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MECP2 Gene

protein-coding GIFtS: 68
GCID: GC0XM153287

Methyl CpG Binding Protein 2 (Rett Syndrome)

(Previous names: mental retardation, X-linked 16, mental retardation, X-linked...)
(Previous symbols: RTT, MRX16, MRX79)

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Aliases
Methyl CpG Binding Protein 2 (Rett Syndrome)¹ ²		PPMX² ⁵
MRX16¹ ² ⁵		Mental Retardation, X-Linked 16¹
MRX79¹ ² ⁵		Mental Retardation, X-Linked 79¹
RTT¹ ² ⁵		RS²
MeCp-2 Protein² ³		RTS²
AUTSX3² ⁵		Methyl-CpG-Binding Protein 2²
MRXS13² ⁵		MeCp2³
MRXSL² ⁵

External Ids:	HGNC: 6990¹	Entrez Gene: 4204²	Ensembl: ENSG00000169057⁷	OMIM: 300005⁵	UniProtKB: P51608³

Export aliases for MECP2 gene to outside databases

Previous GC identifers: GC0XM147424 GC0XM149742 GC0XM150872 GC0XM151755 GC0XM152808 GC0XM152940 GC0XM141928

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for MECP2 Gene:

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 mental retardation in females. (provided by RefSeq, Jul 2009)

GeneCards Summary for MECP2 Gene:

MECP2 (methyl CpG binding protein 2 (Rett syndrome)) is a protein-coding gene. Diseases associated with MECP2 include mecp2-related angelman-like syndrome, and atypical rett syndrome. GO annotations related to this gene include transcription factor binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is MBD4.

UniProtKB/Swiss-Prot: MECP2_HUMAN, P51608

Function: Chromosomal protein that binds to methylated DNA. It can bind specifically to a single methyl-CpG pair.

It is not influenced by sequences flanking the methyl-CpGs. Mediates transcriptional repression through

interaction with histone deacetylase and the corepressor SIN3A. Binds both 5-methylcytosine (5mC) and

5-hydroxymethylcytosine (5hmC)-containing DNA, with a preference for 5-methylcytosine (5mC) (By similarity)

Gene Wiki entry for MECP2 Gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:

NC_000023.11 NT_011681.17 NC_018934.2

Regulatory elements:

Regulatory transcription factor binding sites in the MECP2 gene promoter:
TBP ISGF-3 Nkx2-5 IRF-1 STAT5A NF-Y CBF(2) C/EBPalpha
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): MECP2 promoter sequence

Search Chromatin IP Primers for MECP2

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat MECP2

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq28 Ensembl cytogenetic band: Xq28 HGNC cytogenetic band: Xq28

MECP2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MECP2 gene location

GeneLoc information about chromosome X GeneLoc Exon Structure

GeneLoc location for GC0XM153287: view genomic region (about GC identifiers)

Start:	153,287,024 bp from pter	End:	153,363,212 bp from pter
Size:	76,189 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: MECP2_HUMAN, P51608 (See protein sequence)

Recommended Name: Methyl-CpG-binding protein 2

Size: 486 amino acids; 52441 Da

Subunit: Interacts with FNBP3 (By similarity). Interacts with CDKL5

Sequence caution: Sequence=CAD97991.1; Type=Erroneous initiation;

2 PDB 3D structures from and Proteopedia for MECP2:

1QK9 (3D)

3C2I (3D)

Secondary accessions: O15233 Q6QHH9 Q7Z384

Alternative splicing: 2 isoforms: P51608-1 P51608-2 (Ten times higher expression levels than isoform A in brain)

Explore the universe of human proteins at neXtProt for MECP2: NX_P51608

Explore proteomics data for MECP2 at MOPED

Post-translational modifications:

Phosphorylated on Ser-423 in brain upon synaptic activity, which attenuates its repressor activity and seems to

regulate dendritic growth and spine maturation (By similarity)¹

Ubiquitination² at Lys130

Modification sites at PhosphoSitePlus

See MECP2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts):

NP_001104262.1 NP_004983.1

ENSEMBL proteins:

