Atlas of Genetics and Cytogenetics in Oncology and Haematology


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HDAC1 (histone deacetylase 1)

Identity

Alias_namesRPD3L1
Alias_symbol (synonym)HD1
GON-10
Other aliasRPD3
HGNC (Hugo) HDAC1
LocusID (NCBI) 3065
Atlas_Id 40802
Location 1p35.1  [Link to chromosome band 1p35]
Location_base_pair Starts at 32757708 and ends at 32799224 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
BSDC1 (1p35.1) / HDAC1 (1p35.1)EIF3I (1p35.1) / HDAC1 (1p35.1)HDAC1 (1p35.1) / KPNA6 (1p35.1)
HDAC1 (1p35.1) / LRRC42 (1p32.3)HDAC1 (1p35.1) / PEPD (19q13.11)HDAC1 (1p35.1) / PGA3 (11q12.2)
HDAC1 (1p35.1) / SERINC2 (1p35.2)RPS5 (19q13.43) / HDAC1 (1p35.1)ZNF592 (15q25.3) / HDAC1 (1p35.1)
BSDC1 1p35.1 / HDAC1 1p35.1HDAC1 1p35.1 / KPNA6 1p35.1HDAC1 1p35.1 / LRRC42 1p32.3
HDAC1 1p35.1 / PEPD 19q13.11HDAC1 1p35.1 / SERINC2 1p35.2

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) [ 28 ]
  del(11)(q23q23) KMT2A/CBL::t(11;11)(q23;q23) KMT2A/CBL
del(11)(q23q23) KMT2A/ARHGEF12
t(1;3)(q25;q27) GAS5/BCL6
t(1;11)(p32;q23) KMT2A/EPS15
t(2;11)(q37;q23) KMT2A/SEPT2
t(3;3)(q25;q27) MBNL1/BCL6
t(3;3)(q27;q27) ST6GAL1/BCL6::del(3)(q27q27) ST6GAL1/BCL6
t(3;3)(q27;q28) EIF4A2/BCL6
t(3;3)(q27;q29) TFRC/BCL6
t(3;6)(q27;p21) SRSF3/BCL6
t(3;6)(q27;p21) PIM1/BCL6
t(3;6)(q27;p21)
t(3;6)(q27;p22) HIST1H4I/BCL6
t(3;6)(q27;q14) SNHG5/BCL6
t(3;6)(q27;q15) ?/BCL6
t(3;7)(q27;q32) FRA7H/BCL6
t(3;9)(q27;p13) GRHPR/BCL6
t(3;9)(q27;p24) DMRT1/BCL6
t(3;11)(q21;q23) KMT2A/EEFSEC
t(3;11)(q27;q23) POU2AF1/BCL6
t(3;12)(q27;p12) LRMP/BCL6
t(3;12)(q27;p13) GAPDH/BCL6
t(3;14)(q27;q32) HSP90AA1/BCL6
t(3;19)(q27;q13) NAPA/BCL6
t(9;13)(p12;q21) PAX5/DACH1
t(9;17)(p13;p12) PAX5/NCOR1
t(10;17)(p15;q21) ZMYND11/MBTD1
t(12;12)(p13;q13) ETV6/BAZ2A


