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25 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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HDAC3
histone deacetylase 3
Chromosome 5 · 5q31.3
NCBI Gene: 8841Ensembl: ENSG00000171720.11HGNC: HGNC:4854UniProt: O15379
509PubMed Papers
20Diseases
14Drugs
2Pathogenic Variants
FUNCTIONAL ROLE
Hub GeneTranscription Factor
RESEARCH IMPACT
Highly StudiedTrending
CLINICAL
FDA Approved Target
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
cellular response to fluid shear stresstranscription corepressor bindingnegative regulation of transcription by RNA polymerase IIestablishment of mitotic spindle orientationneoplasmmultiple myelomaCutaneous T-cell lymphomaneurodegenerative disease
✦AI Summary

HDAC3 is a histone deacetylase that catalyzes deacetylation of lysine residues on core histones (H2A, H2B, H3, H4) and non-histone substrates, playing crucial roles in transcriptional repression, cell cycle progression, and development 1. HDAC3 functions within large multiprotein complexes, notably the N-CoR repressor complex, which enhances its enzymatic activity 1. Beyond classical deacetylation, HDAC3 exhibits broader deacylase activities, removing crotonyl, lactyl, and other acyl groups from lysine residues 2. Mechanistically, HDAC3 participates in BCL6-mediated transcriptional repression by deacetylating H3K27 on enhancer elements 1 and regulates circadian clock genes through deacetylase activity-independent mechanisms involving BMAL1 and CRY proteins [UniProt source]. In disease contexts, HDAC3 dysregulation contributes to multiple pathologies. In atherosclerosis, TRAP1-mediated lactate accumulation promotes histone H4K12 lactylation by downregulating HDAC3, activating senescence-associated secretory phenotype genes in vascular smooth muscle cells 3. HDAC3 deletion in intestinal epithelial cells restricts tuft cell differentiation and impairs type 2 immunity, with microbiota-derived butyrate suppressing HDAC3 activity 4. In osteoarthritis, ECM stiffening downregulates HDAC3, increasing Parkin acetylation and excessive mitophagy in chondrocytes 5. Conversely, HDAC3 shows neuroprotective properties in neurodegenerative diseases 6. Clinically, HDAC3 represents a therapeutic target for metabolic diseases, immune disorders, and cancer-related conditions, with potential interventions including HDAC3 activation through microbiota-derived metabolites 7 or inhibition in specific disease contexts.

Sources cited
1
HDAC3 catalyzes histone deacetylation for epigenetic repression and functions within N-CoR repressor complex; participates in BCL6-mediated H3K27 deacetylation
PMID: 23911289
2
HDAC3 exhibits deacylase activities beyond acetylation, including removal of crotonyl and other acyl groups
PMID: 28497810
3
In atherosclerosis, TRAP1 downregulates HDAC3, promoting H4K12 lactylation and SASP gene expression in vascular smooth muscle cell senescence
PMID: 39088352
4
HDAC3 deletion in intestinal epithelium inhibits tuft cell expansion and impairs type 2 immunity; microbiota-derived butyrate suppresses HDAC3 activity
PMID: 38295798
5
ECM stiffening downregulates HDAC3, increasing Parkin acetylation and mitophagy in chondrocyte senescence and osteoarthritis
PMID: 38789434
6
HDAC3 has neuroprotective properties in neurodegenerative disorders compared to HDAC1 and HDAC2
PMID: 34151764
7
Microbiota-derived inositol-1,4,5-trisphosphate promotes HDAC3 activity in intestinal epithelial cells for epithelial repair
PMID: 32731255
Disease Associationsⓘ20
neoplasmOpen Targets
0.58Moderate
multiple myelomaOpen Targets
0.57Moderate
