This gene encodes a zinc finger protein transcriptional repressor. The encoded protein is part of the methyl-CpG-binding protein-1 complex, which represses gene expression by deacetylating methylated nucleosomes. Mutations in this gene are linked to intellectual disability and dysmorphic features associated with cognitive disability. [provided by RefSeq, Jun 2016] See more...

Aliases for GATAD2B Gene

Aliases for GATAD2B Gene

  • GATA Zinc Finger Domain Containing 2B 2 3 5
  • Transcription Repressor P66 Beta Component Of The MeCP1 Complex 2 3
  • GATA Zinc Finger Domain-Containing Protein 2B 3 4
  • Transcriptional Repressor P66-Beta 3 4
  • P66beta 2 3
  • KIAA1150 4
  • GATAD2B 5
  • P66/P68 4
  • MRD18 3
  • P68 3

External Ids for GATAD2B Gene

Previous GeneCards Identifiers for GATAD2B Gene

  • GC01M150593
  • GC01M152044
  • GC01M153777
  • GC01M125139

Summaries for GATAD2B Gene

Entrez Gene Summary for GATAD2B Gene

  • This gene encodes a zinc finger protein transcriptional repressor. The encoded protein is part of the methyl-CpG-binding protein-1 complex, which represses gene expression by deacetylating methylated nucleosomes. Mutations in this gene are linked to intellectual disability and dysmorphic features associated with cognitive disability. [provided by RefSeq, Jun 2016]

GeneCards Summary for GATAD2B Gene

GATAD2B (GATA Zinc Finger Domain Containing 2B) is a Protein Coding gene. Diseases associated with GATAD2B include Mental Retardation, Autosomal Dominant 18 and Meninges Sarcoma. Among its related pathways are Regulation of TP53 Activity through Acetylation and Chromatin organization. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is GATAD2A.

UniProtKB/Swiss-Prot Summary for GATAD2B Gene

  • Transcriptional repressor. Enhances MBD2-mediated repression. Efficient repression requires the presence of GATAD2A. Targets MBD3 to discrete loci in the nucleus. May play a role in synapse development.

Gene Wiki entry for GATAD2B Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GATAD2B Gene

Genomics for GATAD2B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for GATAD2B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GATAD2B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GATAD2B

Top Transcription factor binding sites by QIAGEN in the GATAD2B gene promoter:
  • c-Myb
  • CUTL1
  • ER-alpha
  • GATA-2
  • Nkx2-5
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c
  • RREB-1

Genomic Locations for GATAD2B Gene

Genomic Locations for GATAD2B Gene
chr1:153,789,030-153,923,953
(GRCh38/hg38)
Size:
134,924 bases
Orientation:
Minus strand
chr1:153,777,201-153,895,451
(GRCh37/hg19)
Size:
118,251 bases
Orientation:
Minus strand

Genomic View for GATAD2B Gene

Genes around GATAD2B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GATAD2B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GATAD2B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GATAD2B Gene

Proteins for GATAD2B Gene

  • Protein details for GATAD2B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WXI9-P66B_HUMAN
    Recommended name:
    Transcriptional repressor p66-beta
    Protein Accession:
    Q8WXI9
    Secondary Accessions:
    • D3DUZ2
    • Q5VUR2
    • Q7LG68
    • Q9ULS0

    Protein attributes for GATAD2B Gene

    Size:
    593 amino acids
    Molecular mass:
    65261 Da
    Quaternary structure:
    • Interacts with MBD2 and MBD3 (PubMed:11756549, PubMed:12183469, PubMed:16415179). Interaction with MBD2 is required for the enhancement of MBD2-mediated repression and for targeting to the chromatin (PubMed:11756549, PubMed:12183469, PubMed:16415179). Component of the MeCP1 histone deacetylase complex (PubMed:11756549). Interacts with histone tails, including that of histones H2A, H2B, H3 and H4 (PubMed:16415179). Interacts with ERCC6 (PubMed:26030138).

neXtProt entry for GATAD2B Gene

Post-translational modifications for GATAD2B Gene

  • Ubiquitination at Lys44 and Lys467
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Boster Bio Antibodies for GATAD2B
  • Santa Cruz Biotechnology (SCBT) Antibodies for GATAD2B

