Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

CHD4 (chromodomain helicase DNA binding protein 4)

Identity

Alias_symbol (synonym)Mi-2b
Mi2-BETA
Other aliasCHD-4
SIHIWES
HGNC (Hugo) CHD4
LocusID (NCBI) 1108
Atlas_Id 40072
Location 12p13.31  [Link to chromosome band 12p13]
Location_base_pair Starts at 6570082 and ends at 6607433 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CHD4 (12p13.31) / CHD4 (12p13.31)CHD4 (12p13.31) / CLEC9A (12p13.2)CHD4 (12p13.31) / DTX1 (12q24.13)
CHD4 (12p13.31) / EI24 (11q24.2)CHD4 (12p13.31) / FAM96B (16q22.1)CHD4 (12p13.31) / ISM1 (20p12.1)
CHD4 (12p13.31) / NOP2 (12p13.31)CHD4 (12p13.31) / PRELP (1q32.1)CHD4 (12p13.31) / ZBTB40 (1p36.12)
GALNT8 (12p13.32) / CHD4 (12p13.31)GPX3 (5q33.1) / CHD4 (12p13.31)RELL2 (5q31.3) / CHD4 (12p13.31)
TBC1D24 (16p13.3) / CHD4 (12p13.31)CHD4 12p13.31 / CLEC9A 12p13.2CHD4 12p13.31 / DTX1 12q24.13
GPX3 5q33.1 / CHD4 12p13.31

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

 


