The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains an MBD domain at the N-terminus that functions both in binding to met... See more...

Aliases for MBD4 Gene

Aliases for MBD4 Gene

  • Methyl-CpG Binding Domain 4, DNA Glycosylase 2 3 5
  • MED1 2 3 4
  • Methyl-CpG Binding Domain Protein 4 2 3
  • Methyl-CpG-Binding Domain Protein 4 3 4
  • Mismatch-Specific DNA N-Glycosylase 3 4
  • Methyl-CpG-Binding Endonuclease 1 3 4
  • Methyl-CpG-Binding Protein MBD4 3 4
  • G/5-Fluorouracil Mismatch Glycosylase With Biphasic Kinetics 3
  • Putative Methyl-CpG Binding Protein 3
  • 3,N(4)-Ethenocytosine Glycosylase 3
  • G/T Mismatch Glycosylase 3
  • G/U Mismatch Glycosylase 3
  • EC 3.2.2.- 4
  • MBD4 5

External Ids for MBD4 Gene

Previous GeneCards Identifiers for MBD4 Gene

  • GC03M125975
  • GC03M129786
  • GC03M130431
  • GC03M130470
  • GC03M130632
  • GC03M129149
  • GC03M126533

Summaries for MBD4 Gene

Entrez Gene Summary for MBD4 Gene

  • The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains an MBD domain at the N-terminus that functions both in binding to methylated DNA and in protein interactions and a C-terminal mismatch-specific glycosylase domain that is involved in DNA repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]

CIViC Summary for MBD4 Gene

GeneCards Summary for MBD4 Gene

MBD4 (Methyl-CpG Binding Domain 4, DNA Glycosylase) is a Protein Coding gene. Diseases associated with MBD4 include Rett Syndrome and Angelman Syndrome. Among its related pathways are DNA Double-Strand Break Repair and Chks in Checkpoint Regulation. Gene Ontology (GO) annotations related to this gene include endodeoxyribonuclease activity and pyrimidine-specific mismatch base pair DNA N-glycosylase activity. An important paralog of this gene is MECP2.

UniProtKB/Swiss-Prot Summary for MBD4 Gene

  • Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.

Gene Wiki entry for MBD4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MBD4 Gene

Genomics for MBD4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for MBD4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MBD4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for MBD4

Top Transcription factor binding sites by QIAGEN in the MBD4 gene promoter:
  • AML1a
  • AP-4
  • C/EBPalpha
  • deltaCREB
  • GATA-1
  • Nkx2-5
  • Pax-3
  • Pbx1a
  • RSRFC4

Genomic Locations for MBD4 Gene

Latest Assembly
chr3:129,430,947-129,440,179
(GRCh38/hg38)
Size:
9,233 bases
Orientation:
Minus strand

Previous Assembly
chr3:129,149,790-129,158,791
(GRCh37/hg19 by Entrez Gene)
Size:
9,002 bases
Orientation:
Minus strand

chr3:129,149,787-129,158,878
(GRCh37/hg19 by Ensembl)
Size:
9,092 bases
Orientation:
Minus strand

Genomic View for MBD4 Gene

Genes around MBD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MBD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MBD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MBD4 Gene

Proteins for MBD4 Gene

  • Protein details for MBD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95243-MBD4_HUMAN
    Recommended name:
    Methyl-CpG-binding domain protein 4
    Protein Accession:
    O95243
    Secondary Accessions:
    • B4DZN2
    • D3DNC3
    • D3DNC4
    • E9PEE4
    • Q2MD36
    • Q7Z4T3
    • Q96F09

    Protein attributes for MBD4 Gene

    Size:
    580 amino acids
    Molecular mass:
    66051 Da
    Quaternary structure:
    • Interacts with MLH1.
    Miscellaneous:
    • [Isoform 4]: Possesses uracil DNA glycosylase but not thymine DNA glycosylase activity.

