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Aliases for MBD5 Gene

Aliases for MBD5 Gene

  • Methyl-CpG Binding Domain Protein 5 2 3 5
  • Methyl-CpG-Binding Protein MBD5 3 4
  • Methyl-CpG-Binding Domain Protein 5 3
  • KIAA1461 4
  • MRD1 3

External Ids for MBD5 Gene

Previous GeneCards Identifiers for MBD5 Gene

  • GC02P147594
  • GC02P149238
  • GC02P149426
  • GC02P149049
  • GC02P148932
  • GC02P148495
  • GC02P148778
  • GC02P140776

Summaries for MBD5 Gene

Entrez Gene Summary for MBD5 Gene

  • This gene encodes a member of the methyl-CpG-binding domain (MBD) family. The MBD consists of about 70 residues and is the minimal region required for a methyl-CpG-binding protein binding specifically to methylated DNA. In addition to the MBD domain, this protein contains a PWWP domain (Pro-Trp-Trp-Pro motif), which consists of 100-150 amino acids and is found in numerous proteins that are involved in cell division, growth and differentiation. Mutations in this gene cause an autosomal dominant type of cognitive disability. The encoded protein interacts with the polycomb repressive complex PR-DUB which catalyzes the deubiquitination of a lysine residue of histone 2A. Haploinsufficiency of this gene is associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures. Alternatively spliced transcript variants have been found, but their full-length nature is not determined. [provided by RefSeq, Jul 2017]

GeneCards Summary for MBD5 Gene

MBD5 (Methyl-CpG Binding Domain Protein 5) is a Protein Coding gene. Diseases associated with MBD5 include Mbd5 Haploinsufficiency and Autosomal Dominant Non-Syndromic Intellectual Disability. Among its related pathways are Metabolism of proteins and Deubiquitination. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is MBD6.

UniProtKB/Swiss-Prot for MBD5 Gene

  • Binds to heterochromatin. Does not interact with either methylated or unmethylated DNA (in vitro).

Additional gene information for MBD5 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MBD5 Gene

Genomics for MBD5 Gene

GeneHancer (GH) Regulatory Elements for MBD5 Gene

Promoters and enhancers for MBD5 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J148018 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 650.7 +0.5 533 5.3 CLOCK DMAP1 YBX1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC ORC4 MBD5 GC02M148014 LOC105373673
GH02J148438 Promoter 0.5 EPDnew 650 +417.8 417804 0.1 MBD5 GC02M148438 GC02M148427
GH02J148976 Enhancer 0.7 Ensembl 13.9 +955.1 955090 0.2 ZNF202 ZNF680 ZBTB11 ZFP64 ZNF140 ZNF266 ZC3H11A REST ZBTB8A ZNF623 EPC2 MBD5 LOC101928553 LYPD6B KIF5C
GH02J148201 Enhancer 0.8 ENCODE 0.1 +180.5 180536 0.2 ELF3 FOXA2 ARID4B DMAP1 ZNF48 ZSCAN9 RAD21 ZNF614 ZNF143 THAP11 GC02M148193 ENSG00000212181 GC02M148261 MBD5
GH02J148259 Enhancer 0.8 FANTOM5 0.1 +238.8 238815 0.3 BACH1 CHAMP1 ZNF316 RBAK ZNF26 ZNF169 ZNF143 NFE2 ATF7 TRIM24 GC02M148261 ENSG00000212181 ACVR2A EPC2 GC02M148193 MBD5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MBD5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MBD5 gene promoter:
  • FOXI1
  • Nkx2-5
  • HFH-3
  • HSF1 (long)
  • TBP
  • HSF1short
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • FOXO4

Genomic Locations for MBD5 Gene

Genomic Locations for MBD5 Gene
495,961 bases
Plus strand
497,226 bases
Plus strand

Genomic View for MBD5 Gene

Genes around MBD5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MBD5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MBD5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MBD5 Gene

Proteins for MBD5 Gene

  • Protein details for MBD5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Methyl-CpG-binding domain protein 5
    Protein Accession:
    Secondary Accessions:
    • A5HMQ4
    • A7E2B1
    • Q53SR1
    • Q9NUV6

    Protein attributes for MBD5 Gene

    1494 amino acids
    Molecular mass:
    159895 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA92013.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA95985.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for MBD5 Gene


neXtProt entry for MBD5 Gene

Post-translational modifications for MBD5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for MBD5 Gene

Domains & Families for MBD5 Gene

Gene Families for MBD5 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for MBD5 Gene

Suggested Antigen Peptide Sequences for MBD5 Gene

Graphical View of Domain Structure for InterPro Entry



  • Both MBD and PWWP domains are necessary for chromocentric localization.
  • Both MBD and PWWP domains are necessary for chromocentric localization.
genes like me logo Genes that share domains with MBD5: view

Function for MBD5 Gene

Molecular function for MBD5 Gene

UniProtKB/Swiss-Prot Function:
Binds to heterochromatin. Does not interact with either methylated or unmethylated DNA (in vitro).