ENSP00000301948 ENSP00000395535 ENSP00000384865 ENSP00000358973 ENSP00000416267

MECP2 Human Recombinant Protein Products:

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MECP2 Assay Products:

	Browse Kits and Assays available from EMD Millipore
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	GenScript Custom Assay Services for MECP2
	Browse Enzo Life Sciences for kits & assays
	Cloud-Clone Corp. ELISAs for MECP2 Cloud-Clone Corp. CLIAs for MECP2

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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4 InterPro protein domains:

IPR017956 AT_hook_DNA-bd_motif

IPR001739 Methyl_CpG_DNA-bd

IPR017353 Me_CpG-bd_MeCP2

IPR016177 DNA-bd_dom

Graphical View of Domain Structure for InterPro Entry P51608

ProtoNet protein and cluster: P51608

1 Blocks protein domain: IPB001739 Methyl-CpG binding

UniProtKB/Swiss-Prot: MECP2_HUMAN, P51608

Similarity: Contains 2 A.T hook DNA-binding domains

Similarity: Contains 1 MBD (methyl-CpG-binding) domain

MECP2 for domains About GeneDecksing

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

UniProtKB/Swiss-Prot Summary: MECP2_HUMAN, P51608

Function: Chromosomal protein that binds to methylated DNA. It can bind specifically to a single methyl-CpG pair.

It is not influenced by sequences flanking the methyl-CpGs. Mediates transcriptional repression through

interaction with histone deacetylase and the corepressor SIN3A. Binds both 5-methylcytosine (5mC) and

5-hydroxymethylcytosine (5hmC)-containing DNA, with a preference for 5-methylcytosine (5mC) (By similarity)

Genatlas biochemistry entry for MECP2:

methyl CpG-binding protein 2,abundant chromosomal protein,murine Mecp2 homolog,that selectivity binds 5'methyl

cytosine residues in symmetrically positioned GpG dinucleotides,preferentially in the promoter regions of genes

subject to transcriptional silencing after DNA methylation,interacting with histone deacetylase and the

transcriptional corepressor SIN3A,involved in the regulation of gene expression

Gene Ontology (GO): Selected molecular function terms (see all 13): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003677	DNA binding	TAS	9620804
GO:0003682	chromatin binding	IEA	--
GO:0003700	sequence-specific DNA binding transcription factor activity	IEA	--
GO:0003714	transcription corepressor activity	TAS	10773092
GO:0003729	mRNA binding	IEA	--

MECP2 for ontologies About GeneDecksing

Phenotypes:
Selected MGI mutant phenotypes (inferred from 24 alleles) (MGI details for Mecp2) (see all 20):

adipose tissue	behavior/neurological	cellular	craniofacial	embryogenesis
endocrine/exocrine gland	growth/size/body	hearing/vestibular/ear	homeostasis/metabolism	immune system
integument	liver/biliary system	mortality/aging	nervous system	no phenotypic analysis

MECP2 for phenotypes About GeneDecksing

Animal Models:
MGI mouse knock-outs for MECP2: Mecp2^tm1Pplt Mecp2^tm1.1Jae Mecp2^tm1Jchr Mecp2^tm1Hzo Mecp2^tm1.1Bird

inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for MECP2

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genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for MECP2

genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for MECP2

miRNA Products:		miRTarBase miRNAs that target MECP2: hsa-mir-155-5p (MIRT000442), hsa-mir-148b-3p (MIRT019389), hsa-mir-212-3p (MIRT003897), hsa-mir-124-3p (MIRT007282), hsa-mir-122-5p (MIRT003089), hsa-mir-19a-3p (MIRT001795), hsa-mir-199a-3p (MIRT000779), hsa-mir-92a-3p (MIRT049717), hsa-mir-425-3p (MIRT042431), hsa-mir-195-5p (MIRT000795), hsa-mir-802 (MIRT000441), hsa-mir-199a-5p (MIRT004395), hsa-mir-331-3p (MIRT043437)

		Block miRNA regulation of human, mouse, rat MECP2 using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate MECP2 (see all 100):
		hsa-miR-194* hsa-miR-548j hsa-miR-520f hsa-miR-361-5p hsa-miR-3607-3p hsa-miR-199a-3p hsa-miR-106a hsa-miR-218-1*

