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GATAD2B GATA zinc finger domain containing 2B [ Homo sapiens (human) ]

Gene ID: 57459, updated on 3-Nov-2024

Summary

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Official Symbol
GATAD2Bprovided by HGNC
Official Full Name
GATA zinc finger domain containing 2Bprovided by HGNC
Primary source
HGNC:HGNC:30778
See related
Ensembl:ENSG00000143614 MIM:614998; AllianceGenome:HGNC:30778
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p68; GANDS; MRD18; P66beta
Summary
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]
Expression
Ubiquitous expression in brain (RPKM 8.8), spleen (RPKM 5.8) and 25 other tissues See more
Orthologs
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Genomic context

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See GATAD2B in Genome Data Viewer
Location:
1q21.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153804725..153922972, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (152941989..153060229, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153777201..153895448, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904426 Neighboring gene immunoglobulin superfamily DCC subclass member 3 pseudogene Neighboring gene uncharacterized LOC124904425 Neighboring gene adipose differentiation-related protein pseudogene Neighboring gene Sharpr-MPRA regulatory region 14566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:153877149-153877650 Neighboring gene Sharpr-MPRA regulatory region 2699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1755 Neighboring gene uncharacterized LOC101928059 Neighboring gene Sharpr-MPRA regulatory region 4321 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:153897582-153897755 Neighboring gene DENN domain containing 4B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153918384-153918884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1347 Neighboring gene CREB regulated transcription coactivator 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. 1q21.3 deletion involving GATAD2B: An emerging recurrent microdeletion syndrome. Tim-Aroon T, et al. Am J Med Genet A, 2017 Mar. PMID 28211977
  2. Identification of a linkage disequilibrium block in chromosome 1q associated with BMD in premenopausal white women. Ichikawa S, et al. J Bone Miner Res, 2008 Oct. PMID 18505370, Free PMC Article
  3. GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder. Shieh C, et al. Genet Med, 2020 May. PMID 31949314, Free PMC Article
  4. GATAD2B-related intellectual disability due to parental mosaicism and review of literature. Kaur P, et al. Clin Dysmorphol, 2019 Oct. PMID 31205050
  5. Intellectual disability due to monoallelic variant in GATAD2B and mosaicism in unaffected parent. Rabin R, et al. Am J Med Genet A, 2018 Dec. PMID 30346093

See all (161) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Tissue-specific DNase I footprint analysis confirms the association of GATAD2B Q470* variant with intellectual disability.
    Title: Tissue-specific DNase I footprint analysis confirms the association of GATAD2B Q470* variant with intellectual disability.
  2. The enhancer activity of long interspersed nuclear element derived microRNA 625 induced by NF-kappaB.
    Title: The enhancer activity of long interspersed nuclear element derived microRNA 625 induced by NF-κB.
  3. GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder.
    Title: GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder.
  4. GATAD2B-related intellectual disability is a rare condition with subtle yet recognizable clinical features. In this article, we highlight a consistent clinical profile of subjects with GATAD2B-related intellectual disability.
    Title: GATAD2B-related intellectual disability due to parental mosaicism and review of literature.
  5. Our report further supports the importance of GATAD2B in neurodevelopment and contributes to delineation of the phenotype of the recently identified GAND. Mosaicism for the pathogenic variant in unaffected mothers of cases prompts detailed genetic testing with the use of NGS technology and genetic counseling for the parents of children with GAND.
    Title: Intellectual disability due to monoallelic variant in GATAD2B and mosaicism in unaffected parent.
  6. GATAD2B interacts with C-MYC to enhance KRAS driven tumor growth.
    Title: In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer.
  7. This data suggests that 1q21.3 microdeletion is a recurrent microdeletion syndrome with distinguishable phenotypes, and loss of function of GATAD2B is the major contributor of the characteristic facies and ID.
    Title: 1q21.3 deletion involving GATAD2B: An emerging recurrent microdeletion syndrome.
  8. findings suggest that GATAD2B serves as an important mediator of progesterone-progesterone receptor suppression of proinflammatory and contractile genes during pregnancy; decreased GATAD2B expression near term may contribute to the decline in progesterone receptor function, leading to labor
    Title: The transcriptional repressor GATAD2B mediates progesterone receptor suppression of myometrial contractile gene expression.
  9. This is the first report of GATAD2B in Chinese ID patients. Our findings will broaden the spectrum of GATAD2B mutations and facilitate genetic diagnosis and counseling.
    Title: Novel GATAD2B loss-of-function mutations cause intellectual disability in two unrelated cases.
  10. p66beta might be important for the regulation of LOX in the nucleus.
    Title: Nuclear translocation of lysyl oxidase is promoted by interaction with transcription repressor p66β.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
MedGen: C3554448 OMIM: 615074 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2017-12-27)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2017-12-27)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association identifies genetic variants associated with lentiform nucleus volume in N = 1345 young and elderly subjects.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ37346, KIAA1150, MGC138257, MGC138285

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to nucleosomal DNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chromatin remodeling HDA PubMed 
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of cell fate specification NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of stem cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of NuRD complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of NuRD complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of NuRD complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in chromatin HDA PubMed 
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of protein-containing complex HDA PubMed 

General protein information

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Preferred Names
transcriptional repressor p66-beta
Names
GATA zinc finger domain-containing protein 2B
transcription repressor p66 beta component of the MeCP1 complex

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_050988.1 RefSeqGene

    Range
    5004..123251
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_020699.4 → NP_065750.1  transcriptional repressor p66-beta

    See identical proteins and their annotated locations for NP_065750.1

    Status: REVIEWED

    Source sequence(s)
    AF411836, AL513523, BQ446626, DA161156
    Consensus CDS
    CCDS1054.1
    UniProtKB/Swiss-Prot
    D3DUZ2, Q5VUR2, Q7LG68, Q8WXI9, Q9ULS0
    UniProtKB/TrEMBL
    B3KSZ4
    Related
    ENSP00000357644.4, ENST00000368655.5
    Conserved Domains (2) summary
    pfam00320
    Location:420 → 454
    GATA; GATA zinc finger
    pfam16563
    Location:159 → 194
    P66_CC; Coiled-coil and interaction region of P66A and P66B with MBD2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    153804725..153922972 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426115.1 → XP_047282071.1  transcriptional repressor p66-beta isoform X1

  2. XM_047426117.1 → XP_047282073.1  transcriptional repressor p66-beta isoform X2

    UniProtKB/Swiss-Prot
    D3DUZ2, Q5VUR2, Q7LG68, Q8WXI9, Q9ULS0

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315905.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    121426..145051 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    152941989..153060229 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337814.1 → XP_054193789.1  transcriptional repressor p66-beta isoform X1

  2. XM_054337815.1 → XP_054193790.1  transcriptional repressor p66-beta isoform X2

    UniProtKB/Swiss-Prot
    D3DUZ2, Q5VUR2, Q7LG68, Q8WXI9, Q9ULS0
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WXI9.1 GenPept UniProtKB/Swiss-Prot:Q8WXI9

Gene LinkOut

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