ZHX3

gene
On this page

Also known as KIAA0395

Summary

ZHX3 (zinc fingers and homeoboxes 3, HGNC:15935) is a protein-coding gene on chromosome 20q12, encoding Zinc fingers and homeoboxes protein 3 (Q9H4I2). Acts as a transcriptional repressor.

This gene encodes a member of the zinc fingers and homeoboxes (ZHX) gene family. The encoded protein contains two C2H2-type zinc fingers and five homeodomains and forms a dimer with itself or with zinc fingers and homeoboxes family member 1. In the nucleus, the dimerized protein interacts with the A subunit of the ubiquitous transcription factor nuclear factor-Y and may function as a transcriptional repressor.

Source: NCBI Gene 23051 — RefSeq curated summary.

At a glance

  • GWAS associations: 39
  • Clinical variants (ClinVar): 251 total
  • MANE Select transcript: NM_001384317

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15935
Approved symbolZHX3
Namezinc fingers and homeoboxes 3
Location20q12
Locus typegene with protein product
StatusApproved
AliasesKIAA0395
Ensembl geneENSG00000174306
Ensembl biotypeprotein_coding
OMIM609598
Entrez23051

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 19 protein_coding, 7 protein_coding_CDS_not_defined

ENST00000309060, ENST00000373261, ENST00000419740, ENST00000421422, ENST00000432768, ENST00000436099, ENST00000436440, ENST00000485686, ENST00000487057, ENST00000544979, ENST00000558993, ENST00000559028, ENST00000559234, ENST00000559296, ENST00000559436, ENST00000560361, ENST00000560364, ENST00000560456, ENST00000560759, ENST00000561291, ENST00000683867, ENST00000895799, ENST00000895800, ENST00000895801, ENST00000895802, ENST00000912257

RefSeq mRNA: 12 — MANE Select: NM_001384317 NM_001384315, NM_001384316, NM_001384317, NM_001384318, NM_001384319, NM_001384320, NM_001384321, NM_001384322, NM_001384323, NM_001384324, NM_001384325, NM_015035

CCDS: CCDS13315, CCDS93040

Canonical transcript exons

ENST00000683867 — 4 exons

ExonStartEnd
ENSE000015268294126899041269083
ENSE000025460854131750941317731
ENSE000036988034120205741205066
ENSE000039161704117845541185201

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 94.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.0833 / max 160.4231, expressed in 1775 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
18727814.29501763
1872792.6666980
1872801.0539625
1872810.036315
1872760.02743
1872770.00423

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548894.91gold quality
mucosa of stomachUBERON:000119992.56gold quality
calcaneal tendonUBERON:000370192.24gold quality
ventricular zoneUBERON:000305390.26gold quality
corpus callosumUBERON:000233690.21gold quality
stromal cell of endometriumCL:000225590.19gold quality
lower esophagus muscularis layerUBERON:003583390.02gold quality
lower esophagusUBERON:001347389.94gold quality
esophagogastric junction muscularis propriaUBERON:003584189.77gold quality
popliteal arteryUBERON:000225089.47gold quality
tibial arteryUBERON:000761089.46gold quality
tendonUBERON:000004389.09gold quality
medial globus pallidusUBERON:000247788.86gold quality
aortaUBERON:000094788.57gold quality
nucleus accumbensUBERON:000188288.44gold quality
left testisUBERON:000453388.41gold quality
caudate nucleusUBERON:000187388.22gold quality
globus pallidusUBERON:000187588.18gold quality
descending thoracic aortaUBERON:000234588.08gold quality
right testisUBERON:000453487.99gold quality
renal medullaUBERON:000036287.97gold quality
putamenUBERON:000187487.85gold quality
hindlimb stylopod muscleUBERON:000425287.84gold quality
left coronary arteryUBERON:000162687.77gold quality
thoracic aortaUBERON:000151587.50gold quality
amygdalaUBERON:000187687.45gold quality
right coronary arteryUBERON:000162587.39gold quality
coronary arteryUBERON:000162187.38gold quality
ascending aortaUBERON:000149687.29gold quality
dorsal motor nucleus of vagus nerveUBERON:000287087.27gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes14.74