    Three dimensional structures from OCA and Proteopedia for MBD4 Gene

    Alternative splice isoforms for MBD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MBD4 Gene

Post-translational modifications for MBD4 Gene

  • Ubiquitination at Lys484
  • Modification sites at PhosphoSitePlus

Antibodies for research

  • Abcam antibodies for MBD4

No data available for DME Specific Peptides for MBD4 Gene

Domains & Families for MBD4 Gene

Gene Families for MBD4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for MBD4 Gene

InterPro:
Blocks:
  • Methyl-CpG binding

Suggested Antigen Peptide Sequences for MBD4 Gene

GenScript: Design optimal peptide antigens:
  • Mismatch-specific DNA N-glycosylase (MBD4_HUMAN)
genes like me logo Genes that share domains with MBD4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for MBD4 Gene

Function for MBD4 Gene

Molecular function for MBD4 Gene

UniProtKB/Swiss-Prot Function:
Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.
GENATLAS Biochemistry:
methyl-CpG binding protein 4,widely expressed,mutated in carcinoma with microsatellite instability (colorectal carcinoma),encoding an MLH1 interactor

Enzyme Numbers (IUBMB) for MBD4 Gene

Phenotypes From GWAS Catalog for MBD4 Gene

Gene Ontology (GO) - Molecular Function for MBD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA 21873635
GO:0003696 satellite DNA binding TAS 9774669
GO:0003824 catalytic activity IEA --
GO:0004520 endodeoxyribonuclease activity TAS 10097147
GO:0005515 protein binding IPI 12702765
genes like me logo Genes that share ontologies with MBD4: view
genes like me logo Genes that share phenotypes with MBD4: view

Animal Models for MBD4 Gene

MGI Knock Outs for MBD4:

miRNA for MBD4 Gene

miRTarBase miRNAs that target MBD4

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MBD4

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for MBD4 Gene

Localization for MBD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MBD4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MBD4 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MBD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0016607 nuclear speck IDA --
GO:0042025 host cell nucleus IEA --
genes like me logo Genes that share ontologies with MBD4: view

Pathways & Interactions for MBD4 Gene

genes like me logo Genes that share pathways with MBD4: view

Pathways by source for MBD4 Gene

1 Qiagen pathway for MBD4 Gene
  • DNA Repair Mechanisms

Gene Ontology (GO) - Biological Process for MBD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair TAS 10097147
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0032355 response to estradiol IEA --
GO:0045008 depyrimidination TAS --
genes like me logo Genes that share ontologies with MBD4: view

No data available for SIGNOR curated interactions for MBD4 Gene

Drugs & Compounds for MBD4 Gene

(4) Drugs for MBD4 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(9) Additional Compounds for MBD4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with MBD4: view

Transcripts for MBD4 Gene

mRNA/cDNA for MBD4 Gene

5 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MBD4

Alternative Splicing Database (ASD) splice patterns (SP) for MBD4 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c · 2d ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8a · 8b · 8c · 8d
SP1: - - -
SP2: - - - - -
SP3: - - - -
SP4: - - - - -
SP5: - - - - - - - - - - - -
SP6: - - -
SP7: -
SP8:
SP9: -
SP10:

Relevant External Links for MBD4 Gene

GeneLoc Exon Structure for
MBD4

Expression for MBD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MBD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for MBD4 Gene

This gene is overexpressed in Lavage (58.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for MBD4 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for MBD4

SOURCE GeneReport for Unigene cluster for MBD4 Gene:

Hs.35947

Evidence on tissue expression from TISSUES for MBD4 Gene

  • Nervous system(4.7)
  • Lung(4.4)
  • Intestine(2.8)
  • Blood(2.4)
  • Lymph node(2.3)
  • Skin(2.3)
  • Liver(2.3)
  • Spleen(2.2)
  • Pancreas(2.2)
  • Kidney(2.2)
  • Heart(2)
genes like me logo Genes that share expression patterns with MBD4: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for MBD4 Gene