External links

Nomenclature
HGNC (Hugo)HDAC1   4852
Cards
Entrez_Gene (NCBI)HDAC1  3065  histone deacetylase 1
AliasesGON-10; HD1; RPD3; RPD3L1
GeneCards (Weizmann)HDAC1
Ensembl hg19 (Hinxton)ENSG00000116478 [Gene_View]  chr1:32757708-32799224 [Contig_View]  HDAC1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000116478 [Gene_View]  chr1:32757708-32799224 [Contig_View]  HDAC1 [Vega]
ICGC DataPortalENSG00000116478
TCGA cBioPortalHDAC1
AceView (NCBI)HDAC1
Genatlas (Paris)HDAC1
WikiGenes3065
SOURCE (Princeton)HDAC1
Genetics Home Reference (NIH)HDAC1
Genomic and cartography
GoldenPath hg19 (UCSC)HDAC1  -     chr1:32757708-32799224 +  1p35.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)HDAC1  -     1p35.1   [Description]    (hg38-Dec_2013)
EnsemblHDAC1 - 1p35.1 [CytoView hg19]  HDAC1 - 1p35.1 [CytoView hg38]
Mapping of homologs : NCBIHDAC1 [Mapview hg19]  HDAC1 [Mapview hg38]
OMIM601241   
Gene and transcription
Genbank (Entrez)AB451297 AB451430 AK225555 AK296308 AK299241
RefSeq transcript (Entrez)NM_004964
RefSeq genomic (Entrez)NC_000001 NC_018912 NT_032977 NW_004929290
Consensus coding sequences : CCDS (NCBI)HDAC1
Cluster EST : UnigeneHs.88556 [ NCBI ]
CGAP (NCI)Hs.88556
Alternative Splicing GalleryENSG00000116478
Gene ExpressionHDAC1 [ NCBI-GEO ]   HDAC1 [ EBI - ARRAY_EXPRESS ]   HDAC1 [ SEEK ]   HDAC1 [ MEM ]
Gene Expression Viewer (FireBrowse)HDAC1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3065
GTEX Portal (Tissue expression)HDAC1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13547   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13547  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13547
Splice isoforms : SwissVarQ13547
PhosPhoSitePlusQ13547
Domains : Interpro (EBI)His_deacetylse    His_deacetylse_1    His_deacetylse_dom   
Domain families : Pfam (Sanger)Hist_deacetyl (PF00850)   
Domain families : Pfam (NCBI)pfam00850   
Conserved Domain (NCBI)HDAC1
DMDM Disease mutations3065
Blocks (Seattle)HDAC1
PDB (SRS)1TYI    4BKX   
PDB (PDBSum)1TYI    4BKX   
PDB (IMB)1TYI    4BKX   
PDB (RSDB)1TYI    4BKX   
Structural Biology KnowledgeBase1TYI    4BKX   
SCOP (Structural Classification of Proteins)1TYI    4BKX   
CATH (Classification of proteins structures)1TYI    4BKX   
SuperfamilyQ13547
Human Protein AtlasENSG00000116478
Peptide AtlasQ13547
HPRD03143
IPIIPI00013774   IPI00910637   IPI01009997   IPI01010320   IPI00848042   IPI00514649   
Protein Interaction databases
DIP (DOE-UCLA)Q13547
IntAct (EBI)Q13547
FunCoupENSG00000116478
BioGRIDHDAC1
STRING (EMBL)HDAC1
ZODIACHDAC1
Ontologies - Pathways
QuickGOQ13547
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  negative regulation of transcription from RNA polymerase II promoter  chromatin  nuclear chromatin  transcription regulatory region sequence-specific DNA binding  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II distal enhancer sequence-specific DNA binding  core promoter binding  RNA polymerase II transcription factor binding  RNA polymerase II repressing transcription factor binding  RNA polymerase II transcription corepressor activity  transcription factor activity, sequence-specific DNA binding  histone deacetylase activity  histone deacetylase activity  histone deacetylase activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  cytosol  chromatin remodeling  transcription, DNA-templated  protein deacetylation  blood coagulation  transcription factor binding  transcription factor binding  positive regulation of cell proliferation  epidermal cell differentiation  negative regulation of gene expression  negative regulation of myotube differentiation  positive regulation of receptor biosynthetic process  viral process  chromatin modification  histone deacetylation  Sin3 complex  NuRD complex  deacetylase activity  enzyme binding  nucleosomal DNA binding  NAD-dependent histone deacetylase activity (H3-K14 specific)  circadian regulation of gene expression  protein deacetylase activity  protein deacetylase activity  activating transcription factor binding  odontogenesis of dentin-containing tooth  embryonic digit morphogenesis  histone deacetylase binding  ATP-dependent chromatin remodeling  negative regulation of apoptotic process  protein complex  negative regulation by host of viral transcription  transcription regulatory region DNA binding  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  protein N-terminus binding  NF-kappaB binding  negative regulation of androgen receptor signaling pathway  hair follicle placode formation  eyelid development in camera-type eye  fungiform papilla formation  repressing transcription factor binding  histone H3 deacetylation  histone H4 deacetylation  negative regulation of canonical Wnt signaling pathway  regulation of signal transduction by p53 class mediator  beta-catenin-TCF complex assembly  
