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CHD2 chromodomain helicase DNA binding protein 2 [ Homo sapiens (human) ]

Gene ID: 1106, updated on 11-Apr-2024

Summary

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Official Symbol
CHD2provided by HGNC
Official Full Name
chromodomain helicase DNA binding protein 2provided by HGNC
Primary source
HGNC:HGNC:1917
See related
Ensembl:ENSG00000173575 MIM:602119; AllianceGenome:HGNC:1917
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EEOC; DEE94
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 26.2), thyroid (RPKM 13.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
15q26.1
Exon count:
39
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (92900324..93027996)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (90662587..90790268)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (93443554..93571226)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903558 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93351993-93352843 Neighboring gene FAM174B-LINC01578 intergenic CAGE-defined high expression enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93368032-93368688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10125 Neighboring gene MPRA-validated peak2429 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10127 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:93425915-93426556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10129 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:93447162-93448361 Neighboring gene CHD2 adjacent suppressive regulatory RNA Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:93460529-93461365 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93464712-93465911 Neighboring gene microRNA 3175 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:93488387-93488611 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:93492919-93494118 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:93523977-93525176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93571676-93572182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93575221-93575725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93595001-93595610 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93605093-93605890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93606687-93607483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:93608443-93609406 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:93616734-93616872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:93617029-93617786 Neighboring gene repulsive guidance molecule BMP co-receptor a Neighboring gene uncharacterized LOC101927025 Neighboring gene YBX2 pseudogene 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:93648672-93649381 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:93678957-93679495 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:93679496-93680033

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2. Lewis EMA, et al. Sci Rep, 2022 Sep 17. PMID 36115870, Free PMC Article
  2. Novel Loss-of-Function Variants in CHD2 Cause Childhood-Onset Epileptic Encephalopathy in Chinese Patients. Wang X, et al. Genes (Basel), 2022 May 19. PMID 35627293, Free PMC Article
  3. CHD2-Related CNS Pathologies. Wilson MM, et al. Int J Mol Sci, 2021 Jan 8. PMID 33435571, Free PMC Article
  4. Chromatin remodeling dysfunction extends the etiological spectrum of schizophrenia: a case report. Poisson A, et al. BMC Med Genet, 2020 Jan 8. PMID 31914951, Free PMC Article
  5. A regulatory role for CHD2 in myelopoiesis. Shahin Varnoosfaderani F, et al. Epigenetics, 2020 Jun-Jul. PMID 31900031, Free PMC Article

See all (82) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of CircCHD2 in the pathogenesis of gestational diabetes mellitus by regulating autophagy via miR-33b-3p/ULK1 axis.
    Title: Role of CircCHD2 in the pathogenesis of gestational diabetes mellitus by regulating autophagy via miR-33b-3p/ULK1 axis.
  2. CircCHD2/miR-200b-3p/HLF Axis Promotes Liver Cirrhosis.
    Title: CircCHD2/miR-200b-3p/HLF Axis Promotes Liver Cirrhosis.
  3. Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2.
    Title: Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2.
  4. Novel Loss-of-Function Variants in CHD2 Cause Childhood-Onset Epileptic Encephalopathy in Chinese Patients.
    Title: Novel Loss-of-Function Variants in CHD2 Cause Childhood-Onset Epileptic Encephalopathy in Chinese Patients.
  5. CHD1 and SPOP synergistically protect prostate epithelial cells from DNA damage.
    Title: CHD1 and SPOP synergistically protect prostate epithelial cells from DNA damage.
  6. A regulatory role for CHD2 in myelopoiesis.
    Title: A regulatory role for CHD2 in myelopoiesis.
  7. CHD2-Related CNS Pathologies.
    Title: CHD2-Related CNS Pathologies.
  8. Study finds that Q1392TfsX17 maybe the hot-spot mutation of CHD2 and that West syndrome could be a new phenotype of CHD2 mutation.
    Title: CHD2-related epilepsy: novel mutations and new phenotypes.
  9. CHD2 encodes a member of the chromodomain helicase DNA-binding (CHD) family involved in chromatin remodeling. This observation adds schizophrenia to the phenotypic spectrum of chromodomain remodeling disorders, which may lead to innovative therapeutic approaches.
    Title: Chromatin remodeling dysfunction extends the etiological spectrum of schizophrenia: a case report.
  10. DNA helicases CHD2 and CHD7 could reduce BAP1 promoter activity, likely through unwinding its G4 structures.
    Title: G-quadruplexes in the BAP1 promoter positively regulate its expression.
Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2019-10-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2019-10-23)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ATP-dependent chromatin remodeler activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding HDA PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IEA
Inferred from Electronic Annotation
more info
  
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in hematopoietic stem cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in muscle organ development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in nucleosome organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
chromodomain-helicase-DNA-binding protein 2
Names
ATP-dependent helicase CHD2
CHD-2
NP_001036037.1
NP_001262.3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012826.2 RefSeqGene

    Range
    5004..132676
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1425

mRNA and Protein(s)

  1. NM_001042572.3 → NP_001036037.1  chromodomain-helicase-DNA-binding protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001036037.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks multiple 3' exons and has an alternate 3' end, as compared to variant 1. The encoded isoform (2) has a much shorter and distinct C-terminus, as compared to isoform 1.
    Source sequence(s)
    BC007347, BU630151, CN277753
    Consensus CDS
    CCDS45356.1
    UniProtKB/TrEMBL
    Q8N677
    Related
    ENSP00000406581.2, ENST00000420239.7
    Conserved Domains (3) summary
    cd18661
    Location:376 → 447
    CD2_tandem_CHD1-2_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
    cd18666
    Location:259 → 343
    CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
    cl28899
    Location:464 → 501
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

  2. NM_001271.4 → NP_001262.3  chromodomain-helicase-DNA-binding protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001262.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA907775, AC013394, AF006514, CT003638, DB111282, DB121252
    Consensus CDS
    CCDS10374.2
    UniProtKB/Swiss-Prot
    C6G482, O14647, Q96IP5
    Related
    ENSP00000377747.4, ENST00000394196.9
    Conserved Domains (8) summary
    cd00024
    Location:282 → 344
    CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
    cd00046
    Location:503 → 648
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00176
    Location:487 → 768
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:790 → 905
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:379 → 447
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam08648
    Location:1661 → 1749
    DUF1777; Protein of unknown function (DUF1777)
    pfam13907
    Location:1471 → 1553
    DUF4208; Domain of unknown function (DUF4208)
    pfam17104
    Location:1042 → 1165
    DUF5102; Domain of unknown function (DUF5102)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    92900324..93027996
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    90662587..90790268
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14647.2 GenPept UniProtKB/Swiss-Prot:O14647

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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