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

TargetRegulation
HK2Repression
ZHX2
ZHX3

Upstream regulators (CollecTRI, top): ZHX2, ZHX3

miRNA regulators (miRDB)

192 targeting ZHX3, 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-5011-5P100.0083.465820
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-4533100.0069.482758
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-4283100.0066.422097
HSA-MIR-4455100.0065.481587
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-150-5P99.9966.691976
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-480399.9871.993117
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-211099.9666.681930
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-1236-3P99.9468.041695

Literature-anchored findings (GeneRIF, showing 6)

  • dimerizes with both ZHX1 and ZHX3, also interacts with the activation domain of the NF-YA (PMID:12659632)
  • ZHX proteins 1, 2 and 3 are major transcriptional mediators of podocyte disease (PMID:17056598)
  • ZHX3 is involved in the switch from the undifferentiated state of mesenchymal stem cells to an osteogenic program (PMID:21174497)
  • ZHX3 expression in renal cell carcinoma (PMID:28152006)
  • ZHX3 promotes the progression of urothelial carcinoma of the bladder via repressing of RGS2 and is a novel substrate of TRIM21. (PMID:33440047)
  • Loss of the transcription repressor ZHX3 induces senescence-associated gene expression and mitochondrial-nucleolar activation. (PMID:35085309)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriozhx3bENSDARG00000019774
danio_reriozhx3aENSDARG00000087186
mus_musculusZhx3ENSMUSG00000035877
rattus_norvegicusZhx3ENSRNOG00000027988

Paralogs (3): ZHX1 (ENSG00000165156), ZHX2 (ENSG00000178764), HOMEZ (ENSG00000290292)

Protein

Protein identifiers

Zinc fingers and homeoboxes protein 3Q9H4I2 (reviewed: Q9H4I2)

Alternative names: Triple homeobox protein 1, Zinc finger and homeodomain protein 3

All UniProt accessions (8): Q9H4I2, A0A0A0MST6, A0A0A0MSU5, F6UBH9, F6UQN6, H0Y6F5, H0YLR4, H0YNY7

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a transcriptional repressor. Involved in the early stages of mesenchymal stem cell (MSC) osteogenic differentiation. Is a regulator of podocyte gene expression during primary glomerula disease. Binds to promoter DNA.

Subunit / interactions. Homodimer (via homeobox domain 1). Heterodimer with ZHX1 (via homeobox domain 1). Heterodimer with ZHX2 (via homeobox domain 1). Heterodimerization with ZHX1 is a prerequisite for repressor activity. Interacts with NFYA.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed. High expression in kidney. Expressed during osteogenic differentiation.

Induction. Up-regulated during osteogenic differentiation of mesenchymal stem cells.

Similarity. Belongs to the ZHX family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H4I2-11yes
Q9H4I2-22

RefSeq proteins (12): NP_001371244, NP_001371245, NP_001371246, NP_001371247, NP_001371248, NP_001371249, NP_001371250, NP_001371251, NP_001371252, NP_001371253, NP_001371254, NP_055850 (=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 (40 total): region of interest 8, modified residue 7, helix 7, DNA-binding region 5, compositionally biased region 3, strand 3, zinc finger region 2, sequence conflict 2, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2DA5SOLUTION NMR
2DN0SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H4I2-F160.800.23

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 (7): 599, 604, 680, 708, 723, 927, 946

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (5): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), cell differentiation (GO:0030154), positive regulation of osteoblast differentiation (GO:0045669), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (9): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), protein homodimerization activity (GO:0042803), protein heterodimerization activity (GO:0046982), DNA binding (GO:0003677), 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
transcription cis-regulatory region binding2
protein dimerization activity2
cellular anatomical structure2
negative regulation of DNA-templated transcription1
cellular developmental process1
osteoblast differentiation1
positive regulation of cell differentiation1
regulation of osteoblast differentiation1
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
transcription regulator activity1
transition metal ion binding1
identical protein binding1
nucleic acid binding1
binding1
cation binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1