External links

Nomenclature
HGNC (Hugo)CHD4   1919
Cards
Entrez_Gene (NCBI)CHD4  1108  chromodomain helicase DNA binding protein 4
AliasesCHD-4; Mi-2b; Mi2-BETA; SIHIWES
GeneCards (Weizmann)CHD4
Ensembl hg19 (Hinxton)ENSG00000111642 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000111642 [Gene_View]  chr12:6570082-6607433 [Contig_View]  CHD4 [Vega]
ICGC DataPortalENSG00000111642
TCGA cBioPortalCHD4
AceView (NCBI)CHD4
Genatlas (Paris)CHD4
WikiGenes1108
SOURCE (Princeton)CHD4
Genetics Home Reference (NIH)CHD4
Genomic and cartography
GoldenPath hg38 (UCSC)CHD4  -     chr12:6570082-6607433 -  12p13.31   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CHD4  -     12p13.31   [Description]    (hg19-Feb_2009)
EnsemblCHD4 - 12p13.31 [CytoView hg19]  CHD4 - 12p13.31 [CytoView hg38]
Mapping of homologs : NCBICHD4 [Mapview hg19]  CHD4 [Mapview hg38]
OMIM603277   617159   
Gene and transcription
Genbank (Entrez)AA099889 AK128741 BC014964 BC025962 BC038596
RefSeq transcript (Entrez)NM_001273 NM_001297553
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CHD4
Cluster EST : UnigeneHs.162233 [ NCBI ]
CGAP (NCI)Hs.162233
Alternative Splicing GalleryENSG00000111642
Gene ExpressionCHD4 [ NCBI-GEO ]   CHD4 [ EBI - ARRAY_EXPRESS ]   CHD4 [ SEEK ]   CHD4 [ MEM ]
Gene Expression Viewer (FireBrowse)CHD4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1108
GTEX Portal (Tissue expression)CHD4
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14839   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ14839  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14839
Splice isoforms : SwissVarQ14839
Catalytic activity : Enzyme3.6.4.12 [ Enzyme-Expasy ]   3.6.4.123.6.4.12 [ IntEnz-EBI ]   3.6.4.12 [ BRENDA ]   3.6.4.12 [ KEGG ]   
PhosPhoSitePlusQ14839
Domaine pattern : Prosite (Expaxy)CHROMO_1 (PS00598)    CHROMO_2 (PS50013)    DEAH_ATP_HELICASE (PS00690)    HELICASE_ATP_BIND_1 (PS51192)    HELICASE_CTER (PS51194)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)CHD4    CHD_C2    CHD_N    Chromo/chromo_shadow_dom    Chromo_domain    Chromodomain-like    DNA/RNA_helicase_DEAH_CS    DUF1086    DUF1087    Helicase_ATP-bd    Helicase_C    P-loop_NTPase    SNF2_N    Zinc_finger_PHD-type_CS    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)CHDCT2 (PF08074)    CHDNT (PF08073)    Chromo (PF00385)    DUF1086 (PF06461)    DUF1087 (PF06465)    Helicase_C (PF00271)    PHD (PF00628)    SNF2_N (PF00176)   
Domain families : Pfam (NCBI)pfam08074    pfam08073    pfam00385    pfam06461    pfam06465    pfam00271    pfam00628    pfam00176   
Domain families : Smart (EMBL)CHROMO (SM00298)  DEXDc (SM00487)  DUF1086 (SM01146)  DUF1087 (SM01147)  HELICc (SM00490)  PHD (SM00249)  
Conserved Domain (NCBI)CHD4
DMDM Disease mutations1108
Blocks (Seattle)CHD4
PDB (SRS)1MM2    1MM3    2EE1    2L5U    2L75    2N5N    4O9I   
PDB (PDBSum)1MM2    1MM3    2EE1    2L5U    2L75    2N5N    4O9I   
PDB (IMB)1MM2    1MM3    2EE1    2L5U    2L75    2N5N    4O9I   
PDB (RSDB)1MM2    1MM3    2EE1    2L5U    2L75    2N5N    4O9I   
Structural Biology KnowledgeBase1MM2    1MM3    2EE1    2L5U    2L75    2N5N    4O9I   
SCOP (Structural Classification of Proteins)1MM2    1MM3    2EE1    2L5U    2L75    2N5N    4O9I   
CATH (Classification of proteins structures)1MM2    1MM3    2EE1    2L5U    2L75    2N5N    4O9I   
SuperfamilyQ14839
Human Protein AtlasENSG00000111642
Peptide AtlasQ14839
HPRD04472
IPIIPI00000846   IPI00455210   IPI01012026   IPI00847420   IPI01013311   IPI01013556   
Protein Interaction databases
DIP (DOE-UCLA)Q14839
IntAct (EBI)Q14839
FunCoupENSG00000111642
BioGRIDCHD4
STRING (EMBL)CHD4
ZODIACCHD4
Ontologies - Pathways
QuickGOQ14839
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II distal enhancer sequence-specific DNA binding  RNA polymerase II repressing transcription factor binding  DNA binding  ATP-dependent DNA helicase activity  histone deacetylase activity  protein binding  ATP binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  centrosome  transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  microtubule binding  zinc ion binding  membrane  histone deacetylation  NuRD complex  nucleosomal DNA binding  DNA duplex unwinding  protein-DNA complex  histone deacetylase binding  ATP-dependent chromatin remodeling  protein complex  spindle assembly  terminal button organization  regulation of signal transduction by p53 class mediator  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II distal enhancer sequence-specific DNA binding  RNA polymerase II repressing transcription factor binding  DNA binding  ATP-dependent DNA helicase activity  histone deacetylase activity  protein binding  ATP binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  centrosome  transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  microtubule binding  zinc ion binding  membrane  histone deacetylation  NuRD complex  nucleosomal DNA binding  DNA duplex unwinding  protein-DNA complex  histone deacetylase binding  ATP-dependent chromatin remodeling  protein complex  spindle assembly  terminal button organization  regulation of signal transduction by p53 class mediator  
Pathways : KEGGViral carcinogenesis   
NDEx NetworkCHD4
Atlas of Cancer Signalling NetworkCHD4
Wikipedia pathwaysCHD4
Orthology - Evolution
OrthoDB1108
GeneTree (enSembl)ENSG00000111642
Phylogenetic Trees/Animal Genes : TreeFamCHD4
HOVERGENQ14839
HOGENOMQ14839
Homologs : HomoloGeneCHD4
Homology/Alignments : Family Browser (UCSC)CHD4
Gene fusions - Rearrangements
Fusion : MitelmanCHD4/CLEC9A [12p13.31/12p13.2]  
Fusion : MitelmanCHD4/DTX1 [12p13.31/12q24.13]  [t(12;12)(p13;q24)]  
Fusion : MitelmanGPX3/CHD4 [5q33.1/12p13.31]  [t(5;12)(q33;p13)]  
Fusion: TCGACHD4 12p13.31 CLEC9A 12p13.2 BRCA
Fusion: TCGACHD4 12p13.31 DTX1 12q24.13 BRCA
Fusion: TCGAGPX3 5q33.1 CHD4 12p13.31 THCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCHD4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CHD4
dbVarCHD4
ClinVarCHD4
1000_GenomesCHD4 
Exome Variant ServerCHD4
ExAC (Exome Aggregation Consortium)CHD4 (select the gene name)
Genetic variants : HAPMAP1108
Genomic Variants (DGV)CHD4 [DGVbeta]
DECIPHERCHD4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCHD4 
Mutations
ICGC Data PortalCHD4 
TCGA Data PortalCHD4 
Broad Tumor PortalCHD4
OASIS PortalCHD4 [ Somatic mutations - Copy number]
Cancer Gene: CensusCHD4 
Somatic Mutations in Cancer : COSMICCHD4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCHD4
intOGen PortalCHD4
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
BioMutasearch CHD4
DgiDB (Drug Gene Interaction Database)CHD4
DoCM (Curated mutations)CHD4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CHD4 (select a term)
intoGenCHD4
Cancer3DCHD4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603277    617159   
Orphanet
MedgenCHD4
Genetic Testing Registry CHD4
NextProtQ14839 [Medical]
TSGene1108
GENETestsCHD4
Target ValidationCHD4
Huge Navigator CHD4 [HugePedia]
snp3D : Map Gene to Disease1108
BioCentury BCIQCHD4
ClinGenCHD4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1108
Chemical/Pharm GKB GenePA26455
Clinical trialCHD4
Miscellaneous
canSAR (ICR)CHD4 (select the gene name)
Probes
Litterature
PubMed131 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCHD4
EVEXCHD4
GoPubMedCHD4
iHOPCHD4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Jun 7 12:28:14 CEST 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.