-NFE2L2 pathway711.2×8e-04

GO biological processes:

GO termPartnersFoldFDR
cellular response to retinoic acid512.7×4e-03
chromatin remodeling107.9×8e-05
transcription by RNA polymerase II86.1×4e-03
positive regulation of apoptotic process95.5×3e-03
positive regulation of gene expression104.2×8e-03
negative regulation of apoptotic process114.2×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance96
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

786 predictions. Top by Δscore:

VariantEffectΔscore
8:123250318:CAG:Cacceptor_gain1.0000
8:123250321:C:CCacceptor_gain1.0000
8:123267271:A:ACdonor_gain1.0000
8:123267272:C:CCdonor_gain1.0000
8:123267274:TGCC:Tdonor_gain1.0000
8:123267284:T:TAdonor_gain1.0000
8:123269030:T:Adonor_gain1.0000
8:123250138:T:TAdonor_gain0.9900
8:123250138:TCC:Tdonor_gain0.9900
8:123250320:GC:Gacceptor_loss0.9900
8:123267273:TTGC:Tdonor_gain0.9900
8:123274125:T:Adonor_gain0.9900
8:123250122:T:Cdonor_gain0.9800
8:123250127:A:Cdonor_gain0.9800
8:123250316:GGCAG:Gacceptor_gain0.9800
8:123250317:GCAG:Gacceptor_gain0.9800
8:123250318:CAGC:Cacceptor_gain0.9800
8:123250319:AG:Aacceptor_gain0.9800
8:123253320:A:ACdonor_gain0.9800
8:123253321:C:CCdonor_gain0.9800
8:123267290:G:Cdonor_gain0.9800
8:123267387:C:CCacceptor_gain0.9800
8:123250137:TTC:Tdonor_gain0.9700
8:123253321:CATTT:Cdonor_gain0.9700
8:123267272:CTTG:Cdonor_gain0.9700
8:123250159:A:Cdonor_gain0.9600
8:123250319:A:Tacceptor_gain0.9600
8:123253321:CATT:Cdonor_gain0.9600
8:123267275:G:Adonor_gain0.9600
8:123267386:CCTA:Cacceptor_loss0.9600

AlphaMissense

5783 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:123253494:A:GF818S1.000
8:123253498:A:GW817R1.000
8:123253498:A:TW817R1.000
8:123253506:A:TV814D1.000
8:123253539:A:GL803P1.000
8:123253548:A:GL800P1.000
8:123253593:A:GL785P1.000
8:123253593:A:TL785H1.000
8:123253781:C:AW722C1.000
8:123253781:C:GW722C1.000
8:123253783:A:GW722R1.000
8:123253783:A:TW722R1.000
8:123253812:C:GR712P1.000
8:123253813:G:TR712S1.000
8:123253823:A:CF708L1.000
8:123253823:A:TF708L1.000
8:123253824:A:GF708S1.000
8:123253825:A:GF708L1.000
8:123253828:A:GW707R1.000
8:123253828:A:TW707R1.000
8:123253893:G:TP685Q1.000
8:123253910:A:CF679L1.000
8:123253910:A:TF679L1.000
8:123253912:A:GF679L1.000
8:123253919:C:AK676N1.000
8:123253919:C:GK676N1.000
8:123253923:A:GL675P1.000
8:123253923:A:TL675H1.000
8:123254127:A:GL607P1.000
8:123254399:C:AR516S1.000

dbSNP variants (sampled 300 via entrez): RS1000020950 (8:123272139 C>T), RS1000074255 (8:123258737 T>C), RS1000194978 (8:123269329 C>T), RS1000208535 (8:123276385 G>A,T), RS1000245260 (8:123273453 G>A), RS1000351038 (8:123275735 C>T), RS1000461655 (8:123251151 G>T), RS1000640549 (8:123267943 G>C), RS1000664087 (8:123276131 T>C), RS1000691396 (8:123267626 C>T), RS1000794212 (8:123258439 G>A,C), RS1000887800 (8:123258124 C>A,T), RS1000935091 (8:123261563 G>A), RS1001007443 (8:123264714 C>A,G,T), RS1001039128 (8:123254250 T>A)

Disease associations

OMIM: gene MIM:604764 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, increases expression3
sodium arsenitedecreases expression, increases expression2
entinostatdecreases expression, affects cotreatment2
Tretinoindecreases expression, increases expression2
p-Chloromercuribenzoic Aciddecreases expression, affects cotreatment2
FR900359affects phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
beta-lapachonedecreases expression, increases expression1
methylparabendecreases expression1
coumarinincreases phosphorylation1
perfluorooctane sulfonic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Diazinonincreases methylation1
Estradiolincreases expression1
Formaldehydeincreases expression1
Methyl Methanesulfonateincreases expression1
Tetrachlorodibenzodioxinincreases expression1
Thiramdecreases expression1
Cyclosporinedecreases expression1
Antirheumatic Agentsincreases expression1
Copper Sulfatedecreases expression1

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.