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GeneE
50 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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MECP2
methyl-CpG binding protein 2
Chromosome X Β· Xq28
NCBI Gene: 4204Ensembl: ENSG00000169057.26HGNC: HGNC:6990UniProt: A0A140VKC4
740PubMed Papers
26Diseases
0Drugs
819Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub GeneTranscription Factor
RESEARCH IMPACT
Highly StudiedTrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
negative regulation of angiogenesisnegative regulation of blood vessel endothelial cell migrationnucleic acid bindingnegative regulation of DNA-templated transcriptionRett syndromeX-linked intellectual disability-psychosis-macroorchidism syndromesevere neonatal-onset encephalopathy with microcephalyX-linked intellectual disability - psychosis - macroorchidism
✦AI Summary

MECP2 encodes methyl-CpG-binding protein 2, an X-linked epigenetic regulator that binds methylated DNA at CpG sites with preference for 5-methylcytosine 1. In human neurons, MECP2 occupies CpG-rich promoter-proximal regions of over 4,000 genes, including autism risk genes, and directly interacts with RNA polymerase II to function as a positive cofactor for gene expression rather than exclusively as a repressor 1. MECP2 operates as a multifunctional epigenetic hub that orchestrates neuronal gene regulation, chrX structure, and transcriptional processes through interactions with DNA, RNA, and transcription factors 2. Mutations in MECP2 cause Rett syndrome, a severe neurodevelopmental disorder affecting predominantly females, characterized by developmental regression, language impairment, loss of purposeful hand skills, and stereotypies 3. Beyond neurological manifestations, MECP2 dysfunction contributes to metabolic dysregulation, including perturbed lipid metabolism in brain and peripheral tissues 4. Loss of MECP2 function reduces expression of genes occupied by both MECP2 and RNA Pol II, accounting for RTT pathogenesis 1. Emerging gene therapy approaches show promise, though careful dose regulation is essential to avoid toxicity 5. MECP2 mutations are also implicated in related neurodevelopmental disorders including autism and neonatal encephalopathy, underscoring the gene's critical role in neuronal development and function.

Sources cited
1
MECP2 occupies CpG-rich promoter-proximal regions of >4000 genes, interacts directly with RNA Pol II, and functions as a positive cofactor for gene expression in human neurons
PMID: 38697112
2
MECP2 functions as an interacting hub for DNA, RNA and transcription factors, orchestrating neuronal gene regulation and chromatin structure
PMID: 40360671
3
Rett syndrome is a neurodevelopmental disorder caused by MECP2 mutations, characterized by developmental regression, language impairment, and loss of hand skills
PMID: 39331775
4
MECP2 dysfunction contributes to metabolic components including perturbed lipid metabolism in brain and peripheral tissues
PMID: 29445033
5
Gene therapy for RTT requires dose-regulated MECP2 expression to avoid dose-dependent toxicity
PMID: 38723617
6
MECP2 mutations are associated with a spectrum of neurodevelopmental disorders including autism spectrum disorders
PMID: 24615633
Disease Associationsβ“˜26
Rett syndromeOpen Targets