		Browse SwitchGear 3'UTR luciferase reporter plasmids

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Gene Editing
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DNA2.0 Custom Protein Engineering Service for MECP2

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		GenScript: all cDNA clones in your preferred vector (see all 2): MECP2 (NM_004992)
		Sino Biological Human cDNA Clone for MECP2
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for MECP2
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat MECP2

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for MECP2
		Browse ESI BIO Cell Lines and PureStem Progenitors for MECP2

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MECP2

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot

MECP2_HUMAN, P51608: Nucleus. Note=Colocalized with methyl-CpG in the genome

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
nucleus	5
cytosol	2
cytoskeleton	1

About this image

Gene Ontology (GO): 5 cellular component terms (see first 5): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000792	heterochromatin	IDA	11441023
GO:0005615	extracellular space	IDA	--
GO:0005634	nucleus	IDA	--
GO:0005737	cytoplasm	--	--
GO:0005829	cytosol	IEA	--

MECP2 for ontologies About GeneDecksing

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for MECP2 About

See pathways by source

SuperPath

Contained pathways About

GABA signaling in brain

GABA signaling in brain

0.32

Macrophage Differentiation and Growth Inhibition by METS

DNA Methylation and Transcriptional Repression

0.30

SIDS Susceptibility Pathways

SIDS Susceptibility Pathways

Neuroscience

Neuroscience

Chromatin Regulation / Acetylation

Chromatin Regulation / Acetylation

Pathways by source See SuperPaths
Show all pathways

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for MECP2

DNA Methylation and Transcriptional Repression

2 Cell Signaling Technology (CST) Pathways for MECP2

	Chromatin Regulation / Acetylation
	Neuroscience

1 BioSystems Pathway for MECP2

SIDS Susceptibility Pathways

MECP2 for pathways About GeneDecksing

Pathway & Disease-focused RT² Profiler PCR Array including MECP2:

Epigenetic Chromatin Remodeling Factors in human mouse rat

Interactions:

GeneGlobe Interaction Network for MECP2

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for MECP2 (P51608^{1, 2, 3} ENSP00000395535⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 58)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
HIPK2	Q9H2X6¹^,²^,³	EBI-1189067,EBI-348345 MINT-7308929 MINT-7308914 I2D: score=1
SMARCA2	P51531¹^,³, ENSP00000265773⁴	EBI-1189067,EBI-679562 I2D: score=5 STRING: ENSP00000265773
HIST2H3A	Q71DI3³, ENSP00000385479⁴	I2D: score=1 STRING: ENSP00000385479
HIST2H3C	Q71DI3³	I2D: score=1
HIST2H3D	Q71DI3³	I2D: score=1

About this table

Gene Ontology (GO): Selected biological process terms (see all 56): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	TAS	9620804
GO:0001662	behavioral fear response	IEA	--
GO:0001666	response to hypoxia	IEA	--
GO:0001964	startle response	IEA	--
GO:0001976	neurological system process involved in regulation of systemic arterial blood pressure	IEA	--

MECP2 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse compounds at ApexBio

Browse Tocris compounds for MECP2

Selected Novoseek inferred chemical compound relationships for MECP2 gene (see all 18) About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
5-aza-2'deoxycytidine	64.5	2	15247904 (1), 16848908 (1)
cytosine	53.2	3	10390525 (1), 10319871 (1), 18313390 (1)
5-methylcytosine	41.6	6	11331619 (1), 15917437 (1), 17309881 (1)
hpaii	17.5	2	11691937 (2)
azathioprine	13.9	1	17036333 (1)
valproate	6.55	1	15870696 (1)
gaba	6.37	5	17363207 (1), 18302128 (1)
folate	3.82	5	18058624 (1), 12939425 (1)
oligonucleotide	0	2	19324899 (1), 15689352 (1)
guanosine	0	3	11453972 (1)

MECP2 for compounds About GeneDecksing

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for MECP2 gene (2 alternative transcripts):

NM_001110792.1 NM_004992.3

Unigene Cluster for MECP2:

Methyl CpG binding protein 2 (Rett syndrome)

Hs.200716 [show with all ESTs]

Unigene Representative Sequence: GQ203295

11 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000303391(uc004fjv.2 uc004fjw.2) ENST00000453960 ENST00000407218

ENST00000486506 ENST00000369957 ENST00000496908 ENST00000481807 ENST00000463644

ENST00000460227 ENST00000415944 ENST00000488293

miRNA Products:		Block miRNA regulation of human, mouse, rat MECP2 using miScript Target Protectors
		Selected qRT-PCR Assays for microRNAs that regulate MECP2 (see all 100):
		hsa-miR-194* hsa-miR-548j hsa-miR-520f hsa-miR-361-5p hsa-miR-3607-3p hsa-miR-199a-3p hsa-miR-106a hsa-miR-218-1*

		Browse SwitchGear 3'UTR luciferase reporter plasmids

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		GenScript: all cDNA clones in your preferred vector (see all 2): MECP2 (NM_004992)
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		QuantiTect SYBR Green Assays in human, mouse, rat MECP2
		QuantiFast Probe-based Assays in human, mouse, rat MECP2

Additional mRNA sequence:

AB209464.1 AF158180.1 AJ132917.1 AK289444.1 AY541280.1 BC011612.1 BX538060.1 DQ656049.2

GQ203293.1 GQ203294.1 GQ203295.1 GQ896382.1 GU479943.1 GU812285.1 GU812286.1 HM020402.1

HM156732.1 HM156733.1 HQ127345.1 HQ141377.1 HQ141378.1 L37298.1 X89430.1 X99686.1

Y12643.1

13 DOTS entries:

DT.92046808 DT.92434186 DT.453173 DT.100730813 DT.100798087 DT.92434188 DT.100798090 DT.100831459

DT.121294059 DT.75101285 DT.86846848 DT.91868594 DT.121294031

Selected AceView cDNA sequences (see all 269):

BI821242 BM850695 BU621700 CA436384 BM696151 CK821012 AI955326 BQ681323

BU679576 AL157555 AI439398 R09924 CD516820 AA888593 BU678549 BX509998

BC011612 CB242738 AA351289 BM986904 BQ067965 BG741923 N26870 AA543089

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for MECP2 About this scheme

ExUns:	1	^	2	^	3	^	4	^	5	^	6
SP1:			-				-
SP2:			-		-		-
SP3:
SP4:

ECgene alternative splicing isoforms for MECP2

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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MECP2 expression in normal human tissues (normalized intensities) MECP2 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: CCAAGGCCAA

About this image

MECP2 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 10) fully expand


Brain (Nervous System) fully expand to see all 9 entries
Cerebral Cortex

Neural Tube (Nervous System) fully expand to see all 3 entries
Metencephalon

Ovary (Reproductive System) fully expand to see all 2 entries
Ovarian Mesenchymal Stroma Cells Ovary Interstitium
Oviduct

Blood (Hematopoietic System) fully expand to see all 2 entries
Peripheral blood-derived hematopoietic stem cells (family)

Bone (Muscoskeletal System)
Bone Marrow

MECP2 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

MECP2 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.200716

UniProtKB/Swiss-Prot: MECP2_HUMAN, P51608

Tissue specificity: Present in all adult somatic tissues tested

Pathway & Disease-focused RT² Profiler PCR Array including MECP2:

Epigenetic Chromatin Remodeling Factors in human mouse rat

Primer Products:		OriGene qSTAR qPCR primer pairs in human, mouse for MECP2
		Pre-validated RT² qPCR Primer Assay in human, mouse, rat MECP2
		QuantiTect SYBR Green Assays in human, mouse, rat MECP2
		QuantiFast Probe-based Assays in human, mouse, rat MECP2