No data available for DME Specific Peptides for GATAD2B Gene

Domains & Families for GATAD2B Gene

Gene Families for GATAD2B Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for GATAD2B Gene

InterPro:
Blocks:
  • Zn-finger, GATA type
ProtoNet:

Suggested Antigen Peptide Sequences for GATAD2B Gene

GenScript: Design optimal peptide antigens:
  • p66/p68 (P66B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8WXI9

UniProtKB/Swiss-Prot:

P66B_HUMAN :
  • Both CR1 and CR2 regions are required for speckled nuclear localization.
Domain:
  • Both CR1 and CR2 regions are required for speckled nuclear localization.
genes like me logo Genes that share domains with GATAD2B: view

Function for GATAD2B Gene

Molecular function for GATAD2B Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor. Enhances MBD2-mediated repression. Efficient repression requires the presence of GATAD2A. Targets MBD3 to discrete loci in the nucleus. May play a role in synapse development.

Phenotypes From GWAS Catalog for GATAD2B Gene

Gene Ontology (GO) - Molecular Function for GATAD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 contributes_to RNA polymerase II proximal promoter sequence-specific DNA binding HDA 16217013
GO:0005515 protein binding IPI 24722188
GO:0008270 zinc ion binding IEA --
GO:0031492 contributes_to nucleosomal DNA binding HDA 16217013
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with GATAD2B: view
genes like me logo Genes that share phenotypes with GATAD2B: view

Human Phenotype Ontology for GATAD2B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GATAD2B Gene

MGI Knock Outs for GATAD2B:
  • Gatad2b Gatad2b<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

miRNA for GATAD2B Gene

miRTarBase miRNAs that target GATAD2B

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GATAD2B

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for GATAD2B Gene

Localization for GATAD2B Gene

Subcellular locations from UniProtKB/Swiss-Prot for GATAD2B Gene

Nucleus speckle. Note=Speckled nuclear localization requires both CR1 and CR2 regions. {ECO:0000269 PubMed:16415179}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GATAD2B gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for GATAD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin HDA 16217013
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0016581 NuRD complex IBA 21873635
GO:0016607 nuclear speck IEA --
genes like me logo Genes that share ontologies with GATAD2B: view

Pathways & Interactions for GATAD2B Gene

genes like me logo Genes that share pathways with GATAD2B: view

Pathways by source for GATAD2B Gene

1 GeneGo (Thomson Reuters) pathway for GATAD2B Gene
  • Transcription Sin3 and NuRD in transcription regulation

Gene Ontology (GO) - Biological Process for GATAD2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA,IBA 21873635
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0043044 ATP-dependent chromatin remodeling HDA 16217013
genes like me logo Genes that share ontologies with GATAD2B: view

No data available for SIGNOR curated interactions for GATAD2B Gene

Drugs & Compounds for GATAD2B Gene

No Compound Related Data Available

Transcripts for GATAD2B Gene

mRNA/cDNA for GATAD2B Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GATAD2B

Alternative Splicing Database (ASD) splice patterns (SP) for GATAD2B Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1: -
SP2:

Relevant External Links for GATAD2B Gene

GeneLoc Exon Structure for
GATAD2B

Expression for GATAD2B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GATAD2B Gene

Protein differential expression in normal tissues from HIPED for GATAD2B Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (11.1), CD8 Tcells (10.8), and Cervix (10.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GATAD2B Gene



Protein tissue co-expression partners for GATAD2B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GATAD2B

SOURCE GeneReport for Unigene cluster for GATAD2B Gene:

Hs.4779

mRNA Expression by UniProt/SwissProt for GATAD2B Gene:

Q8WXI9-P66B_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for GATAD2B Gene

  • Nervous system(4.6)
  • Liver(4.4)
  • Lung(4.4)
  • Muscle(2.4)
  • Kidney(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GATAD2B Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • face
  • head
  • lip
  • nose
  • skull
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with GATAD2B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for GATAD2B Gene

Orthologs for GATAD2B Gene

This gene was present in the common ancestor of animals.