Phenotypes From GWAS Catalog for MBD5 Gene

Gene Ontology (GO) - Molecular Function for MBD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 NOT DNA binding IDA 20700456
GO:0003682 chromatin binding IDA 20700456
genes like me logo Genes that share ontologies with MBD5: view
genes like me logo Genes that share phenotypes with MBD5: view

Human Phenotype Ontology for MBD5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for MBD5 Gene

MGI Knock Outs for MBD5:
  • Mbd5 Mbd5<tm1b(EUCOMM)Wtsi>
  • Mbd5 Mbd5<tm1.2Gxu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MBD5

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for MBD5 Gene

Localization for MBD5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MBD5 Gene

Isoform 1: Nucleus. Chromosome. Note=Associated with pericentric heterochromatin.
Isoform 2: Nucleus. Note=Not associated with pericentric heterochromatin.

Subcellular locations from

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 MBD5 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Midbody (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MBD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 20700456
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0010369 chromocenter IDA 20700456
GO:0030496 midbody IDA --
genes like me logo Genes that share ontologies with MBD5: view

Pathways & Interactions for MBD5 Gene

genes like me logo Genes that share pathways with MBD5: view

Pathways by source for MBD5 Gene

Gene Ontology (GO) - Biological Process for MBD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007399 nervous system development IMP 23587880
GO:0016579 protein deubiquitination TAS --
GO:0040014 regulation of multicellular organism growth ISS --
GO:0042593 glucose homeostasis ISS --
GO:0050795 regulation of behavior IMP 23587880
genes like me logo Genes that share ontologies with MBD5: view

No data available for SIGNOR curated interactions for MBD5 Gene

Drugs & Compounds for MBD5 Gene

No Compound Related Data Available

Transcripts for MBD5 Gene

Unigene Clusters for MBD5 Gene

Methyl-CpG binding domain protein 5:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MBD5

Alternative Splicing Database (ASD) splice patterns (SP) for MBD5 Gene

No ASD Table

Relevant External Links for MBD5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MBD5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MBD5 Gene

Protein differential expression in normal tissues from HIPED for MBD5 Gene

This gene is overexpressed in Tlymphocyte (68.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for MBD5 Gene

Protein tissue co-expression partners for MBD5 Gene

NURSA nuclear receptor signaling pathways regulating expression of MBD5 Gene:


SOURCE GeneReport for Unigene cluster for MBD5 Gene:


mRNA Expression by UniProt/SwissProt for MBD5 Gene:

Tissue specificity: Detected in heart, placenta, liver, skeletal muscle, kidney and pancreas.

Evidence on tissue expression from TISSUES for MBD5 Gene

  • Nervous system(4.5)
  • Muscle(2.6)
  • Thyroid gland(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for MBD5 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • pharynx
  • skull
  • tooth
  • chest wall
  • heart
  • abdominal wall
  • intestine
  • large intestine
  • rectum
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with MBD5: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for MBD5 Gene

Orthologs for MBD5 Gene

This gene was present in the common ancestor of animals.

Orthologs for MBD5 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia MBD5 34 33
  • 99.53 (n)
(Canis familiaris)
Mammalia MBD5 34 33
  • 96.71 (n)
(Bos Taurus)
Mammalia MBD5 34 33
  • 95.65 (n)
(Mus musculus)
Mammalia Mbd5 16 34 33
  • 93.75 (n)
(Monodelphis domestica)
Mammalia MBD5 34
  • 90 (a)
(Ornithorhynchus anatinus)
Mammalia MBD5 34
  • 48 (a)
(Gallus gallus)
Aves MBD5 34 33
  • 86 (n)
(Anolis carolinensis)
Reptilia MBD5 34
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia mbd5 33
  • 75.16 (n)
(Danio rerio)
Actinopterygii mbd5 34
  • 56 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.14069 33
fruit fly
(Drosophila melanogaster)
Insecta sba 34
  • 11 (a)
Species where no ortholog for MBD5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 MBD5 Gene

Gene Tree for MBD5 (if available)
Gene Tree for MBD5 (if available)
Evolutionary constrained regions (ECRs) for MBD5: view image

