MBD1: Methyl-CpG Binding Domain Protein 1
A key epigenetic reader involved in transcriptional repression and chromatin remodeling
Gene Information Card
| Symbol | MBD1 |
|---|---|
| Full Name | Methyl-CpG Binding Domain Protein 1 |
| Gene Type | Protein coding |
| Chromosomal Location | 18q21.1 |
| NCBI Gene ID | 4152 ncbi.nlm.nih.gov/gene/4152 |
| Ensembl ID | ENSG00000141644 |
| UniProt ID | Q9UIS9 |
| OMIM ID | 603519 |
| HGNC ID | 6917 |
| Aliases | CXXC3, PCM1, RFT |
Description
MBD1 (Methyl-CpG Binding Domain Protein 1) is a protein-coding gene that encodes a member of the methyl-CpG-binding domain (MBD) family. The protein binds specifically to methylated DNA, particularly at CpG islands, and recruits histone deacetylases and chromatin remodeling complexes to repress transcription. MBD1 plays a critical role in epigenetic gene silencing, genomic imprinting, and maintenance of heterochromatin. It contains a methyl-CpG binding domain (MBD) and a CXXC zinc finger domain that can bind unmethylated CpG sites. Alternative splicing generates multiple isoforms with distinct functional properties.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Cancer (various types) | MBD1 is frequently downregulated or mutated in cancers, leading to loss of transcriptional repression of oncogenes and reactivation of silenced tumor suppressor genes. | COSMIC; ClinVar |
| Rett syndrome | Mutations in MBD1 have been reported in patients with Rett-like phenotypes, though less common than MECP2 mutations. | OMIM; ClinVar |
| Neurodevelopmental disorders | MBD1 variants are associated with intellectual disability and autism spectrum disorder, likely due to disrupted epigenetic regulation of neuronal genes. | ClinVar; NCBI |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Testis | 8.3 | Low |
| Lung | 6.1 | Low |
| Liver | 4.7 | Low |
| Kidney | 5.2 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK293 | 9.8 | Embryonic kidney cells; moderate expression |
| HeLa | 7.4 | Cervical cancer cells; low expression |
| SH-SY5Y | 11.2 | Neuroblastoma cells; higher expression |
| MCF7 | 6.5 | Breast cancer cells; low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1A>G (p.Met1?) | Missense | <0.01% | Loss of start codon; likely loss of function |
| c.103C>T (p.Arg35Cys) | Missense | <0.01% | Disrupts methyl-CpG binding domain; reduced DNA binding |
| c.286G>A (p.Gly96Arg) | Missense | <0.01% | Located in CXXC domain; altered chromatin binding |
| c.421_423del (p.Lys141del) | Deletion | <0.01% | In-frame deletion; impaired protein stability |
Mutation functional classification
Loss of Function (LOF)
Most MBD1 mutations result in loss of DNA binding or protein stability, leading to derepression of target genes.
Gain of Function (GOF)
No gain-of-function mutations have been reported for MBD1.
Dominant Negative (DN)
Some missense mutations in the MBD domain may act in a dominant-negative manner by competing with wild-type MBD1 for methylated DNA binding.
View complete mutation data：
Gene Ontology (GO)
Pathways
• Epigenetic regulation of gene expression
• Chromatin organization
• Transcriptional repression by methyl-CpG binding proteins
Protein Summary
MBD1 is a 605-amino acid protein (isoform 1) with a molecular weight of approximately 66 kDa. It contains an N-terminal methyl-CpG binding domain (MBD) that specifically recognizes symmetrically methylated CpG dinucleotides, and a C-terminal CXXC zinc finger domain that binds unmethylated CpG sequences. The protein also includes a transcriptional repression domain (TRD) that interacts with histone deacetylases (HDACs) and other co-repressors. MBD1 is predominantly nuclear and localizes to heterochromatic foci. It is involved in silencing of imprinted genes, retrotransposons, and tumor suppressor genes. Post-translational modifications include phosphorylation and sumoylation, which modulate its stability and DNA binding affinity.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| MBD1 Knockout HEK293 Cell Line | EDJ-KQ3211 | Human | 4152 | Details Get a Quote |
| MBD1 Knockout A-549 Cell Line | EDJ-KQ24682 | Human | 4152 | Details Get a Quote |
| MBD1 Knockout HCT 116 Cell Line | EDJ-KQ24683 | Human | 4152 | Details Get a Quote |
| MBD1 Knockout HeLa Cell Line | EDJ-KQ24684 | Human | 4152 | Details Get a Quote |
