Gene Gene information from NCBI Gene database.
Entrez ID 57459
Gene name GATA zinc finger domain containing 2B
Gene symbol GATAD2B
Synonyms (NCBI Gene)
GANDSMRD18P66betap68
Chromosome 1
Chromosome location 1q21.3
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 intel
SNPs SNP information provided by dbSNP.
40
SNP ID Visualize variation Clinical significance Consequence
rs587776931 G>A Pathogenic Stop gained, coding sequence variant
rs756062872 A>- Likely-pathogenic Frameshift variant, coding sequence variant
rs761820222 G>A,T Pathogenic Stop gained, synonymous variant, coding sequence variant
rs797045594 C>- Pathogenic Coding sequence variant, frameshift variant
rs886037647 CT>- Pathogenic Frameshift variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
1481
miRTarBase ID miRNA Experiments Reference
MIRT016222 hsa-miR-590-3p Sequencing 20371350
MIRT025107 hsa-miR-181a-5p Sequencing 20371350
MIRT028270 hsa-miR-32-5p Sequencing 20371350
MIRT028420 hsa-miR-30a-5p Proteomics 18668040
MIRT051773 hsa-let-7c-5p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
26
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:0000781 Component Chromosome, telomeric region IDA 25150861
GO:0000785 Component Chromatin HDA 16217013
GO:0005515 Function Protein binding IPI 24722188, 25123934, 25150861, 25416956, 26030138, 26816381, 29961565, 31413325, 31515488, 32296183, 33961781, 35512704
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
614998 30778 ENSG00000143614
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q8WXI9
Protein name Transcriptional repressor p66-beta (GATA zinc finger domain-containing protein 2B) (p66/p68)
Protein function Transcriptional repressor (PubMed:12183469, PubMed:16415179). Acts as a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin (PubMed:16428440, PubMed:28977666). Enhances MBD2-mediated repression (Pu
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF16563 P66_CC 157 200 Coiled-coil and interaction region of P66A and P66B with MBD2 Coiled-coil
PF00320 GATA 420 454 GATA zinc finger Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:12183469}.
Sequence
MDRMTEDALRLNLLKRSLDPADERDDVLAKRLKMEGHEAMERLKMLALLKRKDLANLEVP
HELPTKQDGSGVKGYEEKLNGNLRPHGDNRTAGRPGKENINDEPVDMSARRSEPERGRLT
PSPDIIVLSDNEASSPRSSSRMEERLKAANLEMFKGKGIEERQQLIKQLRDELRLEEARL
VLLKKLRQSQLQKENVVQKT
PVVQNAASIVQPSPAHVGQQGLSKLPSRPGAQGVEPQNLR
TLQGHSVIRSATNTTLPHMLMSQRVIAPNPAQLQGQRGPPKPGLVRTTTPNMNPAINYQP
QSSSSVPCQRTTSSAIYMNLASHIQPGTVNRVSSPLPSPSAMTDAANSQAAAKLALRKQL
EKTLLEIPPPKPPAPLLHFLPSAANSEFIYMVGLEEVVQSVIDSQGKSCASLLRVEPFVC
AQCRTDFTPHWKQEKNGKILCEQCMTSNQKKALK
AEHTNRLKNAFVKALQQEQEIEQRLQ
QQAALSPTTAPAVSSVSKQETIMRHHTLRQAPQPQSSLQRGIPTSARSMLSNFAQAPQLS
VPGGLLGMPGVNIAYLNTGIGGHKGPSLADRQREYLLDMIPPRSISQSISGQK
Sequence length 593
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  ATP-dependent chromatin remodeling   HDACs deacetylate histones
Regulation of TP53 Activity through Acetylation
RNA Polymerase I Transcription Initiation
Regulation of PTEN gene transcription
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
16
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)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
GATAD2B-related disorder Pathogenic rs886041621, rs1553188054 RCV000844949
RCV000709796
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
GATAD2B-related intellectual disability syndrome Pathogenic rs886041621 RCV001270782
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glioma susceptibility 1 Pathogenic rs1553189681 RCV005900407
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability Pathogenic rs1553188463, rs1674353589, rs1674950708, rs1674353634 RCV001260616
RCV001255339
RCV001260615
RCV001263166
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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
ANDROGENETIC ALOPECIA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATOPIC ECZEMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autism spectrum disorder Uncertain significance ClinVar
GWAS catalog
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Anaplasia Anaplasia BEFREE 28165114
★☆☆☆☆
Found in Text Mining only
Apraxia of Phonation Apraxia CLINVAR_DG 28077840
★☆☆☆☆
Found in Text Mining only
Atypical Ductal Breast Hyperplasia Breast Hyperplasia BEFREE 7501973
★☆☆☆☆
Found in Text Mining only
Autistic behavior Autism HPO_DG
★☆☆☆☆
Found in Text Mining only
Autoimmune Diseases Autoimmune Diseases BEFREE 1697098
★☆☆☆☆
Found in Text Mining only
Behavioral tic Tourette syndrome HPO_DG
★☆☆☆☆
Found in Text Mining only
Blepharophimosis Blepharophimosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma BEFREE 19718048, 21766210, 25499975, 30417346, 7501973
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 36770598 Associate
★☆☆☆☆
Found in Text Mining only
Byzanthine arch palate High palate HPO_DG
★☆☆☆☆
Found in Text Mining only