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MECP2 methyl-CpG binding protein 2 [ Homo sapiens (human) ]

Gene ID: 4204, updated on 8-Jul-2018
Official Symbol
MECP2provided by HGNC
Official Full Name
methyl-CpG binding protein 2provided by HGNC
Primary source
HGNC:HGNC:6990
See related
Ensembl:ENSG00000169057 MIM:300005; Vega:OTTHUMG00000024229
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
RS; RTS; RTT; PPMX; MRX16; MRX79; MRXSL; AUTSX3; MRXS13
Summary
DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 is dispensible in stem cells, but is essential for embryonic development. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of cognitive disability in females. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]
Expression
Ubiquitous expression in ovary (RPKM 10.4), brain (RPKM 8.2) and 25 other tissues See more
Orthologs
mouse all
See MECP2 in Genome Data Viewer
Location:
Xq28
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (154021800..154097731, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153287025..153363188, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NFE2L2 motif-containing MPRA enhancer 190/191 Neighboring gene interleukin 1 receptor associated kinase 1 Neighboring gene microRNA 718 Neighboring gene opsin locus control region Neighboring gene opsin 1, long wave sensitive Neighboring gene testis expressed 28 pseudogene 2

Go to nucleotide: Graphics FASTA GenBank

  • 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

Related articles in PubMed

  1. First report of an unusual novel double mutation affecting the transcription repression domain of MeCP2 and causing a severe phenotype of Rett syndrome: Molecular analyses and computational investigation. Ghorbel R, et al. Biochem Biophys Res Commun, 2018 Feb 26. PMID 29421650
  2. Clinical and molecular genetic characterization of familial MECP2 duplication syndrome in a Chinese family. Li X, et al. BMC Med Genet, 2017 Nov 15. PMID 29141583, Free PMC Article
  3. Biophysical characterization of the basic cluster in the transcription repression domain of human MeCP2 with AT-rich DNA. Mushtaq AU, et al. Biochem Biophys Res Commun, 2018 Jan 1. PMID 29101034
  4. Identification of autism-related MECP2 mutations by whole-exome sequencing and functional validation. Wen Z, et al. Mol Autism, 2017. PMID 28785396, Free PMC Article
  5. MECP2 expression in gastric cancer and its correlation with clinical pathological parameters. Zhang J, et al. Medicine (Baltimore), 2017 Aug. PMID 28767600, Free PMC Article

See all (556) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  1. This study suggests that methylation of Wnt pathway genes, in addition to known CpG island methylator phenotype markers, may help predict treatment outcome and survival in patients with CRC[colorectal cancer.
    Title: CpG Island Methylator Phenotype and Methylation of Wnt Pathway Genes Together Predict Survival in Patients with Colorectal Cancer.
  2. Results show that highly expressed phospho-MeCP2-S421 and its association with VEGF in proliferative diabetic retinopathy (PDR) membranes suggests that phospho-MeCP2-S421 might involve in the pathogenesis of PDR.
    Title: The significance of the increased expression of phosphorylated MeCP2 in the membranes from patients with proliferative diabetic retinopathy.
  3. MeCP2 behaves similarly to histone H1 and HMGD1 in creating a higher-order chromatin structure, which is susceptible to chromatin remodeling by ISWI.
    Title: Comparative analysis of linker histone H1, MeCP2, and HMGD1 on nucleosome stability and target site accessibility.
  4. these lines of evidence strongly suggest that MeCP2-P152L, MeCP2-R294X, and MeCP2-P376S, identified in autism patients, affect the proper physiological functions of the MeCP2 protein and thus may contribute the pathogenesis of autism.
    Title: Identification of autism-related <i>MECP2</i> mutations by whole-exome sequencing and functional validation.
  5. Data show that miR-98 could inhibit Mecp2 expression by binding the 3'-untranslated region (UTR) of methyl CpG binding protein 2 (Mecp2).
    Title: Up-regulation of miR-98 and unraveling regulatory mechanisms in gestational diabetes mellitus.
  6. Missense mutations in the gene disrupt the interaction of the MeCP2 with TBLR1 resulting in Rett syndrome and related disorders.
    Title: Structure of the MeCP2-TBLR1 complex reveals a molecular basis for Rett syndrome and related disorders.
  7. Two putative modulators of MeCP2, HIPK2 (homeodomain-interacting protein kinase 2) and PP2A (protein phosphatase 2A), were validated as stabilizers of MeCP2 in vivo.
    Title: An RNA interference screen identifies druggable regulators of MeCP2 stability.
  8. This study identified 2 RTT patients each with pathogenic double MECP2 mutation. Indeed, the first one was a novel double mutation.
    Title: Clinical, Molecular, and Computational Analysis in Patients With a Novel Double Mutation and a New Synonymous Variant in MeCP2: Report of the First Missense Mutation Within the AT-hook1 Cluster in Rett Syndrome.
  9. MBD family is involved in the pathogenesis of Chronic Hepatitis B and is correlated with disease progression, suggesting the value in evaluating disease severity.
    Title: Alteration of methyl-CpG binding domain family in patients with chronic hepatitis B.
  10. MeCP2 tunes gene expression in neurons by binding within the transcribed regions of genes to impede the elongation of RNA polymerase
    Title: DNA methylation in the gene body influences MeCP2-mediated gene repression.
Submit: New GeneRIF Correction See all GeneRIFs (415)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-05)