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  negative regulation of transcription from RNA polymerase II promoter  chromatin  nuclear chromatin  transcription regulatory region sequence-specific DNA binding  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II distal enhancer sequence-specific DNA binding  core promoter binding  RNA polymerase II transcription factor binding  RNA polymerase II repressing transcription factor binding  RNA polymerase II transcription corepressor activity  transcription factor activity, sequence-specific DNA binding  histone deacetylase activity  histone deacetylase activity  histone deacetylase activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  cytosol  chromatin remodeling  transcription, DNA-templated  protein deacetylation  blood coagulation  transcription factor binding  transcription factor binding  positive regulation of cell proliferation  epidermal cell differentiation  negative regulation of gene expression  negative regulation of myotube differentiation  positive regulation of receptor biosynthetic process  viral process  chromatin modification  histone deacetylation  Sin3 complex  NuRD complex  deacetylase activity  enzyme binding  nucleosomal DNA binding  NAD-dependent histone deacetylase activity (H3-K14 specific)  circadian regulation of gene expression  protein deacetylase activity  protein deacetylase activity  activating transcription factor binding  odontogenesis of dentin-containing tooth  embryonic digit morphogenesis  histone deacetylase binding  ATP-dependent chromatin remodeling  negative regulation of apoptotic process  protein complex  negative regulation by host of viral transcription  transcription regulatory region DNA binding  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  protein N-terminus binding  NF-kappaB binding  negative regulation of androgen receptor signaling pathway  hair follicle placode formation  eyelid development in camera-type eye  fungiform papilla formation  repressing transcription factor binding  histone H3 deacetylation  histone H4 deacetylation  negative regulation of canonical Wnt signaling pathway  regulation of signal transduction by p53 class mediator  beta-catenin-TCF complex assembly  
Pathways : BIOCARTAWNT Signaling Pathway [Genes]    Downregulated of MTA-3 in ER-negative Breast Tumors [Genes]    Sumoylation by RanBP2 Regulates Transcriptional Repression [Genes]    The PRC2 Complex Sets Long-term Gene Silencing Through Modification of Histone Tails [Genes]    Cell Cycle: G1/S Check Point [Genes]    Multi-step Regulation of Transcription by Pitx2 [Genes]    CARM1 and Regulation of the Estrogen Receptor [Genes]    Inhibition of Huntington's disease neurodegeneration by histone deacetylase inhibitors [Genes]    Control of Gene Expression by Vitamin D Receptor [Genes]    Role of MEF2D in T-cell Apoptosis [Genes]    Overview of telomerase protein component gene hTert Transcriptional Regulation [Genes]   
Pathways : KEGGCell cycle    Notch signaling pathway    Thyroid hormone signaling pathway    Huntington's disease    Amphetamine addiction    Alcoholism    Epstein-Barr virus infection    Pathways in cancer    Transcriptional misregulation in cancer    Viral carcinogenesis    MicroRNAs in cancer    Chronic myeloid leukemia   
NDEx NetworkHDAC1
Atlas of Cancer Signalling NetworkHDAC1
Wikipedia pathwaysHDAC1
Orthology - Evolution
OrthoDB3065
GeneTree (enSembl)ENSG00000116478
Phylogenetic Trees/Animal Genes : TreeFamHDAC1
HOVERGENQ13547
HOGENOMQ13547
Homologs : HomoloGeneHDAC1
Homology/Alignments : Family Browser (UCSC)HDAC1
Gene fusions - Rearrangements
Fusion : MitelmanBSDC1/HDAC1 [1p35.1/1p35.1]  [t(1;1)(p35;p35)]  
Fusion : MitelmanHDAC1/KPNA6 [1p35.1/1p35.1]  [t(1;1)(p35;p35)]  
Fusion : MitelmanHDAC1/LRRC42 [1p35.1/1p32.3]  [t(1;1)(p32;p35)]  
Fusion : MitelmanHDAC1/PEPD [1p35.1/19q13.11]  [t(1;19)(p35;q13)]  
Fusion : MitelmanHDAC1/SERINC2 [1p35.1/1p35.2]  [t(1;1)(p35;p35)]  
Fusion: TCGABSDC1 1p35.1 HDAC1 1p35.1 LUSC
Fusion: TCGAHDAC1 1p35.1 KPNA6 1p35.1 BRCA
Fusion: TCGAHDAC1 1p35.1 LRRC42 1p32.3 LGG
Fusion: TCGAHDAC1 1p35.1 PEPD 19q13.11 BLCA
Fusion: TCGAHDAC1 1p35.1 SERINC2 1p35.2 GBM
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHDAC1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HDAC1
dbVarHDAC1
ClinVarHDAC1
1000_GenomesHDAC1 
Exome Variant ServerHDAC1
ExAC (Exome Aggregation Consortium)HDAC1 (select the gene name)
Genetic variants : HAPMAP3065
Genomic Variants (DGV)HDAC1 [DGVbeta]
DECIPHER (Syndromes)1:32757708-32799224  ENSG00000116478
CONAN: Copy Number AnalysisHDAC1 
Mutations
ICGC Data PortalHDAC1 
TCGA Data PortalHDAC1 
Broad Tumor PortalHDAC1
OASIS PortalHDAC1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHDAC1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHDAC1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch HDAC1
DgiDB (Drug Gene Interaction Database)HDAC1
DoCM (Curated mutations)HDAC1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HDAC1 (select a term)
intoGenHDAC1
Cancer3DHDAC1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601241   
Orphanet
MedgenHDAC1
Genetic Testing Registry HDAC1
NextProtQ13547 [Medical]
TSGene3065
GENETestsHDAC1
Huge Navigator HDAC1 [HugePedia]
snp3D : Map Gene to Disease3065
BioCentury BCIQHDAC1
ClinGenHDAC1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3065
Chemical/Pharm GKB GenePA29226
Clinical trialHDAC1
Miscellaneous
canSAR (ICR)HDAC1 (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHDAC1
EVEXHDAC1
GoPubMedHDAC1
iHOPHDAC1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Mar 30 15:03:30 CEST 2017

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