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MECP2

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for MECP2 gene from Selected species (see all 12) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Mecp2^{1 , 5}	methyl CpG binding protein 2^{1, 5}	90.15(n)¹ 94.83(a)¹		X (37.63 cM)⁵ 17257¹ NM_010788.3¹ NP_034918.1¹ 74026592⁵
lizard (Anolis carolinensis)	Reptilia	MECP2⁶	methyl CpG binding protein 2 (Rett syndrome)	66(a)	1 ↔ 1	2(88474297-88595647)
African clawed frog (Xenopus laevis)	Amphibia	MECP2²	methyl-CpG-binding protein MeCP2	76.69(n)		AF106951.1
zebrafish (Danio rerio)	Actinopterygii	wufk96a04²	Danio rerio methyl-cytosine binding protein 2 (mecp2) more	74.06(n)		AY298900.2

ENSEMBL Gene Tree for MECP2 (if available)
TreeFam Gene Tree for MECP2 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
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Paralogs for MECP2 gene

MBD4²

1 SIMAP similar gene for MECP2 using alignment to 17 protein entries: MECP2_HUMAN (see all proteins):

MBD4

MECP2 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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SNP ID	Valid	Clinical significance	Chr X pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs28935468^1,2,,4	C	Rett syndrome (RTT)⁴ pathogenic¹	153164502(-)	`AGAAGC/TGCAAG`	6	R C	mis¹ ese³		2		NA	4
rs28934906^1,2,,4	C	Rett syndrome (RTT)⁴ pathogenic¹	153164945(-)	`CTTCAC/TGGTAA`	6	T M	mis¹ ese³		2		NA	4
rs28934905^1,2,,4	C	Rett syndrome (RTT)⁴ pathogenic¹	153164954(-)	`TGATTC/G/TTGACT`	9	S C F	mis¹		0	--	--	--	--
rs28934908^1,2,,4	C	Mental retardation, X-linked, syndromic, 13 (MRXS13)⁴ pathogenic¹	153164999(-)	`GATTGC/TGTACT`	6	A V	mis¹ ese³		0	--	--	--	--
rs28934904^1,2,,4	C	Rett syndrome (RTT)⁴ pathogenic¹	153165021(-)	`CCTTTC/G/TGCTCT`	9	R G C	mis¹		2		NA	4
rs28934907^1,2,,4	C	Rett syndrome (RTT)⁴ pathogenic¹	153165858(-)	`GGACAC/G/TGGAAG`	9	R G W	mis¹ ese³		2		NA	4
rs28935168^1,2,,4	C	Rett syndrome (RTT)⁴ pathogenic¹	153165876(-)	`CCACCC/GTGCCT`	6	L V	mis¹ ese³		0	--	--	--	--
VAR_018206⁴		Rett syndrome (RTT)⁴	--	see VAR_018206	2	P A	mis⁴		0	--	--	--	--
VAR_023557⁴		Rett syndrome (RTT)⁴	--	see VAR_023557	2	T A	mis⁴		0	--	--	--	--
VAR_037665⁴		Mental retardation, X-linked, syndromic, 13 (MRXS13)⁴	--	see VAR_037665	2	P S	mis⁴		0	--	--	--	--

HapMap Linkage Disequilibrium report for MECP2 (153287024 - 153363212 bp)

Structural Variations
Database of Genomic Variants (DGV) 4 variations for MECP2: About this table

Variant ID	Type	Subtype	PubMed ID
nsv517994	CNV	Gain	19592680
nsv519042	CNV	Gain	19592680
esv33199	CNV	Gain+Loss	17666407
esv33784	CNV	Gain+Loss	17666407

Human Gene Mutation Database (HGMD): MECP2
Locus Specific Mutation Databases (LSDB): MECP2

Site Specific Mutation Identification with PCR Assays

1 Copy Number PCR Panel containing MECP2:

Intellectual Disability

SeqTarget long-range PCR primers for resequencing MECP2

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 300005
OMIM disorders: 312750 300055 300673 300496 105830 300260
UniProtKB/Swiss-Prot: MECP2_HUMAN, P51608

Angelman syndrome (AS) [MIM:105830]: A neurodevelopmental disorder characterized by severe motor and

intellectual retardation, ataxia, frequent jerky limb movements and flapping of the arms and hands, hypotonia,

seizures, absence of speech, frequent smiling and episodes of paroxysmal laughter, open-mouthed expression

revealing the tongue. Note=The disease may be caused by mutations affecting the gene represented in this entry

Mental retardation, X-linked, syndromic, 13 (MRXS13) [MIM:300055]: A disorder characterized by

significantly below average general intellectual functioning associated with impairments in adaptive behavior and

manifested during the developmental period. MRXS13 patients manifest mental retardation associated with other

variable features such as spasticity, episodes of manic depressive psychosis, increased tone and macroorchidism.