Paralogs for MBD5 Gene

Paralogs for MBD5 Gene

(2) SIMAP similar genes for MBD5 Gene using alignment to 4 proteins:

  • A1L0W4_HUMAN
  • H7C066_HUMAN
genes like me logo Genes that share paralogs with MBD5: view

Variants for MBD5 Gene

Sequence variations from dbSNP and Humsavar for MBD5 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1031744379 likely-benign, Mental retardation, autosomal dominant 1 148,469,863(+) T/C coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1057522316 likely-benign, uncertain-significance, not specified, Mental retardation, autosomal dominant 1 148,489,831(+) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1060501150 uncertain-significance, Mental retardation, autosomal dominant 1 148,470,221(+) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1060501151 pathogenic, Mental retardation, autosomal dominant 1 148,512,906(+) CCCCCC/CCCCC/CCCCCCC coding_sequence_variant, frameshift, genic_downstream_transcript_variant
rs1060501152 uncertain-significance, Mental retardation, autosomal dominant 1 148,470,369(+) C/G coding_sequence_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for MBD5 Gene

Variant ID Type Subtype PubMed ID
dgv4092n100 CNV loss 25217958
dgv743e214 CNV loss 21293372
esv1091060 CNV deletion 17803354
esv1092103 CNV deletion 17803354
esv2450736 CNV deletion 19546169
esv2660027 CNV deletion 23128226
esv27183 CNV loss 19812545
esv2720941 CNV deletion 23290073
esv2720942 CNV deletion 23290073
esv2751831 CNV gain 17911159
esv2762913 CNV gain 21179565
esv29150 CNV loss 19812545
esv3336236 CNV insertion 20981092
esv3393608 CNV insertion 20981092
esv3584100 CNV loss 25503493
esv3584101 CNV loss 25503493
esv3592833 CNV loss 21293372
esv3592834 CNV loss 21293372
esv3592835 CNV gain 21293372
esv3592836 CNV loss 21293372
esv3592839 CNV gain 21293372
esv3592840 CNV loss 21293372
esv3592841 CNV loss 21293372
esv3592842 CNV gain 21293372
esv3592843 CNV loss 21293372
esv3592844 CNV loss 21293372
esv3592845 CNV loss 21293372
esv3592846 CNV loss 21293372
esv3893492 CNV loss 25118596
nsv1004431 CNV loss 25217958
nsv1004663 CNV gain 25217958
nsv1009608 CNV loss 25217958
nsv1012123 CNV loss 25217958
nsv1012275 CNV gain 25217958
nsv1015003 CNV gain 25217958
nsv1141368 CNV duplication 24896259
nsv1151248 CNV deletion 26484159
nsv477271 CNV novel sequence insertion 20440878
nsv518198 CNV loss 19592680
nsv523090 CNV loss 19592680
nsv583289 CNV loss 21841781
nsv583290 CNV loss 21841781
nsv961895 CNV duplication 23825009
nsv999952 CNV gain 25217958

Variation tolerance for MBD5 Gene

Residual Variation Intolerance Score: 2.01% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.81; 47.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MBD5 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MBD5 Gene

Disorders for MBD5 Gene

MalaCards: The human disease database

(13) MalaCards diseases for MBD5 Gene - From: HGMD, ClinVar, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mbd5 haploinsufficiency
  • 2q23.1 microdeletion syndrome
autosomal dominant non-syndromic intellectual disability
  • autosomal dominant mental retardation
senile entropion
  • involutional entropion
paralytic lagophthalmos
- elite association - COSMIC cancer census association via MalaCards
Search MBD5 in MalaCards View complete list of genes associated with diseases


  • Mental retardation, autosomal dominant 1 (MRD1) [MIM:156200]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269 PubMed:17847001, ECO:0000269 PubMed:22726846}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for MBD5

genes like me logo Genes that share disorders with MBD5: view

No data available for Genatlas for MBD5 Gene

Publications for MBD5 Gene

  1. Copy-number variations measured by single-nucleotide-polymorphism oligonucleotide arrays in patients with mental retardation. (PMID: 17847001) Wagenstaller J … Strom TM (American journal of human genetics 2007) 3 4 22 58
  2. Comparative study of methyl-CpG-binding domain proteins. (PMID: 12529184) Roloff TC … Nuber UA (BMC genomics 2003) 2 3 4 58
  3. The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA. (PMID: 20700456) Laget S … Defossez PA (PloS one 2010) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for MBD5 Gene

Sources for MBD5 Gene

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