0.88Strong
X-linked intellectual disability-psychosis-macroorchidism syndromeOpen Targets
0.81Strong
severe neonatal-onset encephalopathy with microcephalyOpen Targets
0.80Strong
X-linked intellectual disability - psychosis - macroorchidismOpen Targets
0.77Strong
syndromic X-linked intellectual disability Lubs typeOpen Targets
0.74Strong
Angelman syndromeOpen Targets
0.63Moderate
atypical Rett syndromeOpen Targets
0.61Moderate
genetic disorderOpen Targets
0.56Moderate
Intellectual disabilityOpen Targets
0.55Moderate
Neurodevelopmental delayOpen Targets
0.53Moderate
cancerOpen Targets
0.49Moderate
SeizureOpen Targets
0.48Moderate
Abnormality of the nervous systemOpen Targets
0.46Moderate
chromosome Xq28 duplication syndromeOpen Targets
0.46Moderate
autismOpen Targets
0.45Moderate
non-syndromic X-linked intellectual disabilityOpen Targets
0.45Moderate
Neurodevelopmental disorderOpen Targets
0.43Moderate
Global developmental delayOpen Targets
0.43Moderate
Delayed speech and language developmentOpen Targets
0.43Moderate
Developmental regressionOpen Targets
0.43Moderate
Angelman syndromeUniProt
Autism, X-linked 3UniProt
Encephalopathy, neonatal severe, due to MECP2 mutationsUniProt
Intellectual developmental disorder, X-linked, syndromic 13UniProt
Intellectual developmental disorder, X-linked, syndromic, Lubs typeUniProt
Rett syndromeUniProt
Pathogenic Variants819
NM_001110792.2(MECP2):c.800G>C (p.Arg267Pro)Pathogenic
Inborn genetic diseases|not provided|Severe neonatal-onset encephalopathy with microcephaly|Rett syndrome
β˜…β˜…β˜…β˜†2026β†’ Residue 267
NM_001110792.2(MECP2):c.1497A>G (p.Ter499Trp)Pathogenic
not specified|Severe neonatal-onset encephalopathy with microcephaly|Rett syndrome|not provided
β˜…β˜…β˜…β˜†2025β†’ Residue 499
NM_001110792.2(MECP2):c.947A>G (p.Lys316Arg)Pathogenic
not specified|not provided|Rett syndrome
β˜…β˜…β˜…β˜†2025β†’ Residue 316
NM_001110792.2(MECP2):c.1A>T (p.Met1Leu)Likely pathogenic
not provided|Rett syndrome
β˜…β˜…β˜…β˜†2024β†’ Residue 1
NM_001110792.2(MECP2):c.686C>T (p.Pro229Leu)Likely pathogenic
Rett syndrome|Severe neonatal-onset encephalopathy with microcephaly
β˜…β˜…β˜…β˜†2024β†’ Residue 229
NM_001110792.2(MECP2):c.872C>T (p.Ala291Val)Likely pathogenic
Rett syndrome|Syndromic X-linked intellectual disability Lubs type;Rett syndrome;Severe neonatal-onset encephalopathy with microcephaly;X-linked intellectual disability-psychosis-macroorchidism syndrome|Severe neonatal-onset encephalopathy with microcephaly
β˜…β˜…β˜…β˜†2024β†’ Residue 291
NM_001110792.2(MECP2):c.428C>A (p.Ala143Asp)Pathogenic
Rett syndrome|not provided
β˜…β˜…β˜…β˜†2024β†’ Residue 143
NM_001110792.2(MECP2):c.380G>A (p.Arg127His)Pathogenic
not provided|Severe neonatal-onset encephalopathy with microcephaly|Rett syndrome
β˜…β˜…β˜…β˜†2024β†’ Residue 127
NM_001110792.2(MECP2):c.948G>C (p.Lys316Asn)Pathogenic
Severe neonatal-onset encephalopathy with microcephaly|Inborn genetic diseases|Rett syndrome
β˜…β˜…β˜…β˜†2024β†’ Residue 316
NM_001110792.2(MECP2):c.488A>G (p.Asp163Gly)Likely pathogenic
Rett syndrome|Severe neonatal-onset encephalopathy with microcephaly
β˜…β˜…β˜…β˜†2023β†’ Residue 163
NM_001110792.2(MECP2):c.907_1080del (p.Ile305_Ser362del)Likely pathogenic
Rett syndrome|Severe neonatal-onset encephalopathy with microcephaly