Protein interactions and networks

STRING

854 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZHX3NFYAP23511856
ZHX3ZHX2Q9Y6X8485
ZHX3RPN2P04844472
ZHX3TBC1D31Q96DN5456
ZHX3DHX35Q9H5Z1437
ZHX3SACK1AQ86UY5426
ZHX3LPIN3Q9BQK8419
ZHX3GGT7Q9UJ14418
ZHX3RAB5IFQ9BUV8415
ZHX3BTBD9Q96Q07411
ZHX3TOP1P11387407
ZHX3ZFRQ96KR1403
ZHX3DERL1Q9BUN8395
ZHX3ATAD2Q6PL18384
ZHX3ARHGAP31Q2M1Z3376

IntAct

30 interactions, top by confidence:

ABTypeScore
ZHX3NLKpsi-mi:“MI:0915”(physical association)0.670
ZHX3RPL7Apsi-mi:“MI:0915”(physical association)0.400
ZHX3psi-mi:“MI:0915”(physical association)0.370
NTAQ1SBNO1psi-mi:“MI:0914”(association)0.350
PDIA6PLS1psi-mi:“MI:0914”(association)0.350
ARID1Apsi-mi:“MI:0914”(association)0.350
CSNK2BOSBPL8psi-mi:“MI:0914”(association)0.350
HDAC1psi-mi:“MI:0914”(association)0.350
HDAC2psi-mi:“MI:0914”(association)0.350
ECHDC2DBTpsi-mi:“MI:0914”(association)0.350
ARMED6psi-mi:“MI:2364”(proximity)0.270
RAVER1KDM6Apsi-mi:“MI:2364”(proximity)0.270
SRFZNF292psi-mi:“MI:2364”(proximity)0.270
KLF12psi-mi:“MI:2364”(proximity)0.270
KLF3MCRIP1psi-mi:“MI:2364”(proximity)0.270
SOX5SMCHD1psi-mi:“MI:2364”(proximity)0.270
SOX6SMCHD1psi-mi:“MI:2364”(proximity)0.270
YY1SMCHD1psi-mi:“MI:2364”(proximity)0.270
SWSAP1NACApsi-mi:“MI:2364”(proximity)0.270
TLK2SBNO1psi-mi:“MI:2364”(proximity)0.270
SMC5DKFZp686H10254psi-mi:“MI:2364”(proximity)0.270
ZHX3psi-mi:“MI:0915”(physical association)0.000
ATXN1ZHX3psi-mi:“MI:0915”(physical association)0.000

BioGRID (62): NLK (Two-hybrid), ZHX3 (Affinity Capture-MS), ZHX3 (Two-hybrid), ZHX3 (Proximity Label-MS), NLK (Two-hybrid), ZHX3 (Affinity Capture-MS), ZHX3 (Affinity Capture-MS), ZHX3 (Affinity Capture-MS), ZHX3 (Reconstituted Complex), ZHX2 (Reconstituted Complex), ZHX2 (Two-hybrid), ZHX3 (Affinity Capture-RNA), ZHX3 (Proximity Label-MS), ZHX1 (Two-hybrid), ZHX3 (Reconstituted Complex)

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

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 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.

GO biological processes:

GO termPartnersFoldFDR
chromatin remodeling512.2×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance166
Likely benign61
Benign14

Top pathogenic / likely-pathogenic (0)

SpliceAI

2127 predictions. Top by Δscore:

