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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
MBD4
methyl-CpG binding domain 4, DNA glycosylase
Chromosome 3 Β· 3q21.3
NCBI Gene: 8930Ensembl: ENSG00000129071.11HGNC: HGNC:6919UniProt: O95243
107PubMed Papers
22Diseases
0Drugs
123Pathogenic Variants
FUNCTIONAL ROLE
DNA Repair
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
pyrimidine-specific mismatch base pair DNA N-glycosylase activitynuclear speckprotein bindingDNA bindingtumor predisposition syndrome 2Uveal Melanomagenetic disordercolorectal cancer
✦AI Summary

MBD4 (methyl-CpG binding domain 4, DNA glycosylase) is a mismatch-specific DNA N-glycosylase that plays a crucial role in base excision repair by removing thymine, uracil, and 5-fluorouracil from G:T and G:U mismatches, particularly within CpG contexts 1. The protein contains an N-terminal methyl-CpG binding domain and a C-terminal catalytic domain with glycosylase activity, allowing it to repair G:T mismatches arising from spontaneous deamination of 5-methylcytosine to thymine 1. MBD4 functions as a caretaker of genomic fidelity at CpG sites and interacts with the mismatch repair protein MLH1 1. Germline bi-allelic loss-of-function variants in MBD4 cause an autosomal recessive multi-tumor predisposition syndrome characterized by adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma 2. The colorectal adenomas from MBD4-deficient individuals exhibit a mutator phenotype consistent with mutational signature SBS1 2. MBD4 represents one of the major G:T glycosylases alongside TDG and has been implicated in apoptosis regulation 3. Clinical significance includes its role in hereditary adenomatous polyposis syndromes and various cancers, warranting inclusion in genetic testing panels for polyposis and multi-tumor phenotypes 24.

Sources cited
1
MBD4 is a mismatch-specific DNA N-glycosylase with thymine glycosylase activity, contains MBD and catalytic domains, and interacts with MLH1
PMID: 11267993
2
Bi-allelic MBD4 variants cause multi-tumor predisposition syndrome with colorectal polyposis, AML, and uveal melanoma
PMID: 35460607
3
MBD4 is one of two major G:T glycosylases and has been linked to apoptosis regulation
PMID: 23195996
4
MBD4 is involved in autosomal recessive adenomatous polyposis syndromes through base excision repair deficiency
PMID: 40237887
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜22
tumor predisposition syndrome 2Open Targets
0.73Strong
Uveal MelanomaOpen Targets
0.69Moderate
genetic disorderOpen Targets
0.56Moderate
colorectal cancerOpen Targets
0.50Moderate
acute myeloid leukemiaOpen Targets
0.50Moderate
Familial adenomatous polyposisOpen Targets
0.49Moderate
classic familial adenomatous polyposisOpen Targets
0.49Moderate
cranioectodermal dysplasiaOpen Targets
0.45Moderate
hereditary neoplastic syndromeOpen Targets
0.27Weak
Inherited cancer-predisposing syndromeOpen Targets
0.27Weak
O'Donnell-Luria-Rodan syndromeOpen Targets
0.12Weak
neoplasmOpen Targets
0.11Weak
cancerOpen Targets
0.09Suggestive
colorectal carcinomaOpen Targets
0.08Suggestive
systemic lupus erythematosusOpen Targets
0.08Suggestive
ulnar-mammary syndromeOpen Targets
0.08Suggestive
breast cancerOpen Targets
0.06Suggestive
inherited hemoglobinopathyOpen Targets
0.05Suggestive
Tietze syndromeOpen Targets
0.05Suggestive
rheumatoid arthritisOpen Targets
0.04Suggestive
Melanoma, uveal, 1UniProt
Tumor predisposition syndrome 2UniProt
Pathogenic Variants123
NM_001276270.2(MBD4):c.104+1G>ALikely pathogenic
Tumor predisposition syndrome 2|not provided
β˜…β˜…β˜†β˜†2026
NM_001276270.2(MBD4):c.1425del (p.Leu476fs)Pathogenic
not provided|MBD4-related disorder|Inborn genetic diseases|Tumor predisposition syndrome 2
β˜…β˜…β˜†β˜†2026β†’ Residue 476
NM_001276270.2(MBD4):c.1273C>T (p.Arg425Ter)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 425
NM_001276270.2(MBD4):c.1544-1G>TPathogenic
