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

    Gene ID: 57459, updated on 10-Dec-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
    mouse all
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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
    • 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
    		not available

    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)

    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

      UniProtKB/TrEMBL
      B3KSZ4

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

      UniProtKB/Swiss-Prot
      D3DUZ2, Q5VUR2, Q7LG68, Q8WXI9, Q9ULS0
      UniProtKB/TrEMBL
      B3KSZ4

    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

      UniProtKB/TrEMBL
      B3KSZ4

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

      UniProtKB/Swiss-Prot
      D3DUZ2, Q5VUR2, Q7LG68, Q8WXI9, Q9ULS0
      UniProtKB/TrEMBL
      B3KSZ4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WXI9.1 GenPept UniProtKB/Swiss-Prot:Q8WXI9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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