Orthologs for GATAD2B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia GATAD2B 30 31
  • 99.61 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia GATAD2B 31
  • 98 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia GATAD2B 30 31
  • 94.37 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Gatad2b 30 17 31
  • 92.97 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Gatad2b 30
  • 92.69 (n)
Dog
(Canis familiaris)
Mammalia GATAD2B 30 31
  • 92.52 (n)
OneToOne
Chicken
(Gallus gallus)
Aves GATAD2B 30 31
  • 76.76 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia GATAD2B 31
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100486823 30
  • 72.47 (n)
Zebrafish
(Danio rerio)
Actinopterygii gatad2b 30
  • 66.33 (n)
ndufa13 31
  • 26 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta simj 31
  • 20 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea dcp-66 31
  • 16 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3981 30
Species where no ortholog for GATAD2B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for GATAD2B Gene

ENSEMBL:
Gene Tree for GATAD2B (if available)
TreeFam:
Gene Tree for GATAD2B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GATAD2B: view image

Paralogs for GATAD2B Gene

Paralogs for GATAD2B Gene

(1) SIMAP similar genes for GATAD2B Gene using alignment to 1 proteins:

  • P66B_HUMAN
genes like me logo Genes that share paralogs with GATAD2B: view

Variants for GATAD2B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GATAD2B Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
638011 Pathogenic: Mental retardation, autosomal dominant 18 153,828,162(-) CT/C FRAMESHIFT_VARIANT
638585 Pathogenic: Mental retardation, autosomal dominant 18 153,818,098(-) TTAGA/T FRAMESHIFT_VARIANT
666293 Likely Pathogenic: Mental retardation, autosomal dominant 18 153,818,790(-) C/T SPLICE_DONOR_VARIANT
713589 Likely Benign: not provided 153,810,279(-) G/A SYNONYMOUS_VARIANT
725557 Benign: not provided 153,817,420(-) A/G SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for GATAD2B Gene

Structural Variations from Database of Genomic Variants (DGV) for GATAD2B Gene

Variant ID Type Subtype PubMed ID
esv3578196 CNV loss 25503493
esv3587594 CNV loss 21293372
esv3587595 CNV loss 21293372
esv3587596 CNV loss 21293372
nsv1078969 CNV deletion 25765185
nsv1120199 CNV tandem duplication 24896259
nsv1130976 CNV deletion 24896259
nsv476590 CNV novel sequence insertion 20440878
nsv547941 CNV loss 21841781

Variation tolerance for GATAD2B Gene

Residual Variation Intolerance Score: 16.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.69; 32.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GATAD2B Gene

Human Gene Mutation Database (HGMD)
GATAD2B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GATAD2B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GATAD2B Gene

Disorders for GATAD2B Gene

MalaCards: The human disease database

(3) MalaCards diseases for GATAD2B Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, autosomal dominant 18
  • mrd18
meninges sarcoma
  • meningeal sarcoma
koolen-de vries syndrome
  • kdvs
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

P66B_HUMAN
  • Mental retardation, autosomal dominant 18 (MRD18) [MIM:615074]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD18 patients have severe intellectual disability and dysmorphic features. {ECO:0000269 PubMed:23033978, ECO:0000269 PubMed:23644463}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GATAD2B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with GATAD2B: view

No data available for Genatlas for GATAD2B Gene

Publications for GATAD2B Gene

  1. Identification and functional characterization of the p66/p68 components of the MeCP1 complex. (PMID: 11756549) Feng Q … Zhang Y (Molecular and cellular biology 2002) 2 3 4
  2. Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain. (PMID: 10574461) Hirosawa M … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  3. Identification of Novel Proteins Co-Purifying with Cockayne Syndrome Group B (CSB) Reveals Potential Roles for CSB in RNA Metabolism and Chromatin Dynamics. (PMID: 26030138) Nicolai S … Proietti-De-Santis L (PloS one 2015) 3 4
  4. GATAD2B loss-of-function mutations cause a recognisable syndrome with intellectual disability and are associated with learning deficits and synaptic undergrowth in Drosophila. (PMID: 23644463) Willemsen MH … Kleefstra T (Journal of medical genetics 2013) 3 4
  5. Diagnostic exome sequencing in persons with severe intellectual disability. (PMID: 23033978) de Ligt J … Vissers LE (The New England journal of medicine 2012) 3 4

Products for GATAD2B Gene

Sources for GATAD2B Gene