Orthologs for MBD4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for MBD4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia MBD4 29 30
  • 99.48 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia MBD4 29 30
  • 86.27 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia MBD4 29 30
  • 82.85 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Mbd4 29 16 30
  • 78.16 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Mbd4 29
  • 77.92 (n)
Oppossum
(Monodelphis domestica)
Mammalia MBD4 30
  • 57 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia MBD4 30
  • 43 (a)
OneToOne
Chicken
(Gallus gallus)
Aves MBD4 30
  • 46 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia MBD4 30
  • 39 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.6790 29
Zebrafish
(Danio rerio)
Actinopterygii Dr.16765 29
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 56 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.8051 29
Species where no ortholog for MBD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for MBD4 Gene

ENSEMBL:
Gene Tree for MBD4 (if available)
TreeFam:
Gene Tree for MBD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for MBD4: view image
Alliance of Genome Resources:
Additional Orthologs for MBD4

Paralogs for MBD4 Gene

Paralogs for MBD4 Gene

(1) SIMAP similar genes for MBD4 Gene using alignment to 3 proteins:

  • MBD4_HUMAN
  • D6RBI7_HUMAN
  • E9PEE4_HUMAN
genes like me logo Genes that share paralogs with MBD4: view

Variants for MBD4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for MBD4 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
985558 Uncertain Significance: Inborn genetic diseases 129,433,856(-) T/C
NM_001276270.2(MBD4):c.1387A>G (p.Thr463Ala)
MISSENSE
985782 Uncertain Significance: Inborn genetic diseases 129,432,595(-) T/G
NM_001276270.2(MBD4):c.1555A>C (p.Thr519Pro)
MISSENSE
rs2005619 Benign: not provided 129,432,560(-) C/T
NM_001276270.2(MBD4):c.1590G>A (p.Gly530=)
SYNONYMOUS
rs2307293 Uncertain Significance: not specified 129,431,542(-) C/Gp.Asp568His
NM_001276270.2(MBD4):c.1684G>C (p.Asp562His)
MISSENSE_VARIANT,THREE_PRIME_UTR
rs895290906 Likely Benign: not provided 129,433,971(-) T/C
NM_001276270.2(MBD4):c.1272A>G (p.Pro424=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for MBD4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for MBD4 Gene

Variant ID Type Subtype PubMed ID
esv2725901 CNV deletion 23290073
esv3597741 CNV loss 21293372
nsv591668 CNV gain 21841781

Variation tolerance for MBD4 Gene

Residual Variation Intolerance Score: 62% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.59; 72.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MBD4 Gene

Human Gene Mutation Database (HGMD)
MBD4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MBD4
Leiden Open Variation Database (LOVD)
MBD4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MBD4 Gene

Disorders for MBD4 Gene

MalaCards: The human disease database

(4) MalaCards diseases for MBD4 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search MBD4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for MBD4

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with MBD4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MBD4 Gene

Publications for MBD4 Gene

  1. MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1. (PMID: 10097147) Bellacosa A … Neri G (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 4 22
  2. Identification and characterization of a family of mammalian methyl-CpG binding proteins. (PMID: 9774669) Hendrich B … Bird A (Molecular and cellular biology 1998) 2 3 4 22
  3. Single nucleotide polymorphism in the methyl-CpG binding domain 4 gene and the risk for immune thrombocytopenic purpura in Chinese population. (PMID: 20100009) Zhao H … Yang R (Platelets 2010) 3 22 40
  4. The Glu346Lys polymorphism and frameshift mutations of the Methyl-CpG Binding Domain 4 gene in gastrointestinal cancer. (PMID: 19469655) Song JH … Park WS (Neoplasma 2009) 3 22 40
  5. Polymorphisms in uracil-processing genes, but not one-carbon nutrients, are associated with altered DNA uracil concentrations in an urban Puerto Rican population. (PMID: 19403629) Chanson A … Mason JB (The American journal of clinical nutrition 2009) 3 22 40

Products for MBD4 Gene

Sources for MBD4 Gene