Human Gene CHD8 (uc001war.2) Description and Page Index
  Description: Homo sapiens chromodomain helicase DNA binding protein 8 (CHD8), transcript variant 1, mRNA.
RefSeq Summary (NM_001170629): This gene encodes a member of the chromodomain-helicase-DNA binding protein family, which is characterized by a SNF2-like domain and two chromatin organization modifier domains. The encoded protein also contains brahma and kismet domains, which are common to the subfamily of chromodomain-helicase-DNA binding proteins to which this protein belongs. This gene has been shown to function in several processes that include transcriptional regulation, epigenetic remodeling, promotion of cell proliferation, and regulation of RNA synthesis. Allelic variants of this gene are associated with autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2016].
Transcript (Including UTRs)
   Position: hg19 chr14:21,853,353-21,899,867 Size: 46,515 Total Exon Count: 37 Strand: -
Coding Region
   Position: hg19 chr14:21,853,772-21,899,802 Size: 46,031 Coding Exon Count: 37 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:21,853,353-21,899,867)mRNA (may differ from genome)Protein (2581 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMGIneXtProtOMIMPubMed
ReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CHD8_HUMAN
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 8; Short=CHD-8; EC=3.6.4.12; AltName: Full=ATP-dependent helicase CHD8; AltName: Full=Helicase with SNF2 domain 1;
FUNCTION: DNA helicase that acts as a chromatin remodeling factor and regulates transcription. Acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. Suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity. Acts as a negative regulator of Wnt signaling pathway by regulating beta-catenin (CTNNB1) activity. Negatively regulates CTNNB1- targeted gene expression by being recruited specifically to the promoter regions of several CTNNB1 responsive genes. Involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. Acts as a suppressor of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. Also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Interacts with p53/TP53, histone H1, CTNNB1, CTCF and PIAS3. Component of some MLL1/MLL complex, at least composed of the core components MLL, ASH2L, HCFC1/HCF1, WDR5 and RBBP5, as well as the facultative components C17orf49, CHD8, E2F6, HSP70, INO80C, KANSL1, LAS1L, MAX, MCRS1, MGA, KAT8/MOF, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9 and TEX10. Interacts with CHD7.
INTERACTION: Q9P2D1:CHD7; NbExp=3; IntAct=EBI-4410319, EBI-3951683;
SUBCELLULAR LOCATION: Nucleus. Note=Localizes to the promoter regions of several CTNNB1-responsive genes. Also present at known CTCF target sites.
PTM: Sumoylated (By similarity).
MISCELLANEOUS: Its gene is located in the 14q11.2 region of the genome which is associated with developmental delay, cognitive impairment and similar minor anomalies in some children, suggesting that it may be a good candidate for the phenotype.
SIMILARITY: Belongs to the SNF2/RAD54 helicase family. CHD8 subfamily.
SIMILARITY: Contains 2 chromo domains.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.

-  MalaCards Disease Associations
  MalaCards Gene Search: CHD8
Diseases sorted by gene-association score: autism 18* (1003), autism spectrum disorder susceptibility, chd8-related* (500), charge syndrome (13), autism spectrum disorder (13), pervasive developmental disorder (10)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.81 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 424.93 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -10.8065-0.166 Picture PostScript Text
3' UTR -152.15419-0.363 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006576 - BRK_domain
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000330 - SNF2_N

Pfam Domains:
PF00176 - SNF2 family N-terminal domain
PF00271 - Helicase conserved C-terminal domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF04851 - Type III restriction enzyme, res subunit
PF07533 - BRK domain

SCOP Domains:
54160 - Chromo domain-like
52540 - P-loop containing nucleoside triphosphate hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2CKA
- NMR MuPIT

2DL6
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9HCK8
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0002039 p53 binding
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0003682 chromatin binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008013 beta-catenin binding
GO:0008094 DNA-dependent ATPase activity
GO:0016787 hydrolase activity
GO:0016817 hydrolase activity, acting on acid anhydrides
GO:0035064 methylated histone binding
GO:0042393 histone binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007420 brain development
GO:0016055 Wnt signaling pathway
GO:0030178 negative regulation of Wnt signaling pathway
GO:0032508 DNA duplex unwinding
GO:0043044 ATP-dependent chromatin remodeling
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0045945 positive regulation of transcription from RNA polymerase III promoter
GO:0048565 digestive tract development
GO:0060070 canonical Wnt signaling pathway
GO:0090090 negative regulation of canonical Wnt signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0032991 macromolecular complex
GO:0071339 MLL1 complex


