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Aliases for CHD2 Gene

Aliases for CHD2 Gene

  • Chromodomain Helicase DNA Binding Protein 2 2 3 5
  • ATP-Dependent Helicase CHD2 3 4
  • CHD-2 3 4
  • Chromodomain-Helicase-DNA-Binding Protein 2 3
  • EC 4
  • EEOC 3

External Ids for CHD2 Gene

Previous GeneCards Identifiers for CHD2 Gene

  • GC15P089886
  • GC15P087276
  • GC15P091030
  • GC15P091173
  • GC15P091244
  • GC15P093443
  • GC15P069580
  • GC15P093533
  • GC15P093924
  • GC15P094240
  • GC15P094584

Summaries for CHD2 Gene

Entrez Gene Summary for CHD2 Gene

  • The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for CHD2 Gene

CHD2 (Chromodomain Helicase DNA Binding Protein 2) is a Protein Coding gene. Diseases associated with CHD2 include Epileptic Encephalopathy, Childhood-Onset and Lennox-Gastaut Syndrome. Among its related pathways are Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include core promoter sequence-specific DNA binding. An important paralog of this gene is CHD1.

UniProtKB/Swiss-Prot for CHD2 Gene

  • DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. Involved in myogenesis via interaction with MYOD1: binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression (By similarity).

Gene Wiki entry for CHD2 Gene

Additional gene information for CHD2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHD2 Gene

Genomics for CHD2 Gene

GeneHancer (GH) Regulatory Elements for CHD2 Gene

Promoters and enhancers for CHD2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J092876 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 661 -17.3 -17278 12.3 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B NEUROD1 SIN3A DMAP1 YY1 CHD2 LINC01578 ENSG00000279765 FAM174B C15orf32
GH15J092898 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 712.4 +9.0 8980 20.4 MLX FEZF1 DMAP1 IRF4 YY1 E2F8 ZNF143 SP3 NFYC PPARGC1A CHD2 ASB9P1 FAM174B HMGN1P38 MIR3175 GC15P095992 LINC01578 ENSG00000279765 LOC105370979
GH15J092892 Promoter/Enhancer 0.9 EPDnew dbSUPER 650.4 -8.1 -8134 0.1 POLR2A RBM22 CHD2 FAM174B LINC01578 GC15P095992 ENSG00000279765
GH15J092927 Promoter 0.5 EPDnew 650.3 +27.1 27066 0.1 CHD2 MIR3175 ENSG00000279765 LOC105370979
GH15J092800 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 107.2 -93.0 -93027 14.1 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ENSG00000258922 ENSG00000274215 FAM174B CHD2 ASB9P1 HMGN1P38 ENSG00000260361
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHD2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHD2 gene promoter:
  • E2F-1
  • PPAR-gamma2
  • E2F
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Pbx1a
  • Pax-5
  • CBF(2)

Genomic Locations for CHD2 Gene

Genomic Locations for CHD2 Gene
127,819 bases
Plus strand
144,712 bases
Plus strand

Genomic View for CHD2 Gene

Genes around CHD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHD2 Gene

Proteins for CHD2 Gene

  • Protein details for CHD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Chromodomain-helicase-DNA-binding protein 2
    Protein Accession:
    Secondary Accessions:
    • C6G482
    • Q96IP5

    Protein attributes for CHD2 Gene

    1828 amino acids
    Molecular mass:
    211344 Da
    Quaternary structure:
    • Interacts with MYOD1. Interacts with histone H3.3 (By similarity).

    Alternative splice isoforms for CHD2 Gene


neXtProt entry for CHD2 Gene

Post-translational modifications for CHD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CHD2 Gene

Domains & Families for CHD2 Gene

Gene Families for CHD2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SNF2/RAD54 helicase family.
  • Belongs to the SNF2/RAD54 helicase family.
genes like me logo Genes that share domains with CHD2: view

Function for CHD2 Gene

Molecular function for CHD2 Gene

UniProtKB/Swiss-Prot Function:
DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. Involved in myogenesis via interaction with MYOD1: binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
GENATLAS Biochemistry:
DNA binding protein with two chromatin organization (chromo) domains,and a helicase domain,2,component of the chromatin remodeling complex

