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

Gene ID: 57459, updated on 10-Dec-2024

Summary

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

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
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

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_020699.4NP_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:420454
    GATA; GATA zinc finger
    pfam16563
    Location:159194
    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_047426115.1XP_047282071.1  transcriptional repressor p66-beta isoform X1

    UniProtKB/TrEMBL
    B3KSZ4
  2. XM_047426117.1XP_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_054337814.1XP_054193789.1  transcriptional repressor p66-beta isoform X1

    UniProtKB/TrEMBL
    B3KSZ4
  2. XM_054337815.1XP_054193790.1  transcriptional repressor p66-beta isoform X2

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