Note=The disease is caused by mutations affecting the gene represented in this entry

Rett syndrome (RTT) [MIM:312750]: An X-linked dominant neurodevelopmental disorder, and one of the most

common causes of mental retardation in females. Patients appear to develop normally until 6 to 18 months of age,

then gradually lose speech and purposeful hand movements, and develop microcephaly, seizures, autism, ataxia,

mental retardation and stereotypic hand movements. After initial regression, the condition stabilizes and

patients usually survive into adulthood. Note=The disease is caused by mutations affecting the gene represented

in this entry

Autism, X-linked 3 (AUTSX3) [MIM:300496]: A complex multifactorial, pervasive developmental disorder

characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped

patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most

individuals with autism also manifest moderate mental retardation. Note=The disease may be caused by mutations

affecting the gene represented in this entry

Encephalopathy, neonatal severe, due to MECP2 mutations (ENS-MECP2) [MIM:300673]: A neurodevelopmental

disorder characterized by severe neonatal encephalopathy, developmental delay, mental retardation, microcephaly,

seizures. Additional features include respiratory insufficiency and central hypoventilation, gastroesophageal

reflux, axial hypotonia, hyperreflexia and dyskinetic movements. Note=The disease is caused by mutations

affecting the gene represented in this entry. The MECP2 gene is mutated in Rett syndrome, a severe

neurodevelopmental disorder that almost always occurs in females. Although it was first thought that MECP2

mutations causing Rett syndrome were lethal in males, later reports identified a severe neonatal encephalopathy

in surviving male sibs of patients with Rett syndrome. Additional reports have confirmed a severe phenotype in

males with Rett syndrome-associated MECP2 mutations

Mental retardation, X-linked, syndromic, Lubs type (MRXSL) [MIM:300260]: A disorder characterized by

significantly below average general intellectual functioning associated with impairments in adaptive behavior and

manifested during the developmental period. MRXSL patients manifest mental retardation associated with variable

features. They include swallowing dysfunction and gastroesophageal reflux with secondary recurrent respiratory

infections, hypotonia, mild myopathy and characteristic facies such as downslanting palpebral fissures,

hypertelorism and a short nose with a low nasal bridge. Note=The disease is caused by mutations affecting the

gene represented in this entry. Increased dosage of MECP2 due to gene duplication appears to be responsible for

the mental retardation phenotype

Selected diseases for MECP2 (see all 86): About MalaCards

mecp2 duplication syndrome lubs x-linked mental retardation syndrome encephalopathy, neonatal severe mecp2-related disorders

classic rett syndrome rett syndrome, preserved speech variant ppm-x syndrome bruxism

mental retardation progressive spasticity autism susceptibility, x-linked 3 pervasive developmental disorder gait apraxia

angelman syndrome infantile hypotonia asperger syndrome epileptic encephalopathy, early infantile, 2

6 diseases from the University of Copenhagen DISEASES database for MECP2:

Rett syndrome Intellectual disability Autistic disorder Angelman syndrome

Microcephaly Gait apraxia

MECP2 for disorders About GeneDecksing

Congresses - knowledge worth sharing:
The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014