Enzyme Numbers (IUBMB) for CHD2 Gene

Phenotypes From GWAS Catalog for CHD2 Gene

Gene Ontology (GO) - Molecular Function for CHD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001046 core promoter sequence-specific DNA binding ISS --
GO:0003677 DNA binding TAS,IEA 9326634
GO:0003723 RNA binding HDA 22658674
GO:0004003 ATP-dependent DNA helicase activity TAS 9326634
GO:0004386 helicase activity IEA --
genes like me logo Genes that share ontologies with CHD2: view
genes like me logo Genes that share phenotypes with CHD2: view

Human Phenotype Ontology for CHD2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CHD2 Gene

MGI Knock Outs for CHD2:
  • Chd2 Chd2<tm1b(EUCOMM)Hmgu>

Animal Model Products

  • Taconic Biosciences Mouse Models for CHD2

miRNA for CHD2 Gene

Clone Products

  • Addgene plasmids for CHD2

No data available for Transcription Factor Targets and HOMER Transcription for CHD2 Gene

Localization for CHD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHD2 Gene

Nucleus. Note=Binds to myogenic gene promoters. {ECO:0000250}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHD2 gene
Compartment Confidence
extracellular 5
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CHD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS,IEA --
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
GO:0070062 extracellular exosome HDA --
genes like me logo Genes that share ontologies with CHD2: view

Pathways & Interactions for CHD2 Gene

genes like me logo Genes that share pathways with CHD2: view

Pathways by source for CHD2 Gene

1 Cell Signaling Technology pathway for CHD2 Gene

Gene Ontology (GO) - Biological Process for CHD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II TAS 9326634
GO:0006974 cellular response to DNA damage stimulus IEA --
genes like me logo Genes that share ontologies with CHD2: view

No data available for SIGNOR curated interactions for CHD2 Gene

Drugs & Compounds for CHD2 Gene

(3) Drugs for CHD2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(1) Additional Compounds for CHD2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with CHD2: view

Transcripts for CHD2 Gene

mRNA/cDNA for CHD2 Gene

Unigene Clusters for CHD2 Gene

Chromodomain helicase DNA binding protein 2:
Representative Sequences:

Clone Products

  • Addgene plasmids for CHD2

Alternative Splicing Database (ASD) splice patterns (SP) for CHD2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1: -
SP2: - -
SP6: - -

ExUns: 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30

Relevant External Links for CHD2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CHD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CHD2 Gene

Protein differential expression in normal tissues from HIPED for CHD2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.7), Rectum (8.1), Adrenal (6.1), and Lung (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CHD2 Gene

Protein tissue co-expression partners for CHD2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CHD2 Gene:


SOURCE GeneReport for Unigene cluster for CHD2 Gene:


Evidence on tissue expression from TISSUES for CHD2 Gene

  • Liver(4.6)
  • Skin(4.3)
  • Blood(4.2)
  • Nervous system(3.6)
  • Lung(3.5)
  • Bone marrow(2.3)
  • Spleen(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CHD2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • cerebellum
  • head
genes like me logo Genes that share expression patterns with CHD2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for CHD2 Gene

Orthologs for CHD2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CHD2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CHD2 34 33
  • 99.77 (n)
(Bos Taurus)
Mammalia CHD2 34
  • 97 (a)
(Monodelphis domestica)
Mammalia CHD2 34
  • 93 (a)
(Canis familiaris)
Mammalia CHD2 34 33
  • 92.88 (n)
(Rattus norvegicus)
Mammalia Chd2 33
  • 90.68 (n)
(Mus musculus)
Mammalia Chd2 16 34 33
  • 90.24 (n)
(Ornithorhynchus anatinus)
Mammalia CHD2 34
  • 89 (a)
(Gallus gallus)
Aves CHD2 34 33
  • 80.53 (n)
(Anolis carolinensis)
Reptilia CHD2 34
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia chd2 33
  • 73.73 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.3342 33
(Danio rerio)
Actinopterygii chd2 34 33
  • 69.54 (n)
Dr.15242 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008698 33
  • 56.7 (n)
fruit fly
(Drosophila melanogaster)
Insecta Chd1 34 35 33
  • 53.49 (n)
(Caenorhabditis elegans)
Secernentea chd-1 34 33
  • 57.03 (n)
H06O01.2 35
  • 53 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHD1 34
  • 35 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons CHR5 33
  • 51.4 (n)
(Oryza sativa)
Liliopsida Os07g0660200 33
  • 52.84 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
Species where no ortholog for CHD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CHD2 Gene

