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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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CBFA2T3
CBFA2/RUNX1 partner transcriptional co-repressor 3
Chromosome 16 · 16q24.3
NCBI Gene: 863Ensembl: ENSG00000129993.15HGNC: HGNC:1537UniProt: O75081
62PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
granulocyte differentiationtranscription corepressor activityprotein bindingnegative regulation of transcription by RNA polymerase IImyeloproliferative disorderskin canceractinic keratosisacute myeloid leukemia
✦AI Summary

CBFA2T3 functions as a master transcriptional corepressor that plays critical roles in hematopoiesis and leukemogenesis 1. The protein regulates cell-fate genes and establishes gene expression signatures associated with leukemia stem cell transformation and relapse in acute myeloid leukemia (AML) 1. Mechanistically, CBFA2T3 inhibits retinoic acid receptor target gene expression by regulating histone acetyltransferase recruitment, histone acetylation, and chr16 accessibility at RARα target sites, thereby blocking myeloid differentiation 2. The gene is particularly significant in pediatric malignancies through oncogenic fusion proteins. CBFA2T3-GLIS2 fusions result from cryptic chromosome 16 inversions and represent the most frequent chimeric oncogene in pediatric non-Down syndrome acute megakaryoblastic leukemia, characterizing an extremely aggressive subtype with 15-30% overall survival rates 34. This fusion is pediatric-specific and drives leukemogenesis through GLIS2-mediated oncogenic properties 4. Additionally, CBFA2T3 alterations occur in group 4 medulloblastoma, where mutations affecting CBFA2T2, CBFA2T3, and related genes converge on the CBFA complex, causing differentiation blockade in cerebellar progenitor cells 5. The protein's role in maintaining stem cell signatures makes it a potential therapeutic target for enhancing differentiation therapies.

Sources cited
1
CBFA2T3 functions as a master transcriptional coregulator and regulates leukemia stem cell gene signatures
PMID: 31040112
2
CBFA2T3 inhibits myeloid differentiation by repressing retinoic acid receptor target genes through chromatin modifications
PMID: 32434928
3
CBFA2T3-GLIS2 fusions are the most frequent oncogene in pediatric megakaryoblastic leukemia with poor prognosis
PMID: 30592296
4
CBFA2T3-GLIS2 fusions drive aggressive pediatric leukemia through GLIS2-mediated oncogenic properties
PMID: 37716355
5
CBFA2T3 alterations occur in group 4 medulloblastoma affecting cerebellar development
PMID: 36131014
Disease Associationsⓘ20
myeloproliferative disorderOpen Targets
0.40Moderate
skin cancerOpen Targets
0.40Weak
actinic keratosisOpen Targets
0.39Weak
acute myeloid leukemiaOpen Targets
0.39Weak
cutaneous melanomaOpen Targets
0.38Weak
Abnormality of the skeletal systemOpen Targets
0.37Weak
pancreatic ductal adenocarcinomaOpen Targets
0.37Weak
lung carcinomaOpen Targets
0.37Weak
breast ductal adenocarcinomaOpen Targets
0.37Weak
thyroid neoplasmOpen Targets
0.37Weak
esophageal adenocarcinomaOpen Targets
0.37Weak
Hepatobiliary NeoplasmOpen Targets
0.37Weak
lymphoid neoplasmOpen Targets
0.37Weak
Ovarian Endometrioid Adenocarcinoma with Squamous DifferentiationOpen Targets
0.37Weak
ACPA-positive rheumatoid arthritisOpen Targets
0.30Weak
rheumatoid arthritisOpen Targets
0.30Weak
glomerulonephritisOpen Targets
0.30Weak
skin diseaseOpen Targets
0.30Weak
squamous cell carcinomaOpen Targets
0.30Weak
basal cell carcinomaOpen Targets
0.29Weak
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
LDB1Protein interaction100%LDB2Protein interaction100%LYL1Protein interaction100%GATA1Protein interaction100%TCF3Protein interaction100%PRDM14Protein interaction97%
Tissue Expression6 tissues
Lung
100%
Bone Marrow
61%
Heart
59%
Liver
50%
Brain
49%
Ovary
7%
Gene Interaction Network
Click a node to explore
CBFA2T3LDB1LDB2LYL1GATA1TCF3PRDM14
PROTEIN STRUCTURE
Preparing viewer…
PDB9DE2 · NMR
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.96LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.70 [0.52–0.96]
RankingsWhere CBFA2T3 stands among ~20K protein-coding genes
  • #7,434of 20,598
    Most Researched62
  • #9,002of 17,882
    Most Constrained (LOEUF)0.96
Genes detectedCBFA2T3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Failure of human rhombic lip differentiation underlies medulloblastoma formation.
PMID: 36131014
Nature · 2022
1.00
2
CBFA2T3-GLIS2-dependent pediatric acute megakaryoblastic leukemia is driven by GLIS2 and sensitive to navitoclax.
PMID: 37716355
Cell Rep · 2023
0.90
3
Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes.
PMID: 28112737
Nat Genet · 2017
0.80
4
Novel classification system and high-risk categories of pediatric acute myeloid leukemia.
PMID: 39781610
Haematologica · 2025
0.70
5
Myeloid translocation gene CBFA2T3 directs a relapse gene program and determines patient-specific outcomes in AML.
PMID: 31040112
Blood Adv · 2019
0.60