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Gene

MECP2

methyl-CpG binding protein 2

Summary

Cytogenetic location
Xq28
Coordinates
Chromosome X: 154,021,573–154,097,717 (GRCh38)
Exons
3 exons across 76.1 kb
Protein
498 amino acids
Inheritance
X-linked dominant X-linked recessive
Previous symbols
RTT, MRX16, MRX79
MANE Select transcript
ENST00000453960.7NM_001110792.2
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Rett Syndrome and MECP2-Related Disorders

    • Rett SyndromeX-linked dominant

      A neurodevelopmental disorder caused by MECP2 variants, usually new (de novo), with regression of language and hand skills, stereotyped hand movements, breathing irregularities and seizures.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong
      What knowing changes

      Multidisciplinary care including seizure, breathing, scoliosis and nutrition management; trofinetide is FDA-approved for Rett syndrome.

    • MECP2 Duplication Syndrome (Lubs Type X-Linked Intellectual Disability)X-linked recessive

      An X-linked disorder mainly affecting boys, caused by duplication of MECP2, with intellectual disability, low muscle tone, seizures and recurrent infections.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Seizure and infection management and genetic counselling for mothers, who are often unaffected carriers.

    • Severe Neonatal-Onset Encephalopathy with Microcephaly (MECP2)

      A severe early-onset encephalopathy in boys caused by MECP2 variants, with small head size, breathing problems and seizures.

      • 1 GenCC submitter rates it definitive or strong

Broader groupings

  • Epilepsy (Full Panel)

    • Epilepsy

      One of 171 genes linked to it

      A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

      • 1 GenCC submitter rates it definitive or strong

  • Intellectual Disability

    • One of 233 genes linked to it

      • 1 GenCC submitter rates it definitive or strong

Inheritance

X-linked dominant
The change is on the X chromosome, and one copy is enough. A mother who has it passes it on to each child with a one-in-two chance; a father, to all of his daughters and none of his sons.
X-linked recessive
The change is on the X chromosome, so one copy affects males, who have one X, while females with one are usually carriers. A carrier mother passes it on to each child with a one-in-two chance.

How MECP2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome X, with a bracket where MECP2 sits. MECP2 and 42 genes near it on chromosome X, from 153,559,645 to 154,559,644.Chromosome XXq28p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q28153.6 Mb153.8 Mb154 Mb154.2 Mb154.4 MbATP2B3: 153,517,620–153,582,939, forward strandATP2B3CCNQ: 153,587,925–153,600,045, reverse strandCCNQDUSP9: 153,642,397–153,651,326, forward strandDUSP9PNCK: 153,669,730–153,689,033, reverse strandPNCKSLC6A8: 153,687,914–153,696,591, forward strandSLC6A8BCAP31: 153,698,006–153,725,957, reverse strandBCAP31ABCD1: 153,724,495–153,744,755, forward strandABCD1PLXNB3: 153,764,179–153,779,346, forward strandSRPK3: 153,781,001–153,785,768, forward strandSRPK3IDH3G: 153,785,735–153,794,535, reverse strandIDH3GSSR4: 153,793,516–153,798,510, forward strandSSR4PDZD4: 153,802,161–153,830,935, reverse strandPDZD4L1CAM: 153,861,511–153,886,204, reverse strandL1CAM: 153,872,221–153,909,223, reverse strandAVPR2: 153,902,531–153,907,169, forward strandAVPR2ARHGAP4: 153,907,367–153,934,999, reverse strandNAA10: 153,928,799–153,935,083, reverse strandNAA10RENBP: 153,935,269–153,944,688, reverse strandRENBPHCFC1: 153,946,434–153,972,427, reverse strandHCFC1TMEM187: 153,972,290–153,983,194, forward strandTMEM187IRAK1: 154,010,501–154,020,650, reverse strandIRAK1MECP2: 154,021,573–154,097,717, reverse strandMECP2OPN1LW: 154,144,243–154,159,032, forward strandOPN1LWOPN1MW: 154,182,596–154,196,861, forward strandOPN1MWOPN1MW2: 154,219,756–154,233,286, forward strandOPN1MW2OPN1MW3: 154,257,582–154,271,090, forward strandOPN1MW3TEX28: 154,271,265–154,295,853, reverse strandTEX28TKTL1: 154,295,795–154,330,350, forward strandTKTL1FLNA: 154,348,524–154,374,643, reverse strandFLNAEMD: 154,379,205–154,381,574, forward strandEMDRPL10: 154,389,955–154,409,168, forward strandRPL10DNASE1L1: 154,401,236–154,412,119, reverse strandDNASE1L1TAFAZZIN: 154,409,456–154,421,726, forward strandATP6AP1: 154,428,618–154,436,517, forward strandGDI1: 154,436,600–154,443,467, forward strandGDI1FAM50A: 154,444,103–154,450,655, forward strandPLXNA3: 154,458,275–154,477,779, forward strandPLXNA3LAGE3: 154,477,598–154,479,291, reverse strandLAGE3UBL4A: 154,483,717–154,486,661, reverse strandUBL4ASLC10A3: 154,487,306–154,490,690, reverse strandFAM3A: 154,505,019–154,516,882, reverse strandG6PD: 154,517,825–154,547,584, reverse strandG6PDIKBKG: 154,541,179–154,568,543, forward strandIKBKGDiagram of MECP2: 3 exons on the reverse strand of chromosome XExon 3: 360 known disease-causing sitesExon 2: 78 known disease-causing sitesExon 1: 11 known disease-causing sitesExon 3: 154,021,573–154,031,450, 9,878 bases. 33 variants with a page in exon 3. List themExon 2: 154,032,207–154,032,557, 351 bases. 8 variants with a page in exon 2. List themExon 1: 154,097,604–154,097,717, 114 bases. 1 variant with a page in exon 1. List them3215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 10.3 kb of the gene's 76.1 kb; 1,497 of those bases code for the protein.

How a genome test reads MECP2

460

positions in MECP2 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 76.1 kb of MECP2, introns included, not only the 10.3 kb of exons.

Variants with a page (45)

The MECP2 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A143Dc.428C>AExon 3154,031,436Pathogenic3 stars out of 4 reviewed by expert panel
A291Vc.872C>TExon 3154,030,992Likely pathogenic3 stars out of 4 reviewed by expert panel
c.1A>TExon 1154,097,665Likely pathogenic3 stars out of 4 reviewed by expert panel
c.62+1G>AIntron 1154,097,603Pathogenic3 stars out of 4 reviewed by expert panel
c.62+2T>GIntron 1154,097,602Pathogenic3 stars out of 4 reviewed by expert panel
c.408G>TExon 2154,032,212Pathogenic3 stars out of 4 reviewed by expert panel
c.414-3C>GIntron 2154,031,453Pathogenic3 stars out of 4 reviewed by expert panel
D163Gc.488A>GExon 3154,031,376Likely pathogenic3 stars out of 4 reviewed by expert panel
D168Gc.503A>GExon 3154,031,361Pathogenic3 stars out of 4 reviewed by expert panel
F169Ic.505T>AExon 3154,031,359Likely pathogenic3 stars out of 4 reviewed by expert panel

See all 45 MECP2 variants →

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). MECP2 gene: methyl-CpG binding protein 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/mecp2

Vancouver

Dante Labs. MECP2 gene: methyl-CpG binding protein 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/mecp2

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