Gene Tree for CHD2 (if available)
Gene Tree for CHD2 (if available)
Evolutionary constrained regions (ECRs) for CHD2: view image

Paralogs for CHD2 Gene

Paralogs for CHD2 Gene

(11) SIMAP similar genes for CHD2 Gene using alignment to 8 proteins:

  • B7Z3I4_HUMAN
  • G3V418_HUMAN
  • G3V4S8_HUMAN
  • H3BU65_HUMAN
  • J3QR73_HUMAN
  • Q8N677_HUMAN
genes like me logo Genes that share paralogs with CHD2: view

Variants for CHD2 Gene

Sequence variations from dbSNP and Humsavar for CHD2 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1015228436 uncertain-significance, Epileptic encephalopathy, childhood-onset 92,984,505(+) T/G genic_downstream_transcript_variant, intron_variant
rs1060503517 pathogenic, Epileptic encephalopathy, childhood-onset 92,942,894(+) GTGGTG/G coding_sequence_variant, frameshift
rs1060503518 uncertain-significance, Epileptic encephalopathy, childhood-onset 92,953,547(+) A/G coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1060503519 uncertain-significance, Epileptic encephalopathy, childhood-onset 92,945,835(+) A/G coding_sequence_variant, missense_variant
rs1060503520 uncertain-significance, Epileptic encephalopathy, childhood-onset 92,953,524(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for CHD2 Gene

Variant ID Type Subtype PubMed ID
dgv1264n106 CNV deletion 24896259
dgv157n21 CNV loss 19592680
dgv2660n100 CNV gain 25217958
esv1010129 CNV deletion 20482838
esv1475283 CNV deletion 17803354
esv2229244 CNV deletion 18987734
esv2567952 CNV deletion 19546169
esv2750049 CNV deletion 23290073
esv3214901 CNV deletion 24192839
esv3304312 CNV mobile element insertion 20981092
esv3327654 CNV insertion 20981092
esv3343910 CNV insertion 20981092
esv3552857 CNV deletion 23714750
esv3637274 CNV gain 21293372
esv4137 CNV loss 18987735
esv9274 CNV loss 19470904
nsv1052724 CNV gain 25217958
nsv1070477 CNV deletion 25765185
nsv1146550 CNV deletion 26484159
nsv520601 CNV loss 19592680
nsv523617 CNV loss 19592680
nsv957969 CNV deletion 24416366

Variation tolerance for CHD2 Gene

Residual Variation Intolerance Score: 0.916% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.89; 48.54% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHD2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHD2 Gene

Disorders for CHD2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for CHD2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CHD2 in MalaCards View complete list of genes associated with diseases


  • Epileptic encephalopathy, childhood-onset (EEOC) [MIM:615369]: A severe form of epilepsy characterized by onset of multiple seizure types in the first few years of life and associated with poor prognosis. Affected individuals have cognitive regression and intellectual disability. {ECO:0000269 PubMed:23708187, ECO:0000269 PubMed:25356899}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CHD2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CHD2: view

No data available for Genatlas for CHD2 Gene

Publications for CHD2 Gene

  1. Characterization of the CHD family of proteins. (PMID: 9326634) Woodage T … Collins FS (Proceedings of the National Academy of Sciences of the United States of America 1997) 2 3 4 58
  2. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1. (PMID: 23708187) Carvill GL … Mefford HC (Nature genetics 2013) 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Analysis of the DNA sequence and duplication history of human chromosome 15. (PMID: 16572171) Zody MC … Nusbaum C (Nature 2006) 3 4 58
  5. PARP1 Links CHD2-Mediated Chromatin Expansion and H3.3 Deposition to DNA Repair by Non-homologous End-Joining. (PMID: 26895424) Luijsterburg MS … van Attikum H (Molecular cell 2016) 3 58

Products for CHD2 Gene

Sources for CHD2 Gene

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