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

    Gene ID: 4204, updated on 26-Jul-2021

    Summary

    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
    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
    NEW
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    Try the new Transcript table

    Genomic context

    See MECP2 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (154021573..154097717, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153287024..153363174, 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

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Autism, susceptibility to, X-linked 3
    MedGen: C1845336 OMIM: 300496 GeneReviews: MECP2 Disorders
    Compare labs
    Common variants on Xq28 conferring risk of schizophrenia in Han Chinese.
    GeneReviews: Not available
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    GeneReviews: Not available
    Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.
    GeneReviews: Not available
    Mental retardation, X-linked, syndromic 13
    MedGen: C1968550 OMIM: 300055 GeneReviews: MECP2 Disorders
    Compare labs
    Rett syndrome
    MedGen: C0035372 OMIM: 312750 GeneReviews: MECP2 Disorders
    Compare labs
    Severe neonatal-onset encephalopathy with microcephaly
    MedGen: C1968556 OMIM: 300673 GeneReviews: MECP2 Disorders
    Compare labs
    Syndromic X-linked intellectual disability Lubs type
    MedGen: C1846058 OMIM: 300260 GeneReviews: MECP2 Duplication Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-02-22)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-02-22)

    ClinGen Genome Curation PagePubMed

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • DKFZp686A24160

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA binding HDA PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables double-stranded methylated DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables double-stranded methylated DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables mRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables methyl-CpG binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables promoter-specific chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein N-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables siRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in adult locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in behavioral fear response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cardiolipin metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular biogenic amine metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cerebellum development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin silencing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dendrite development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in excitatory postsynaptic potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glucocorticoid metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glutamine metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in histone acetylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in histone methylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inositol metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in long-term memory IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in long-term synaptic potentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitotic spindle organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of blood vessel endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of smooth muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nervous system process involved in regulation of systemic arterial blood pressure IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron maturation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phosphatidylcholine metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of G2/M transition of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of histone H3-K9 trimethylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of microtubule nucleation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in post-embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proprioception IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within regulation of gene expression by genetic imprinting IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of respiratory gaseous exchange by nervous system process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in respiratory gaseous exchange by respiratory system IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to other organism IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of pain IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in social behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in startle response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in synapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ventricular system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual learning IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in centrosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular space HDA PubMed 
    is_active_in heterochromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in heterochromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    methyl-CpG-binding protein 2
    Names
    meCp-2 protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_007107.3 RefSeqGene

      Range
      44387..120531
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_764

    mRNA and Protein(s)

    1. NM_001110792.2NP_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)
      AF030876, BC011612, BX538060, U52112
      Consensus CDS
      CCDS48193.1
      UniProtKB/Swiss-Prot
      P51608
      UniProtKB/TrEMBL
      A0A140VKC4, Q59FJ6
      Related
      ENSP00000395535.2, ENST00000453960.7
      Conserved Domains (1) summary
      smart00391
      Location:104181
      MBD; Methyl-CpG binding domain
    2. NM_001316337.2NP_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. Variants 3-7 all encode the same isoform (3).
      Source sequence(s)
      AB209464, AF030876, BC011612, BI767019, U52112
      UniProtKB/Swiss-Prot
      P51608
      UniProtKB/TrEMBL
      Q59FJ6
      Conserved Domains (1) summary
      smart00391
      Location:176
      MBD; Methyl-CpG binding domain
    3. NM_001369391.2NP_001356320.1  methyl-CpG-binding protein 2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) includes exon 2 and some additional exons, 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. Variants 3-7 all encode the same isoform (3).
      Source sequence(s)
      AC244097, AF030876, U52112
      Conserved Domains (1) summary
      smart00391
      Location:176
      MBD; Methyl-CpG binding domain
    4. NM_001369392.2NP_001356321.1  methyl-CpG-binding protein 2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) 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. Variants 3-7 all encode the same isoform (3).
      Source sequence(s)
      AC244097, AF030876, U52112
      Conserved Domains (1) summary
      smart00391
      Location:176
      MBD; Methyl-CpG binding domain
    5. NM_001369393.2NP_001356322.1  methyl-CpG-binding protein 2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks exon 2 and contains 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. Variants 3-7 all encode the same isoform (3).
      Source sequence(s)
      AC244097, AF030876, U52112
      Conserved Domains (1) summary
      smart00391
      Location:176
      MBD; Methyl-CpG binding domain
    6. NM_001369394.2NP_001356323.1  methyl-CpG-binding protein 2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3-7 all encode the same isoform (3).
      Source sequence(s)
      AC244097, AF030876, U52112
      Conserved Domains (1) summary
      smart00391
      Location:176
      MBD; Methyl-CpG binding domain
    7. NM_001386137.1NP_001373066.1  methyl-CpG-binding protein 2 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC244097, AF030876, U52112
    8. NM_001386138.1NP_001373067.1  methyl-CpG-binding protein 2 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC244097, AF030876, U52112
    9. NM_001386139.1NP_001373068.1  methyl-CpG-binding protein 2 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC244097, AF030876, U52112
    10. NM_004992.4NP_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)
      AC244097, AF030876, U52112
      Consensus CDS
      CCDS14741.1
      UniProtKB/Swiss-Prot
      P51608
      UniProtKB/TrEMBL
      D3YJ43, Q59FJ6
      Related
      ENSP00000301948.6, ENST00000303391.11
      Conserved Domains (1) summary
      smart00391
      Location:92169
      MBD; Methyl-CpG binding domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

      Range
      154021573..154097717 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Conserved Domains (1) summary
      smart00391
      Location:176
      MBD; Methyl-CpG binding domain
    2. XM_011531166.2XP_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:176
      MBD; Methyl-CpG binding domain
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