VariantEffectΔscore
20:41268977:A:ACdonor_gain1.0000
20:41268978:C:CCdonor_gain1.0000
20:41268988:A:ACdonor_gain1.0000
20:41268989:C:CCdonor_gain1.0000
20:41268989:CTT:Cdonor_gain1.0000
20:41268991:T:TAdonor_gain1.0000
20:41272205:T:TAdonor_gain1.0000
20:41205063:CAAT:Cacceptor_gain0.9900
20:41205067:C:CCacceptor_gain0.9900
20:41218657:T:TAdonor_gain0.9900
20:41238686:A:ACdonor_gain0.9900
20:41238687:C:CCdonor_gain0.9900
20:41268989:CTTCA:Cdonor_gain0.9900
20:41269079:CAGTC:Cacceptor_gain0.9900
20:41184989:T:Cdonor_gain0.9800
20:41184993:G:Adonor_gain0.9800
20:41185004:G:Adonor_gain0.9800
20:41185978:C:CCacceptor_gain0.9800
20:41205062:TCAAT:Tacceptor_gain0.9800
20:41205063:CAATC:Cacceptor_gain0.9800
20:41205065:AT:Aacceptor_gain0.9800
20:41217118:A:Tacceptor_gain0.9800
20:41268983:T:TAdonor_gain0.9800
20:41268988:ACTT:Adonor_gain0.9800
20:41268989:CTTC:Cdonor_gain0.9800
20:41299935:T:Adonor_gain0.9800
20:41184956:A:ACdonor_gain0.9700
20:41184957:C:CCdonor_gain0.9700
20:41200039:AC:Adonor_gain0.9700
20:41200040:CC:Cdonor_gain0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000000650 (20:41290704 A>G), RS1000015065 (20:41192844 T>G), RS1000050729 (20:41190505 A>C), RS1000056477 (20:41276774 G>A), RS1000101660 (20:41239854 A>T), RS1000122405 (20:41206296 A>G), RS1000147342 (20:41186499 G>A), RS1000167580 (20:41301842 C>G), RS1000180815 (20:41233242 A>G), RS1000181172 (20:41260839 T>C,G), RS1000197641 (20:41253168 C>T), RS1000199908 (20:41302141 A>G), RS1000217411 (20:41296615 T>C), RS1000228956 (20:41269894 A>C), RS1000252627 (20:41214786 C>A)

Disease associations

OMIM: gene MIM:609598 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

39 associations (top):

StudyTraitp-value
GCST003804_5Non-response to bupropion and depression8.000000e-07
GCST003818_33Resting heart rate1.000000e-08
GCST005195_109Coronary artery disease1.000000e-08
GCST005196_245Coronary artery disease2.000000e-08
GCST005531_98Multiple sclerosis7.000000e-08
GCST006004_22Low density lipoprotein cholesterol levels7.000000e-09
GCST006034_7Total cholesterol levels4.000000e-09
GCST006661_160Male-pattern baldness2.000000e-15
GCST006979_542Heel bone mineral density7.000000e-45
GCST007515_23Type 2 diabetes7.000000e-06
GCST007517_24Type 2 diabetes9.000000e-08
GCST007518_32Type 2 diabetes (adjusted for BMI)3.000000e-06
GCST007858_9Fasting blood glucose adjusted for BMI4.000000e-07
GCST008077_70LDL cholesterol levels5.000000e-09
GCST008078_102LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)2.000000e-15
GCST008078_32LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)1.000000e-09
GCST008079_43LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)4.000000e-46
GCST008079_57LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)9.000000e-11
GCST008079_84LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)4.000000e-46
GCST008086_66LDL cholesterol levels in current drinkers1.000000e-09
GCST008839_242Height5.000000e-10
GCST009597_310Multiple sclerosis5.000000e-06
GCST009597_38Multiple sclerosis3.000000e-06
GCST010002_67Refractive error7.000000e-10
GCST010703_20Brain morphology (MOSTest)1.000000e-09
GCST010866_166Coronary artery disease5.000000e-10
GCST011011_40Youthful appearance (self-reported)1.000000e-09
GCST011365_7Myocardial infarction2.000000e-08
GCST011494_101Daytime nap1.000000e-14
GCST90020025_1661Waist-to-hip ratio adjusted for BMI7.000000e-10

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004574total cholesterol measurement
EFO:0009270heel bone mineral density
EFO:0004329alcohol drinking
EFO:0004346neuroimaging measurement
EFO:0007828daytime rest measurement
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression3
Benzo(a)pyreneaffects methylation, decreases expression3
Air Pollutantsaffects cotreatment, decreases expression, increases abundance2
Tobacco Smoke Pollutiondecreases expression2
Valproic Acidaffects expression, increases expression2
Cadmium Chloridedecreases expression, increases expression2
FR900359increases phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
bisphenol Aaffects cotreatment, increases expression1
2-butenaldecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
4-aminophenylarsenoxideaffects binding, decreases reaction1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
epigallocatechin gallateaffects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
ICG 001increases expression1
abrinedecreases 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
Temozolomidedecreases expression1
Arsenic Trioxideaffects binding, decreases reaction1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Arsenicaffects expression1
Caffeinedecreases phosphorylation1
Copperaffects binding, increases expression1
Dexamethasoneaffects cotreatment, increases expression1
Disulfiramaffects binding, increases expression1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1

Clinical trials (associated diseases)

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