Atlas of Genetics and Cytogenetics in Oncology and Haematology


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HDAC4 (histone deacetylase 4)

Identity

Alias_namesBDMR
brachydactyly-mental retardation syndrome
Alias_symbol (synonym)KIAA0288
HDAC-A
HDACA
HD4
HA6116
HDAC-4
Other aliasAHO3
HGNC (Hugo) HDAC4
LocusID (NCBI) 9759
Atlas_Id 40805
Location 2q37.3  [Link to chromosome band 2q37]
Location_base_pair Starts at 239048168 and ends at 239400949 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
HDAC4 (2q37.3) / BRAT1 (7p22.3)HDAC4 (2q37.3) / HDAC4 (2q37.3)HDAC4 (2q37.3) / NBPF9 (1q21.1)
HDAC4 (2q37.3) / SATB2 (2q33.1)HDAC4 (2q37.3) / SNX18 (5q11.2)PPM1F (22q11.22) / HDAC4 (2q37.3)
HDAC4 2q37.3 / BRAT1 7p22.3HDAC4 2q37.3 / SATB2 2q33.1HDAC4 2q37.3 / SNX18 5q11.2

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(9;17)(p13;p12) PAX5/NCOR1
t(X;9)(q21;p13) PAX5/DACH2


External links

Nomenclature
HGNC (Hugo)HDAC4   14063
Cards
Entrez_Gene (NCBI)HDAC4  9759  histone deacetylase 4
AliasesAHO3; BDMR; HA6116; HD4; 
HDAC-4; HDAC-A; HDACA
GeneCards (Weizmann)HDAC4
Ensembl hg19 (Hinxton)ENSG00000068024 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000068024 [Gene_View]  chr2:239048168-239400949 [Contig_View]  HDAC4 [Vega]
ICGC DataPortalENSG00000068024
TCGA cBioPortalHDAC4
AceView (NCBI)HDAC4
Genatlas (Paris)HDAC4
WikiGenes9759
SOURCE (Princeton)HDAC4
Genetics Home Reference (NIH)HDAC4
Genomic and cartography
GoldenPath hg38 (UCSC)HDAC4  -     chr2:239048168-239400949 -  2q37.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HDAC4  -     2q37.3   [Description]    (hg19-Feb_2009)
EnsemblHDAC4 - 2q37.3 [CytoView hg19]  HDAC4 - 2q37.3 [CytoView hg38]
Mapping of homologs : NCBIHDAC4 [Mapview hg19]  HDAC4 [Mapview hg38]
OMIM605314   
Gene and transcription
Genbank (Entrez)AB006626 AF070607 AF132607 AI199675 AI654062
RefSeq transcript (Entrez)NM_006037
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)HDAC4
Cluster EST : UnigeneHs.20516 [ NCBI ]
CGAP (NCI)Hs.20516
Alternative Splicing GalleryENSG00000068024
Gene ExpressionHDAC4 [ NCBI-GEO ]   HDAC4 [ EBI - ARRAY_EXPRESS ]   HDAC4 [ SEEK ]   HDAC4 [ MEM ]
Gene Expression Viewer (FireBrowse)HDAC4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9759
GTEX Portal (Tissue expression)HDAC4
Protein : pattern, domain, 3D structure
UniProt/SwissProtP56524   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP56524  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP56524
Splice isoforms : SwissVarP56524
PhosPhoSitePlusP56524
Domains : Interpro (EBI)HDAC4    His_deacetylse    His_deacetylse_dom    Hist_deacetylase_Gln_rich_N    Histone_deAcase_II_euk   
Domain families : Pfam (Sanger)HDAC4_Gln (PF12203)    Hist_deacetyl (PF00850)   
Domain families : Pfam (NCBI)pfam12203    pfam00850   
Conserved Domain (NCBI)HDAC4
DMDM Disease mutations9759
Blocks (Seattle)HDAC4
PDB (SRS)2H8N    2O94    2VQJ    2VQM    2VQO    2VQQ    2VQV    2VQW    3UXG    3UZD    3V31    4CBT    4CBY    5A2S   
PDB (PDBSum)2H8N    2O94    2VQJ    2VQM    2VQO    2VQQ    2VQV    2VQW    3UXG    3UZD    3V31    4CBT    4CBY    5A2S   
PDB (IMB)2H8N    2O94    2VQJ    2VQM    2VQO    2VQQ    2VQV    2VQW    3UXG    3UZD    3V31    4CBT    4CBY    5A2S   
PDB (RSDB)2H8N    2O94    2VQJ    2VQM    2VQO    2VQQ    2VQV    2VQW    3UXG    3UZD    3V31    4CBT    4CBY    5A2S   
Structural Biology KnowledgeBase2H8N    2O94    2VQJ    2VQM    2VQO    2VQQ    2VQV    2VQW    3UXG    3UZD    3V31    4CBT    4CBY    5A2S   
SCOP (Structural Classification of Proteins)2H8N    2O94    2VQJ    2VQM    2VQO    2VQQ    2VQV    2VQW    3UXG    3UZD    3V31    4CBT    4CBY    5A2S   
CATH (Classification of proteins structures)2H8N    2O94    2VQJ    2VQM    2VQO    2VQQ    2VQV    2VQW    3UXG    3UZD    3V31    4CBT    4CBY    5A2S   
SuperfamilyP56524
Human Protein AtlasENSG00000068024
Peptide AtlasP56524
HPRD05610
IPIIPI00010088   IPI01011861   IPI01012936   IPI00892764   IPI01014711   IPI00892631   IPI00894354   IPI00894491   IPI00892542   
