MECP2 (methyl-CpG binding protein 2)

Gene Gene information from NCBI Gene database.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID 4204
Gene name Methyl-CpG binding protein 2
Gene symbol MECP2
Synonyms (NCBI Gene)
AUTSX3MRX16MRX79MRXS13MRXSLPPMXRSRTSRTT
Chromosome X
Chromosome location Xq28
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 bi
SNPs SNP information provided by dbSNP.
446
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (446)
SNP ID Visualize variation Clinical significance Consequence
rs28934904 G>A,C,T Pathogenic, uncertain-significance, likely-pathogenic Coding sequence variant, 5 prime UTR variant, missense variant
rs28934905 A>C,G Not-provided, pathogenic, uncertain-significance Coding sequence variant, intron variant, missense variant
rs28934906 G>A Pathogenic, pathogenic-likely-pathogenic Coding sequence variant, intron variant, missense variant
rs28934907 G>A,C Pathogenic, uncertain-significance, pathogenic-likely-pathogenic Coding sequence variant, 5 prime UTR variant, missense variant
rs28934908 G>A,T Pathogenic, likely-pathogenic Coding sequence variant, 5 prime UTR variant, missense variant
miRNA miRNA information provided by mirtarbase database.
1378
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (1378)
miRTarBase ID miRNA Experiments Reference
MIRT003089 hsa-miR-122-5p Luciferase reporter assayqRT-PCR 19296470
MIRT000795 hsa-miR-195-5p MicroarrayNorthern blot 16331254
MIRT004395 hsa-miR-199a-5p MicroarrayNorthern blot 16331254
MIRT000779 hsa-miR-199a-3p MicroarrayNorthern blot 16331254
MIRT000442 hsa-miR-155-5p ReviewLuciferase reporter assayqRT-PCRMicroarray 20388499
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (1)
Transcription factor Regulation Reference
MEF2C Unknown 20513142
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
110
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (110)
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IBA
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000122 Process Negative regulation of transcription by RNA polymerase II TAS 9620804
GO:0000785 Component Chromatin IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
300005 6990 ENSG00000169057
Protein Protein information from UniProt database.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P51608
Protein name Methyl-CpG-binding protein 2 (MeCp-2 protein) (MeCp2)
Protein 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
PDB 1QK9 , 3C2I , 5BT2 , 6C1Y , 6OGJ , 6OGK , 6YWW , 8AJR , 8ALQ
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01429 MBD 91 → 162 Methyl-CpG binding domain Domain
Tissue specificity TISSUE SPECIFICITY: Present in all adult somatic tissues tested.
Sequence 
MVAGMLGLREEKSEDQDLQGLKDKPLKFKKVKKDKKEEKEGKHEPVQPSAHHSAEPAEAG
KAETSEGSGSAPAVPEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKY
DVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSPSRREQKPPKKPKSPK
APGTGRGRGRPKGSGTTRPKAATSEGVQVKRVLEKSPGKLLVKMPFQTSPGGKAEGGGAT
TSTQVMVIKRPGRKRKAEADPQAIPKKRGRKPGSVVAAAAAEAKKKAVKESSIRSVQETV
LPIKKRKTRETVSIEVKEVVKPLLVSTLGEKSGKGLKTCKSPGRKSKESSPKGRSSSASS
PPKKEHHHHHHHSESPKAPVPLLPPLPPPPPEPESSEDPTSPPEPQDLSSSVCKEEKMPR
GGSLESDGCPKEPAKTQPAVATAATAAEKYKHRGEGERKDIVSSSMPRPNREEPVDSRTP
VTERVS
Sequence length 486
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
  Reactome
    Transcriptional Regulation by MECP2
Loss of MECP2 binding ability to 5hmC-DNA
Loss of MECP2 binding ability to 5mC-DNA
Regulation of MECP2 expression and activity
MECP2 regulates neuronal receptors and channels
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
80
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Show/Hide Causal Diseases (37)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormality of the nervous system Likely pathogenic; Pathogenic rs267608438, rs28934906, rs61749721 RCV001814066
RCV001813975
RCV001813976
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Absent speech Pathogenic rs61749715 RCV000626873
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Angelman syndrome Pathogenic; Likely pathogenic rs267608426, rs63749748, rs61754453, rs1557135251, rs28934904, rs28934906, rs267608434, rs28935468, rs61748396 RCV000473677
RCV000132897
RCV000133058
RCV000170146
RCV000169934
View all (4 more)
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Attention deficit hyperactivity disorder Pathogenic rs786205019 RCV000170149
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Show/Hide Unknown Diseases (43)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign ClinVar
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANXIETY DISORDERS — CTD, Disgenet
CTD, Disgenet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS — Disgenet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER — CTD, Disgenet
CTD, Disgenet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Show/Hide Text Mining Associations (508)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
2-3 toe syndactyly Syndactyly Of The Toes HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Abnormal fear/anxiety-related behavior Behavioral abnormality HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Acquired Kyphoscoliosis Acquired Kyphoscoliosis HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 11710831
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenoma of large intestine Colorectal adenoma BEFREE 28291253
★★★★★
★☆☆☆☆
Found in Text Mining only
Adrenoleukodystrophy Adrenoleukodystrophy Pubtator 11885030, 26686765 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Adult Learning Disorders Learning Disorders CTD_human_DG 19921286
★★★★★
★☆☆☆☆
Found in Text Mining only
Adult type dermatomyositis Dermatomyositis BEFREE 19444718
★★★★★
★☆☆☆☆
Found in Text Mining only
ALPHA-THALASSEMIA/MENTAL RETARDATION SYNDROME, NONDELETION TYPE, X-LINKED alpha-Thalassemia Mental Retardation Syndrome, X-Linked BEFREE 17296936, 22129561
★★★★★
★☆☆☆☆
Found in Text Mining only
Alveolitis, Fibrosing Alveolitis CTD_human_DG 21435439
★★★★★
★☆☆☆☆
Found in Text Mining only