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GeneE
26 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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MBD3
methyl-CpG binding domain protein 3
Chromosome 19 · 19p13.3
NCBI Gene: 53615Ensembl: ENSG00000071655.19HGNC: HGNC:6918UniProt: O95983
180PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
chromatinmethyl-CpG bindingnucleosomal DNA bindingnucleusneurodegenerative diseaseneoplasmCentral precocious pubertyglioma
✦AI Summary

MBD3 (methyl-CpG binding domain protein 3) functions as a key component of the nucleosome remodeling and deacetylase (NuRD) complex, which regulates chr19 structure and gene transcription 1. Unlike other MBD family proteins, MBD3 does not bind methylated DNA but instead associates with both active and repressive chr19 regions, localizing at CpG-rich promoters marked by H3K4me3, gene bodies, and enhancers 1. The protein acts primarily as a transcriptional repressor by recruiting histone deacetylases through the NuRD complex, controlling chr19 accessibility and nucleosome occupancy 12. MBD3 plays critical roles in cellular differentiation and stemness maintenance, particularly in neural progenitor cells where it suppresses neurogenesis-associated genes 3. Its expression and stability are regulated by canonical Wnt signaling through GSK3β-mediated ubiquitination 3. Clinically, MBD3 has significant disease relevance in cancer biology, where its dysregulation contributes to glioblastoma chemoresistance 4, hepatocellular carcinoma progression 2, and acute myeloid leukemia pathogenesis through altered DOCK5/8 expression 5. Lower MBD3 expression correlates with poor prognosis in glioma patients 6, highlighting its potential as both a prognostic biomarker and therapeutic target.

⚠Limited data available — This gene has 0 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.27Weak
neoplasmOpen Targets
0.09Suggestive
Central precocious pubertyOpen Targets
0.08Suggestive
gliomaOpen Targets
0.08Suggestive
hepatocellular carcinomaOpen Targets
0.08Suggestive
gastric cancerOpen Targets
0.07Suggestive
pancreatic neoplasmOpen Targets
0.07Suggestive
glioblastoma multiformeOpen Targets
0.06Suggestive
acute lymphoblastic leukemiaOpen Targets
0.05Suggestive
malignant gliomaOpen Targets
0.03Suggestive
neuroblastomaOpen Targets
0.03Suggestive
breast cancerOpen Targets
0.02Suggestive
cancerOpen Targets
0.02Suggestive
colitisOpen Targets
0.02Suggestive
melanomaOpen Targets
0.02Suggestive
epilepsyOpen Targets
0.02Suggestive
acute myeloid leukemiaOpen Targets
0.02Suggestive
non-small cell lung carcinomaOpen Targets
0.02Suggestive
Miyoshi myopathyOpen Targets
0.02Suggestive
lung cancerOpen Targets
0.01Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
HDAC1Protein interaction91%HDAC2Protein interaction91%RBBP7Protein interaction91%CDK2AP1Protein interaction91%PHF20L1Protein interaction91%ZNF219Protein interaction91%
Tissue Expression6 tissues
Liver
100%
Ovary
81%
Lung
67%
Brain
66%
Heart
51%
Bone Marrow
45%
Gene Interaction Network
Click a node to explore
MBD3HDAC1HDAC2RBBP7CDK2AP1PHF20L1ZNF219
PROTEIN STRUCTURE
Preparing viewer…
PDB6CCG · 1.90 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.68LoF Tolerant
pLIⓘ
0.37Tolerant
Observed/Expected LoF0.40 [0.25–0.68]
RankingsWhere MBD3 stands among ~20K protein-coding genes
  • #2,416of 20,598
    Most Researched180 · top quartile
  • #5,068of 17,882
    Most Constrained (LOEUF)0.68
Genes detectedMBD3
Sources retrieved26 papers
Response time—
📄 Sources
26▼
1
PTMA controls cardiomyocyte proliferation and cardiac repair by enhancing STAT3 acetylation.
PMID: 40408476
Sci Adv · 2025
1.00
2
Epigenetic modulator inhibition overcomes temozolomide chemoresistance and antagonizes tumor recurrence of glioblastoma.
PMID: 33016927
J Clin Invest · 2020
0.90
3
Regulatory landscape and clinical implication of MBD3 in human malignant glioma.
PMID: 27835581
Oncotarget · 2016
0.80
4
MBD3 localizes at promoters, gene bodies and enhancers of active genes.
PMID: 24385926
PLoS Genet · 2013
0.70
5
Analysis of the complex between MBD2 and the histone deacetylase core of NuRD reveals key interactions critical for gene silencing.
PMID: 37552759
Proc Natl Acad Sci U S A · 2023
0.64