Selected Novoseek inferred disease relationships for MECP2 gene (see all 46) About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
rett syndrome	99	776	19652677 (8), 14649549 (5), 18174559 (5), 17986102 (5) (see all 99)
mental retardation	83.3	147	17084570 (4), 19806472 (4), 15814190 (4), 20163734 (4) (see all 78)
encephalopathy neonatal	79.9	17	12719401 (2), 11930274 (2), 19559301 (2), 12447790 (1) (see all 13)
angelman syndrome	79	19	15866439 (2), 15578581 (2), 11283202 (1), 14734626 (1) (see all 16)
autistic	77	41	12770674 (4), 17427193 (3), 11464249 (3), 12707946 (3) (see all 23)
severe mental retardation	72.3	13	18985075 (2), 12447790 (1), 16080119 (1), 11262731 (1) (see all 10)
microcephaly	69	10	15939091 (1), 17936729 (1), 20142466 (1), 19090026 (1) (see all 8)
pervasive developmental disorder	66	8	12027529 (1), 14734626 (1), 19189931 (1), 12555243 (1) (see all 5)
neurological disorders	61.4	28	11242118 (1), 12928486 (1), 14529314 (1), 16354910 (1) (see all 20)
infantile spasms	60.4	2	16806828 (1), 20397747 (1)

GeneTests: MECP2
GeneReviews: MECP2
Genetic Association Database (GAD): MECP2
Human Genome Epidemiology (HuGE) Navigator: MECP2 (78 documents)

Export disorders for MECP2 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for MECP2 gene, integrated from 10 sources (see all 698):
(articles sorted by number of sources associating them with MECP2)

Utopia: connect your pdf to the dynamic
world of online information

Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. (PubMed id 10508514)^{1, 2, 3, 9} Amir R.E....Zoghbi H.Y. (Nat. Genet. 1999)
Low frequency of MECP2 mutations in mentally retarded males. (PubMed id 12111644)^{1, 2, 4} Yntema H.G....van Bokhoven H. (Eur. J. Hum. Genet. 2002)
Diagnostic testing for Rett syndrome by DHPLC and direct sequencing analysis of the MECP2 gene: identification of several novel mutations and polymorphisms. (PubMed id 11055898)^{1, 2, 4} Buyse I.M.... Roa B.B. (Am. J. Hum. Genet. 2000)
Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus. (PubMed id 19333917)^{1, 4, 9} Webb R....Sawalha A.H. (Arthritis Rheum. 2009)
Spectrum of MECP2 mutations in New Zealand Rett syndrome patients. (PubMed id 19652677)^{1, 4, 9} Raizis A.M....George P.M. (N. Z. Med. J. 2009)
Drug-resistant epilepsy and epileptic phenotype-EEG association in MECP2 mutated Rett syndrome. (PubMed id 18842453)^{1, 4, 9} Buoni S....Hayek J. (Clin Neurophysiol 2008)
[Methyl-CpG-binding protein 2 gene and CDKL5 gene mutation in patients with Rett syndrome: analysis of 177 Chinese pediatric patients]. (PubMed id 19552836)^{1, 4, 9} Li M.R....Wu X.R. (Zhonghua Yi Xue Za Zhi 2009)
Structural variation in Xq28: MECP2 duplications in 1% of patients with unexplained XLMR and in 2% of male patients with severe encephalopathy. (PubMed id 18985075)^{1, 4, 9} Lugtenberg D....de Brouwer A.P. (Eur. J. Hum. Genet. 2009)
MECP2 mutation analysis in patients with mental retardation. (PubMed id 15578581)^{1, 4, 9} Ylisaukko-Oja T....JAorvelAo I. (Am. J. Med. Genet. A 2005)
The A140V mutation in the MECP2 gene is not a common etiological factor among Brazilian mentally retarded males. (PubMed id 15814190)^{1, 4, 9} dos Santos J.M....Pimentel M.M. (Neurosci. Lett. 2005)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 4204	HGNC: 6990	AceView: MECP2	Ensembl:ENSG00000169057	euGenes: HUgn4204
ECgene: MECP2	H-InvDB: MECP2

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for MECP2	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for MECP2	Genetics and Cytogenetics in Oncology and Haematology
RettBASE	http://mecp2.chw.edu.au/mecp2/
GeneReviews	http://www.ncbi.nlm.nih.gov/books/NBK1116/?term=MECP2[genesymbol]

Intellectual Property for MECP2 gene
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Patent Information for MECP2 gene:
Search GeneIP for patents involving MECP2

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

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MECP2 Gene

Methyl CpG Binding Protein 2 (Rett Syndrome)

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ENCEPHALOPATHY NEONATAL
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MECP2 Gene

Methyl CpG Binding Protein 2 (Rett Syndrome)

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