Melanoma, uveal, susceptibility to, 1|Tumor predisposition syndrome 2|not provided|MBD4-related disorder|Ovarian serous cystadenocarcinoma|Uveal melanoma
β˜…β˜…β˜†β˜†2026
NM_001276270.2(MBD4):c.1618C>T (p.Arg540Ter)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 540
NM_001276270.2(MBD4):c.939dup (p.Glu314fs)Pathogenic
not specified|Tumor predisposition syndrome 2|not provided|Tumor predisposition syndrome 2;Melanoma, uveal, susceptibility to, 1
β˜…β˜…β˜†β˜†2026β†’ Residue 314
NM_001276270.2(MBD4):c.942_945del (p.Glu314fs)Pathogenic
not provided|Inborn genetic diseases|Tumor predisposition syndrome 2
β˜…β˜…β˜†β˜†2026β†’ Residue 314
NM_001276270.2(MBD4):c.947C>A (p.Ser316Ter)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 316
NM_001276270.2(MBD4):c.335+1G>ALikely pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026
NM_001276270.2(MBD4):c.249dup (p.Lys84Ter)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 84
NM_001276270.2(MBD4):c.1670T>A (p.Leu557Ter)Pathogenic
Tumor predisposition syndrome 2|not provided|Melanoma, uveal, susceptibility to, 1|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 557
NM_001276270.2(MBD4):c.1213_1216del (p.Arg405fs)Pathogenic
not provided|Inborn genetic diseases|Tumor predisposition syndrome 2
β˜…β˜…β˜†β˜†2026β†’ Residue 405
NM_001276270.2(MBD4):c.227dup (p.Thr77fs)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 77
NM_001276270.2(MBD4):c.962C>G (p.Ser321Ter)Pathogenic
not provided|Inborn genetic diseases|Tumor predisposition syndrome 2
β˜…β˜…β˜†β˜†2025β†’ Residue 321
NM_001276270.2(MBD4):c.939del (p.Glu314fs)Pathogenic
not provided|MBD4-related disorder|Inborn genetic diseases|Tumor predisposition syndrome 2
β˜…β˜…β˜†β˜†2025β†’ Residue 314
NM_001276270.2(MBD4):c.229dup (p.Thr77fs)Pathogenic
not provided|Tumor predisposition syndrome 2|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 77
NM_001276270.2(MBD4):c.846_849del (p.Gln283fs)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 283
NM_001276270.2(MBD4):c.541C>T (p.Arg181Ter)Pathogenic
Inborn genetic diseases|Tumor predisposition syndrome 2|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 181
NM_001276270.2(MBD4):c.614_615del (p.Leu204_Ser205insTer)Pathogenic
not provided|Inborn genetic diseases|Tumor predisposition syndrome 2
β˜…β˜…β˜†β˜†2025β†’ Residue 204
NM_001276270.2(MBD4):c.1237dup (p.Ser413fs)Pathogenic
Inborn genetic diseases|Tumor predisposition syndrome 2
β˜…β˜…β˜†β˜†2025β†’ Residue 413
View on ClinVar β†—
Related Genes
MLH1Protein interaction97%DNMT3BProtein interaction96%DNMT1Protein interaction93%DNMT3AProtein interaction90%TRDMT1Protein interaction81%TDGProtein interaction79%
Tissue Expression6 tissues
Bone Marrow
100%
Liver
84%
Ovary
76%
Lung
74%
Heart
57%
Brain
49%
Gene Interaction Network
Click a node to explore
MBD4MLH1DNMT3BDNMT1DNMT3ATRDMT1TDG
PROTEIN STRUCTURE
Preparing viewer…
PDB4OFA Β· 1.55 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.02LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.80 [0.63–1.02]
RankingsWhere MBD4 stands among ~20K protein-coding genes
  • #4,449of 20,598
    Most Researched107 Β· top quartile
  • #638of 5,498
    Most Pathogenic Variants123 Β· top quartile
  • #10,070of 17,882
    Most Constrained (LOEUF)1.02
Genes detectedMBD4
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Germline MBD4 deficiency causes a multi-tumor predisposition syndrome.
PMID: 35460607
Am J Hum Genet Β· 2022
1.00
2
Rapid disuse atrophy of diaphragm fibers in mechanically ventilated humans.
PMID: 18367735
N Engl J Med Β· 2008
0.90
3
Role of MED1 (MBD4) Gene in DNA repair and human cancer.
PMID: 11267993
J Cell Physiol Β· 2001
0.80
4
Genetics, genomics and clinical features of adenomatous polyposis.
PMID: 40237887
Fam Cancer Β· 2025
0.70
5
MBD4 and TDG: multifaceted DNA glycosylases with ever expanding biological roles.
PMID: 23195996
Mutat Res Β· 2013
0.60