Protein Interaction databases
DIP (DOE-UCLA)P56524
IntAct (EBI)P56524
FunCoupENSG00000068024
BioGRIDHDAC4
STRING (EMBL)HDAC4
ZODIACHDAC4
Ontologies - Pathways
QuickGOP56524
Ontology : AmiGOhistone deacetylase complex  negative regulation of transcription from RNA polymerase II promoter  negative regulation of transcription from RNA polymerase II promoter  negative regulation of transcription from RNA polymerase II promoter  RNA polymerase III transcription factor binding  core promoter binding  skeletal system development  osteoblast development  chromatin binding  transcription corepressor activity  histone deacetylase activity  protein binding  nucleus  nucleoplasm  cytoplasm  cytosol  chromatin remodeling  transcription, DNA-templated  protein deacetylation  inflammatory response  nervous system development  transcription factor binding  zinc ion binding  positive regulation of cell proliferation  negative regulation of cell proliferation  positive regulation of lamellipodium assembly  negative regulation of myotube differentiation  regulation of cardiac muscle contraction by calcium ion signaling  response to denervation involved in regulation of muscle adaptation  cardiac muscle hypertrophy in response to stress  positive regulation of smooth muscle cell migration  histone deacetylation  histone deacetylation  transcriptional repressor complex  protein kinase binding  Z disc  B cell differentiation  potassium ion binding  neuromuscular junction  A band  NAD-dependent histone deacetylase activity (H3-K14 specific)  positive regulation of protein sumoylation  protein deacetylase activity  activating transcription factor binding  peptidyl-lysine deacetylation  regulation of gene expression, epigenetic  B cell activation  response to drug  actomyosin  histone deacetylase binding  protein complex  regulation of protein binding  negative regulation of sequence-specific DNA binding transcription factor activity  positive regulation of neuron apoptotic process  sequence-specific DNA binding  transcription regulatory region DNA binding  negative regulation of osteoblast differentiation  negative regulation of glycolytic process  negative regulation of transcription, DNA-templated  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  positive regulation of smooth muscle cell proliferation  regulation of skeletal muscle fiber development  positive regulation of sequence-specific DNA binding transcription factor activity  repressing transcription factor binding  response to interleukin-1  histone H3 deacetylation  histone H4 deacetylation  cellular response to mechanical stimulus  cellular response to tumor necrosis factor  cellular response to parathyroid hormone stimulus  negative regulation of pri-miRNA transcription from RNA polymerase II promoter  positive regulation of reactive oxygen species biosynthetic process  
Ontology : EGO-EBIhistone deacetylase complex  negative regulation of transcription from RNA polymerase II promoter  negative regulation of transcription from RNA polymerase II promoter  negative regulation of transcription from RNA polymerase II promoter  RNA polymerase III transcription factor binding  core promoter binding  skeletal system development  osteoblast development  chromatin binding  transcription corepressor activity  histone deacetylase activity  protein binding  nucleus  nucleoplasm  cytoplasm  cytosol  chromatin remodeling  transcription, DNA-templated  protein deacetylation  inflammatory response  nervous system development  transcription factor binding  zinc ion binding  positive regulation of cell proliferation  negative regulation of cell proliferation  positive regulation of lamellipodium assembly  negative regulation of myotube differentiation  regulation of cardiac muscle contraction by calcium ion signaling  response to denervation involved in regulation of muscle adaptation  cardiac muscle hypertrophy in response to stress  positive regulation of smooth muscle cell migration  histone deacetylation  histone