Cutaneous T-cell lymphomaOpen Targets
0.56Moderate
neurodegenerative diseaseOpen Targets
0.53Moderate
Duchenne muscular dystrophyOpen Targets
0.52Moderate
unspecified peripheral T-cell lymphomaOpen Targets
0.52Moderate
T-cell non-Hodgkin lymphomaOpen Targets
0.50Moderate
mature T-cell and NK-cell non-Hodgkin lymphomaOpen Targets
0.45Moderate
Neurodevelopmental disorderOpen Targets
0.42Moderate
renal cell carcinomaOpen Targets
0.38Weak
viral diseaseOpen Targets
0.38Weak
lymphomaOpen Targets
0.38Weak
breast cancerOpen Targets
0.38Weak
acute myeloid leukemiaOpen Targets
0.37Weak
Intellectual disabilityOpen Targets
0.37Weak
genetic disorderOpen Targets
0.33Weak
Hodgkins lymphomaOpen Targets
0.30Weak
myelodysplastic syndromeOpen Targets
0.30Weak
polycythemia veraOpen Targets
0.30Weak
Abnormality of the skeletal systemOpen Targets
0.29Weak
Pathogenic Variants2
NM_003883.4(HDAC3):c.893A>G (p.Tyr298Cys)Likely pathogenic
Inborn genetic diseases
★☆☆☆2017→ Residue 298
NM_003883.4(HDAC3):c.902G>A (p.Arg301Gln)Likely pathogenic
Inborn genetic diseases
★☆☆☆2015→ Residue 301
View on ClinVar ↗
Drug Targets14
ABEXINOSTATPhase III
Histone deacetylase inhibitor
follicular lymphoma
BELINOSTATApproved
Histone deacetylase inhibitor
T-cell non-Hodgkin lymphoma
CUDC-101Phase I
Epidermal growth factor receptor erbB1 inhibitor
ENTINOSTATApproved
Histone deacetylase inhibitor
neoplasm
FIMEPINOSTATPhase II
Histone deacetylase inhibitor
lymphoma
GIVINOSTATApproved
Histone deacetylase inhibitor
Duchenne muscular dystrophy
GIVINOSTAT HYDROCHLORIDEApproved
Histone deacetylase inhibitor
Duchenne muscular dystrophy
MOCETINOSTATPhase II
Histone deacetylase 11 inhibitor
non-small cell lung carcinoma
PANOBINOSTATApproved
Histone deacetylase inhibitor
multiple myeloma
PANOBINOSTAT LACTATEApproved
Histone deacetylase inhibitor
multiple myeloma
QUISINOSTATPhase II
Histone deacetylase inhibitor
ROMIDEPSINApproved
Histone deacetylase inhibitor
T-cell non-Hodgkin lymphoma
TACEDINALINEPhase II
Histone deacetylase inhibitor
VORINOSTATApproved
Histone deacetylase 2 inhibitor
T-cell non-Hodgkin lymphoma
Related Genes
SKIProtein interaction100%FOXO3Protein interaction100%WDR5Protein interaction100%RBM15Protein interaction100%TBL1YProtein interaction100%EP300Protein interaction97%
Tissue Expression6 tissues
Liver
100%
Bone Marrow
99%
Ovary
98%
Lung
84%
Heart
68%
Brain
46%
Gene Interaction Network
Click a node to explore
HDAC3SKIFOXO3WDR5RBM15TBL1YEP300
PROTEIN STRUCTURE
Preparing viewer…
PDB4A69 · 2.06 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.46Moderately Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.32 [0.23–0.46]
RankingsWhere HDAC3 stands among ~20K protein-coding genes
  • #522of 20,598
    Most Researched509 · top 5%
  • #187of 1,025
    FDA-Approved Drug Targets8 · top quartile
  • #4,196of 5,498
    Most Pathogenic Variants2
  • #2,626of 17,882
    Most Constrained (LOEUF)0.46 · top quartile
Genes detectedHDAC3
Sources retrieved25 papers
Response time—
📄 Sources
25▼
1
TRAP1 drives smooth muscle cell senescence and promotes atherosclerosis via HDAC3-primed histone H4 lysine 12 lactylation.
PMID: 39088352
Eur Heart J · 2024
1.00
2
Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestinal type 2 immunity.
PMID: 38295798
Immunity · 2024
0.90
3
Matrix stiffening promotes chondrocyte senescence and the osteoarthritis development through downregulating HDAC3.
PMID: 38789434
Bone Res · 2024
0.80
4
KDELR2 promotes breast cancer proliferation via HDAC3-mediated cell cycle progression.
PMID: 34146461
Cancer Commun (Lond) · 2021
0.72
5
Microbiota-derived metabolite promotes HDAC3 activity in the gut.
PMID: 32731255
Nature · 2020
0.70