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25 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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RUNX3
RUNX family transcription factor 3
Chromosome 1 · 1p36.11
NCBI Gene: 864Ensembl: ENSG00000020633.19HGNC: HGNC:10473UniProt: Q13761
443PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
Highly StudiedTrending
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
regulation of transcription by RNA polymerase IIprotein phosphorylationprotein bindingnucleoplasmasthmapsoriasisallergic rhinitisallergic disease
✦AI Summary

RUNX3 is a transcription factor that forms a heterodimeric core-binding factor (CBF) complex with CBFB to regulate gene expression by recognizing specific DNA sequences (5'-TGTGGT-3') in target promoters and enhancers. RUNX3 plays critical roles in immune cell differentiation and tissue homeostasis. In CD8+ T cells, RUNX3 is essential for tissue-resident memory (TRM) cell development and homeostasis, supporting expression of tissue-residency genes while suppressing genes associated with tissue egress 1. RUNX3 activity, often in conjunction with RUNX2, promotes differentiation of cytotoxic CD8+CD103+CD49a+ TRM cells with enhanced immunosurveillance capacity 2. Beyond immunity, RUNX3 functions as a gatekeeping regulator in liver sinusoidal endothelial cells; its deficiency leads to IL-6/JAK/STAT3 pathway activation, LRG1 secretion, and subsequent liver fibrosis progression 3. In fallopian tube epithelium, RUNX3 marks an intermediate state during secretory-to-ciliated cell differentiation 4. Regarding cancer, RUNX3 exhibits context-dependent roles. While traditionally considered a tumor suppressor, recent evidence suggests RUNX3 acts as a "conditional" oncogene, with its oncogenic activity dependent on p53 status 5. In esophageal squamous cell carcinoma, low RUNX3 expression correlates with tumor progression and poor outcomes, suggesting tumor-suppressive functions 6. RUNX3 expression is also regulated by HDAC9-mediated deacetylation, affecting intervertebral disc homeostasis 7.

Sources cited
1
RUNX3 is a key regulator of tissue-resident memory CD8+ T cell differentiation and homeostasis
PMID: 29211713
2
Combined RUNX2 and RUNX3 activity promotes differentiation of cytotoxic CD8+CD103+CD49a+ tissue-resident memory cells
PMID: 37269830
3
Endothelial RUNX3 deficiency causes liver sinusoidal endothelial cell dysfunction, IL-6/JAK/STAT3 pathway activation, and liver fibrosis through LRG1 secretion
PMID: 39042837
4
RUNX3 marks an intermediate state in fallopian tube epithelial differentiation from secretory to ciliated cells
PMID: 33852846
5
RUNX3 acts as a conditional oncogene in human cancers, with oncogenic activity dependent on p53 status
PMID: 37190031
6
Low RUNX3 expression in esophageal squamous cell carcinoma correlates with tumor progression and promotes cell migration and invasion
PMID: 25428380
7
HDAC9 deacetylates and stabilizes RUNX3 to protect nucleus pulposus cells from apoptosis in intervertebral disc degeneration
PMID: 38093179
Disease Associationsⓘ20
asthmaOpen Targets
0.54Moderate
psoriasisOpen Targets
0.52Moderate
allergic rhinitisOpen Targets
0.49Moderate
allergic diseaseOpen Targets
0.48Moderate
Eczematoid dermatitisOpen Targets
0.48Moderate
Crohn's diseaseOpen Targets
0.47Moderate
androgenetic alopeciaOpen Targets
0.47Moderate
hypertensionOpen Targets
0.45Moderate
psoriasis vulgarisOpen Targets
0.45Moderate
skin diseaseOpen Targets
0.45Moderate
ankylosing spondylitisOpen Targets
0.44Moderate
respiratory system diseaseOpen Targets
0.44Moderate
atopic eczemaOpen Targets
0.44Moderate
dermatitisOpen Targets
0.42Moderate
deep vein thrombosisOpen Targets
0.41Moderate
Abnormal thrombosisOpen Targets
0.40Moderate
hypothyroidismOpen Targets
0.40Moderate
lower respiratory tract diseaseOpen Targets
0.39Weak
type 2 diabetes mellitusOpen Targets
0.38Weak
alopeciaOpen Targets
0.37Weak
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
CDKN1AProtein interaction100%CDKN2AProtein interaction100%TBX21Protein interaction99%SMAD3Protein interaction99%SMAD4Protein interaction96%CD8AProtein interaction94%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
34%
Liver
7%
Heart
2%
Brain
2%
Ovary
1%
Gene Interaction Network
Click a node to explore
RUNX3CDKN1ACDKN2ATBX21SMAD3SMAD4CD8A
PROTEIN STRUCTURE
Preparing viewer…
PDB5W69 · 2.80 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.70LoF Tolerant
pLIⓘ
0.37Tolerant
Observed/Expected LoF0.40 [0.24–0.70]
RankingsWhere RUNX3 stands among ~20K protein-coding genes
  • #623of 20,598
    Most Researched443 · top 5%
  • #5,303of 17,882
    Most Constrained (LOEUF)0.70
Genes detectedRUNX3
Sources retrieved25 papers
Response time—
📄 Sources
25▼
1
Human skin-resident CD8
PMID: 37269830
Immunity · 2023
1.00
2
Endothelial RUNX3 controls LSEC dysfunction and angiocrine LRG1 signaling to prevent liver fibrosis.
PMID: 39042837
Hepatology · 2025
0.90
3
Single-cell transcriptomics identifies gene expression networks driving differentiation and tumorigenesis in the human fallopian tube.
PMID: 33852846
Cell Rep · 2021
0.80
4
Runx3 programs CD8
PMID: 29211713
Nature · 2017
0.70
5
Differential Runx3, Eomes, and T-bet expression subdivides MS-associated CD4
PMID: 38009648
Eur J Immunol · 2024
0.68