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MBD5 methyl-CpG binding domain protein 5 [ Homo sapiens (human) ]

Gene ID: 55777, updated on 7-Oct-2018

Summary

Official Symbol
MBD5provided by HGNC
Official Full Name
methyl-CpG binding domain protein 5provided by HGNC
Primary source
HGNC:HGNC:20444
See related
Ensembl:ENSG00000204406 MIM:611472; Vega:OTTHUMG00000150440
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MRD1
Summary
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]
Expression
Ubiquitous expression in brain (RPKM 2.6), gall bladder (RPKM 2.4) and 25 other tissues See more
Orthologs

Genomic context

See MBD5 in Genome Data Viewer
Location:
2q23.1
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (148021011..148516923)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (148778580..149271046)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1275, pseudogene Neighboring gene activin A receptor type 2A Neighboring gene uncharacterized LOC105373674 Neighboring gene uncharacterized LOC105373673 Neighboring gene origin recognition complex subunit 4 Neighboring gene ubiquitin specific peptidase 12 pseudogene Neighboring gene ADP ribosylation factor like GTPase 5A pseudogene Neighboring gene ribosomal protein S29 pseudogene 8 Neighboring gene enhancer of polycomb homolog 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, autosomal dominant 1
MedGen: C1969562 OMIM: 156200 GeneReviews: MBD5 Haploinsufficiency
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

Little evidence for dosage pathogenicity (Last evaluated (2016-08-11)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2016-08-11)

ClinGen Genome Curation PagePubMed

Pathways from BioSystems

  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • UCH proteinases, organism-specific biosystem (from REACTOME)
    UCH proteinases, organism-specific biosystemDUBs of the Ub C-terminal Hydrolase (UCH) family are thiol proteases that have an N-terminal catalytic domain sometimes followed by C-terminal extensions that mediate protein-protein interactions. Hu...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11113, FLJ30517, KIAA1461

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NOT DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
glucose homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 
nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of growth hormone receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
protein deubiquitination TAS
Traceable Author Statement
more info
 
regulation of behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of multicellular organism growth ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
chromocenter IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromocenter IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
midbody IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
methyl-CpG-binding domain protein 5
Names
methyl-CpG-binding protein MBD5

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_017003.1 RefSeqGene

    Range
    5001..497467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018328.4NP_060798.2  methyl-CpG-binding domain protein 5

    See identical proteins and their annotated locations for NP_060798.2

    Status: REVIEWED

    Source sequence(s)
    AB040894, CA449443, DA240785, EF542797
    Consensus CDS
    CCDS33302.1
    UniProtKB/Swiss-Prot
    Q9P267
    Related
    ENSP00000386049.1, OTTHUMP00000197369, ENST00000407073.5, OTTHUMT00000318111
    Conserved Domains (2) summary
    cl00110
    Location:2179
    MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
    cl02554
    Location:13831460
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    148021011..148516923
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511472.2XP_011509774.1  methyl-CpG-binding domain protein 5 isoform X1

    See identical proteins and their annotated locations for XP_011509774.1

    Conserved Domains (2) summary
    cd05835
    Location:16161706
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    cl00110
    Location:2179
    MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
  2. XM_011511470.2XP_011509772.1  methyl-CpG-binding domain protein 5 isoform X1

    See identical proteins and their annotated locations for XP_011509772.1

    Conserved Domains (2) summary
    cd05835
    Location:16161706
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    cl00110
    Location:2179
    MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
  3. XM_024452987.1XP_024308755.1  methyl-CpG-binding domain protein 5 isoform X2

    Related
    ENSP00000384672.1, ENST00000404807.5
    Conserved Domains (2) summary
    cl00110
    Location:2179
    MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
    cl02554
    Location:16161693
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
  4. XM_024452990.1XP_024308758.1  methyl-CpG-binding domain protein 5 isoform X5

    Related
    ENSP00000490728.2, ENST00000638043.2
    Conserved Domains (2) summary
    cd05835
    Location:13831473
    Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...
    cl00110
    Location:2179
    MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
  5. XM_024452988.1XP_024308756.1  methyl-CpG-binding domain protein 5 isoform X3

    Conserved Domains (2) summary
    cl00110
    Location:2179
    MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
    cl02554
    Location:16161692
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
  6. XM_024452989.1XP_024308757.1  methyl-CpG-binding domain protein 5 isoform X4

    Conserved Domains (2) summary
    cl00110
    Location:2179
    MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
    cl02554
    Location:16161679
    PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

RNA

  1. XR_002959318.1 RNA Sequence

  2. XR_002959319.1 RNA Sequence

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