β˜…β˜…β˜…β˜†2022β†’ Residue 305
NM_001110792.2(MECP2):c.434G>T (p.Arg145Leu)Pathogenic
Rett syndrome|not provided
β˜…β˜…β˜…β˜†2022β†’ Residue 145
NM_001110792.2(MECP2):c.408G>T (p.Leu136Phe)Pathogenic
Rett syndrome|Severe neonatal-onset encephalopathy with microcephaly
β˜…β˜…β˜…β˜†2022β†’ Residue 136
NM_001110792.2(MECP2):c.946A>G (p.Lys316Glu)Likely pathogenic
Rett syndrome|not provided
β˜…β˜…β˜…β˜†2022β†’ Residue 316
NM_001110792.2(MECP2):c.505T>A (p.Phe169Ile)Likely pathogenic
Severe neonatal-onset encephalopathy with microcephaly|Rett syndrome|not provided
β˜…β˜…β˜…β˜†2022β†’ Residue 169
NM_001110792.2(MECP2):c.507C>G (p.Phe169Leu)Pathogenic
Rett syndrome|Severe neonatal-onset encephalopathy with microcephaly
β˜…β˜…β˜…β˜†2022β†’ Residue 169
NM_001110792.2(MECP2):c.408G>C (p.Leu136Phe)Pathogenic
Rett syndrome
β˜…β˜…β˜…β˜†2022β†’ Residue 136
NM_001110792.2(MECP2):c.961C>T (p.Arg321Trp)Pathogenic
not provided|Autism, susceptibility to, X-linked 3|Rett syndrome|X-linked intellectual disability-psychosis-macroorchidism syndrome|Inborn genetic diseases|Intellectual disability|Severe neonatal-onset encephalopathy with microcephaly|Syndromic X-linked intellectual disability Lubs type|Non-syndromic X-linked intellectual disability
β˜…β˜…β˜…β˜†2022β†’ Residue 321
NM_001110792.2(MECP2):c.1001C>T (p.Pro334Leu)Pathogenic
Rett syndrome|not provided|Severe neonatal-onset encephalopathy with microcephaly|Autism, susceptibility to, X-linked 3;Syndromic X-linked intellectual disability Lubs type;Rett syndrome;Severe neonatal-onset encephalopathy with microcephaly;X-linked intellectual disability-psychosis-macroorchidism syndrome
β˜…β˜…β˜…β˜†2022β†’ Residue 334
NM_001110792.2(MECP2):c.941C>T (p.Pro314Leu)Pathogenic
Rett syndrome|not provided|Severe neonatal-onset encephalopathy with microcephaly
β˜…β˜…β˜…β˜†2022β†’ Residue 314
View on ClinVar β†—
Related Genes
SUV39H1Protein interaction100%H3C12Protein interaction100%H3C13Protein interaction100%PPARGProtein interaction100%TBL1XR1Protein interaction100%GPS2Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Ovary
74%
Heart
63%
Lung
63%
Bone Marrow
52%
Liver
28%
Gene Interaction Network
Click a node to explore
MECP2SUV39H1H3C12H3C13PPARGTBL1XR1GPS2
PROTEIN STRUCTURE
Preparing viewer…
PDB6OGK Β· 1.65 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.28Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.09 [0.04–0.28]
RankingsWhere MECP2 stands among ~20K protein-coding genes
  • #280of 20,598
    Most Researched740 Β· top 5%
  • #54of 5,498
    Most Pathogenic Variants819 Β· top 1%
  • #1,011of 17,882
    Most Constrained (LOEUF)0.28 Β· top 10%
Genes detectedMECP2
Sources retrieved50 papers
Response timeβ€”
πŸ“„ Sources
50β–Ό
1
Rett syndrome: a neurological disorder with metabolic components.
PMID: 29445033
Open Biol Β· 2018
1.00
2
MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons.
PMID: 38697112
Neuron Β· 2024
0.90
3
Human MECP2 transgenic rats show increased anxiety, severe social deficits, and abnormal prefrontal neural oscillation stability.
PMID: 36724557
Biochem Biophys Res Commun Β· 2023
0.82
4
Preclinical Milestones in MECP2 Gene Transfer for Treating Rett Syndrome.
PMID: 38723617
Dev Neurosci Β· 2025
0.80
5
Rett Syndrome: Thinking Beyond Brain Borders.
PMID: 40442389
Adv Exp Med Biol Β· 2025
0.78