-  Descriptions from all associated GenBank mRNAs
  CR749315 - Homo sapiens mRNA; cDNA DKFZp686N17164 (from clone DKFZp686N17164).
AB046784 - Homo sapiens mRNA for KIAA1564 protein, partial cds.
BC156439 - Synthetic construct Homo sapiens clone IMAGE:100063036, MGC:190670 chromodomain helicase DNA binding protein 8 (CHD8) mRNA, encodes complete protein.
AK122910 - Homo sapiens cDNA FLJ16585 fis, clone TESTI4000134, weakly similar to Chromodomain helicase-DNA-binding protein Mi-2.
BC040636 - Homo sapiens, clone IMAGE:4153069, mRNA.
AL834524 - Homo sapiens mRNA; cDNA DKFZp667O149 (from clone DKFZp667O149).
BC036920 - Homo sapiens chromodomain helicase DNA binding protein 8, mRNA (cDNA clone IMAGE:5199722), partial cds.
BC073903 - Homo sapiens chromodomain helicase DNA binding protein 8, mRNA (cDNA clone IMAGE:4415955), partial cds.
AK131077 - Homo sapiens mRNA for FLJ00266 protein.
JD225229 - Sequence 206253 from Patent EP1572962.
JD147106 - Sequence 128130 from Patent EP1572962.
JD427309 - Sequence 408333 from Patent EP1572962.
JD368515 - Sequence 349539 from Patent EP1572962.
JD301450 - Sequence 282474 from Patent EP1572962.
BC011695 - Homo sapiens chromodomain helicase DNA binding protein 8, mRNA (cDNA clone IMAGE:3534143), partial cds.
BC025964 - Homo sapiens chromodomain helicase DNA binding protein 8, mRNA (cDNA clone IMAGE:3534141), partial cds.
BC063693 - Homo sapiens chromodomain helicase DNA binding protein 8, mRNA (cDNA clone IMAGE:4443191), partial cds.
BC098452 - Homo sapiens chromodomain helicase DNA binding protein 8, mRNA (cDNA clone IMAGE:6302978), partial cds.
JD481756 - Sequence 462780 from Patent EP1572962.
JD481755 - Sequence 462779 from Patent EP1572962.
JD479982 - Sequence 461006 from Patent EP1572962.
AK056639 - Homo sapiens cDNA FLJ32077 fis, clone OCBBF1000188, weakly similar to Drosophila melanogaster KISMET-L long isoform (kis) mRNA.
AK098408 - Homo sapiens cDNA FLJ25542 fis, clone JTH01318.
AK122868 - Homo sapiens cDNA FLJ16499 fis, clone FCBBF3025650, moderately similar to Drosophila melanogaster KISMET-L long isoform (kis) mRNA.
JD351174 - Sequence 332198 from Patent EP1572962.
JD455737 - Sequence 436761 from Patent EP1572962.
JD115719 - Sequence 96743 from Patent EP1572962.
JD334314 - Sequence 315338 from Patent EP1572962.
JD375429 - Sequence 356453 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04310 - Wnt signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein Q9HCK8 (Reactome details) participates in the following event(s):

R-HSA-5368580 CHD8 binds beta-catenin to negatively regulate WNT-dependent gene expression
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CHD8_HUMAN, HELSNF1, KIAA1564, NM_001170629, NP_001164100, Q4G0D8, Q68DQ0, Q6DKH9, Q6P440, Q6ZNL7, Q8N3Z9, Q8NCY4, Q8TBR9, Q96F26, Q9HCK8
UCSC ID: uc001war.2
RefSeq Accession: NM_001170629
Protein: Q9HCK8 (aka CHD8_HUMAN)
CCDS: CCDS53885.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001170629.1
exon count: 37CDS single in 3' UTR: no RNA size: 8254
ORF size: 7746CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 15284.00frame shift in genome: no % Coverage: 99.71
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.