ClinGen Genome Curation Page
Triplosensitivity

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-05)

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
Common variants on Xq28 conferring risk of schizophrenia in Han Chinese.
NHGRI GWA Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
NHGRI GWA Catalog
Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.
NHGRI GWA Catalog

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Protein interactions

Protein Gene Interaction Pubs
Nef nef MECP2 mRNA is selectively retained in HIV-1 Nef-expressing cellular exosomes, and eight miRNAs (miR-19a, miR-29b, miR-34a*, miR-146b, miR-181a, miR181c, miR-195, and let-7c) which target MECP2 mRNA are selectively secreted in exosomes from these cells PubMed

Go to the HIV-1, Human Interaction Database

  • Cytosine methylation, organism-specific biosystem (from WikiPathways)
    Cytosine methylation, organism-specific biosystemDNA, namely cytosine, methylation is the key event in epigentics. The degree of methylation influences gene expression and methylation disorders are known to be major causes of some diseases like Ret...
  • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Lung fibrosis, organism-specific biosystem (from WikiPathways)
    Lung fibrosis, organism-specific biosystemLung fibrosis pathway linked to events (molecular initiating event, key events and associative events) in a putative Adverse Outcome Pathway for lung fibrosis.
  • MECP2 and Associated Rett Syndrome, organism-specific biosystem (from WikiPathways)
    MECP2 and Associated Rett Syndrome, organism-specific biosystemMecp2 is in many mammals an important regulator of neuronal function and development. It affects all cell types, especially neurons but also astrocytes, oligodendrocytes, and glial cells. Mecp2 plays...
  • Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • DKFZp686A24160

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
DNA binding TAS
Traceable Author Statement
more info
 PubMed 
RNA binding HDA PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
  
double-stranded methylated DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
double-stranded methylated DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
mRNA binding IEA
Inferred from Electronic Annotation
more info
  
methyl-CpG binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein N-terminus binding IPI
Inferred from Physical Interaction
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
 PubMed 
siRNA binding IEA
Inferred from Electronic Annotation
more info
  
transcription corepressor activity TAS
Traceable Author Statement
more info
 PubMed 
transcription factor binding IEA
Inferred from Electronic Annotation
more info
  
transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
behavioral fear response IEA
Inferred from Electronic Annotation
more info
  
cardiolipin metabolic process IEA
Inferred from Electronic Annotation
more info
  
catecholamine secretion IEA
Inferred from Electronic Annotation
more info
  
cellular biogenic amine metabolic process IEA
Inferred from Electronic Annotation
more info
  
cerebellum development IEA
Inferred from Electronic Annotation
more info
  
chromatin silencing IEA
Inferred from Electronic Annotation
more info
  
dendrite development IEA
Inferred from Electronic Annotation
more info
  
excitatory postsynaptic potential IEA
Inferred from Electronic Annotation
more info
  
glucocorticoid metabolic process IEA
Inferred from Electronic Annotation
more info
  
glutamine metabolic process IEA
Inferred from Electronic Annotation
more info
  
histone acetylation IEA
Inferred from Electronic Annotation
more info
  
histone methylation IEA
Inferred from Electronic Annotation
more info
  
inositol metabolic process IEA
Inferred from Electronic Annotation
more info
  
locomotory behavior IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
long-term memory IEA
Inferred from Electronic Annotation
more info
  
long-term synaptic potentiation IEA
Inferred from Electronic Annotation
more info
  
mitochondrial electron transport, ubiquinol to cytochrome c IEA
Inferred from Electronic Annotation
more info
  