deacetylation  transcriptional repressor complex  protein kinase binding  Z disc  B cell differentiation  potassium ion binding  neuromuscular junction  A band  NAD-dependent histone deacetylase activity (H3-K14 specific)  positive regulation of protein sumoylation  protein deacetylase activity  activating transcription factor binding  peptidyl-lysine deacetylation  regulation of gene expression, epigenetic  B cell activation  response to drug  actomyosin  histone deacetylase binding  protein complex  regulation of protein binding  negative regulation of sequence-specific DNA binding transcription factor activity  positive regulation of neuron apoptotic process  sequence-specific DNA binding  transcription regulatory region DNA binding  negative regulation of osteoblast differentiation  negative regulation of glycolytic process  negative regulation of transcription, DNA-templated  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  positive regulation of smooth muscle cell proliferation  regulation of skeletal muscle fiber development  positive regulation of sequence-specific DNA binding transcription factor activity  repressing transcription factor binding  response to interleukin-1  histone H3 deacetylation  histone H4 deacetylation  cellular response to mechanical stimulus  cellular response to tumor necrosis factor  cellular response to parathyroid hormone stimulus  negative regulation of pri-miRNA transcription from RNA polymerase II promoter  positive regulation of reactive oxygen species biosynthetic process  
Pathways : BIOCARTASumoylation by RanBP2 Regulates Transcriptional Repression [Genes]    CARM1 and Regulation of the Estrogen Receptor [Genes]   
Pathways : KEGGAlcoholism    Epstein-Barr virus infection    Viral carcinogenesis    MicroRNAs in cancer   
NDEx NetworkHDAC4
Atlas of Cancer Signalling NetworkHDAC4
Wikipedia pathwaysHDAC4
Orthology - Evolution
OrthoDB9759
GeneTree (enSembl)ENSG00000068024
Phylogenetic Trees/Animal Genes : TreeFamHDAC4
HOVERGENP56524
HOGENOMP56524
Homologs : HomoloGeneHDAC4
Homology/Alignments : Family Browser (UCSC)HDAC4
Gene fusions - Rearrangements
Fusion : MitelmanHDAC4/BRAT1 [2q37.3/7p22.3]  
Fusion : MitelmanHDAC4/SATB2 [2q37.3/2q33.1]  [t(2;2)(q33;q37)]  
Fusion : MitelmanHDAC4/SNX18 [2q37.3/5q11.2]  [t(2;5)(q37;q11)]  
Fusion: TCGAHDAC4 2q37.3 BRAT1 7p22.3 LGG
Fusion: TCGAHDAC4 2q37.3 SATB2 2q33.1 BLCA
Fusion: TCGAHDAC4 2q37.3 SNX18 5q11.2 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHDAC4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HDAC4
dbVarHDAC4
ClinVarHDAC4
1000_GenomesHDAC4 
Exome Variant ServerHDAC4
ExAC (Exome Aggregation Consortium)HDAC4 (select the gene name)
Genetic variants : HAPMAP9759
Genomic Variants (DGV)HDAC4 [DGVbeta]
DECIPHERHDAC4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHDAC4 
Mutations
ICGC Data PortalHDAC4 
TCGA Data PortalHDAC4 
Broad Tumor PortalHDAC4
OASIS PortalHDAC4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHDAC4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHDAC4
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)X-chromosome gene database
BioMutasearch HDAC4
DgiDB (Drug Gene Interaction Database)HDAC4
DoCM (Curated mutations)HDAC4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HDAC4 (select a term)
intoGenHDAC4
Cancer3DHDAC4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605314   
Orphanet1313   
MedgenHDAC4
Genetic Testing Registry HDAC4
NextProtP56524 [Medical]
TSGene9759
GENETestsHDAC4
Target ValidationHDAC4
Huge Navigator HDAC4 [HugePedia]
snp3D : Map Gene to Disease9759
BioCentury BCIQHDAC4
ClinGenHDAC4 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9759
Chemical/Pharm GKB GenePA29229
Clinical trialHDAC4
Miscellaneous
canSAR (ICR)HDAC4 (select the gene name)
Probes
Litterature
PubMed237 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHDAC4
EVEXHDAC4
GoPubMedHDAC4
iHOPHDAC4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Sep 18 13:55:07 CEST 2017

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