mitotic spindle organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
negative regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
negative regulation of blood vessel endothelial cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
negative regulation of gene expression IDA
Inferred from Direct Assay
more info
 PubMed 
negative regulation of histone acetylation IEA
Inferred from Electronic Annotation
more info
  
negative regulation of histone methylation IEA
Inferred from Electronic Annotation
more info
  
negative regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
  
negative regulation of smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
 PubMed 
neurological system process involved in regulation of systemic arterial blood pressure IEA
Inferred from Electronic Annotation
more info
  
neuron maturation IEA
Inferred from Electronic Annotation
more info
  
pathogenesis IEA
Inferred from Electronic Annotation
more info
  
phosphatidylcholine metabolic process IEA
Inferred from Electronic Annotation
more info
  
positive regulation of DNA methylation IDA
Inferred from Direct Assay
more info
 PubMed 
positive regulation of G2/M transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
positive regulation of histone H3-K9 trimethylation IEA
Inferred from Electronic Annotation
more info
  
positive regulation of microtubule nucleation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
positive regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
  
positive regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
  
post-embryonic development IEA
Inferred from Electronic Annotation
more info
  
proprioception IEA
Inferred from Electronic Annotation
more info
  
protein localization IEA
Inferred from Electronic Annotation
more info
  
regulation of gene expression by genetic imprinting IEA
Inferred from Electronic Annotation
more info
  
regulation of respiratory gaseous exchange by neurological system process IEA
Inferred from Electronic Annotation
more info
  
respiratory gaseous exchange IEA
Inferred from Electronic Annotation
more info
  
response to hypoxia IEA
Inferred from Electronic Annotation
more info
  
response to radiation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
sensory perception of pain IEA
Inferred from Electronic Annotation
more info
  
social behavior IEA
Inferred from Electronic Annotation
more info
  
startle response IEA
Inferred from Electronic Annotation
more info
  
synapse assembly IEA
Inferred from Electronic Annotation
more info
  
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
  
ventricular system development IEA
Inferred from Electronic Annotation
more info
  
visual learning IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
colocalizes_with centrosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
extracellular space HDA PubMed 
colocalizes_with gamma-tubulin complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 
heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
heterochromatin IDA
Inferred from Direct Assay
more info
 PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
  
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
postsynapse IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
methyl-CpG-binding protein 2
Names
meCp-2 protein
testis tissue sperm-binding protein Li 41a

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_007107.2 RefSeqGene

    Range
    44391..120315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001110792.1 → NP_001104262.1  methyl-CpG-binding protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001104262.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as MECP2B, lacks exon 2. Translation is reported to initiate in the first exon resulting in a protein isoform (2) with a distinct N-terminus. This transcript is reported to be abundant in the central nervous system (PMID: 15034579, 17171659).
    Source sequence(s)
    AB209464, BC011612, BX538060
    Consensus CDS
    CCDS48193.1
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    A0A140VKC4, Q59FJ6
    Related
    ENSP00000395535.2, OTTHUMP00000064436, ENST00000453960.6, OTTHUMT00000061145
    Conserved Domains (1) summary
    smart00391
    Location:104 → 181
    MBD; Methyl-CpG binding domain

  2. NM_001316337.1 → NP_001303266.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes exon 2 and an additional exon, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AB209464, AF030876, BC011612, BI767019
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    Q59FJ6
    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  3. NM_004992.3 → NP_004983.1  methyl-CpG-binding protein 2 isoform 1

    See identical proteins and their annotated locations for NP_004983.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as MECP2A, includes exon 2. Translation is reported to initiate in exon 2 resulting in a protein isoform (1) with a distinct N-terminus.
    Source sequence(s)
    AB209464, AC244097, AF158180
    Consensus CDS
    CCDS14741.1
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    D3YJ43, Q59FJ6
    Related
    ENSP00000301948.6, OTTHUMP00000026021, ENST00000303391.10, OTTHUMT00000061144
    Conserved Domains (1) summary
    smart00391
    Location:92 → 169
    MBD; Methyl-CpG binding domain

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_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    154021800..154097731 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452383.1 → XP_024308151.1  methyl-CpG-binding protein 2 isoform X1

    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  2. XM_024452384.1 → XP_024308152.1  methyl-CpG-binding protein 2 isoform X1

    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  3. XM_011531166.2 → XP_011529468.1  methyl-CpG-binding protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011529468.1

    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  4. XM_006724819.3 → XP_006724882.1  methyl-CpG-binding protein 2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51608.1 GenPept UniProtKB/Swiss-Prot:P51608

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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