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

    Gene ID: 1106, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See CHD2 in Genome Data Viewer
    Location:
    15q26.1
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (92900324..93027996)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (90662587..90790268)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Clinical analysis of five CHD2 gene mutations in Chinese children with epilepsy. You C, et al. Seizure, 2024 Oct. PMID 39068850
    2. The first reported case of an inherited pathogenic CHD2 variant in a clinically affected mother and daughter. Petersen AK, et al. Am J Med Genet A, 2018 Jul. PMID 29740950
    3. Autism spectrum disorder recurrence, resulting of germline mosaicism for a CHD2 gene missense variant. Lebrun N, et al. Clin Genet, 2017 Dec. PMID 28960266
    4. CHD2-related epilepsy: novel mutations and new phenotypes. Chen J, et al. Dev Med Child Neurol, 2020 May. PMID 31677157
    5. A regulatory role for CHD2 in myelopoiesis. Shahin Varnoosfaderani F, et al. Epigenetics, 2020 Jun-Jul. PMID 31900031, Free PMC Article

    See all (92) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical analysis of five CHD2 gene mutations in Chinese children with epilepsy.
      Title: Clinical analysis of five CHD2 gene mutations in Chinese children with epilepsy.
    2. Low-grade parental gonosomal mosaicism in CHD2 siblings with Smith-Magenis-like syndrome.
      Title: Low-grade parental gonosomal mosaicism in CHD2 siblings with Smith-Magenis-like syndrome.
    3. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement.
      Title: Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement.
    4. 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.
    5. CircCHD2/miR-200b-3p/HLF Axis Promotes Liver Cirrhosis.
      Title: CircCHD2/miR-200b-3p/HLF Axis Promotes Liver Cirrhosis.
    6. 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.
    7. 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.
    8. CHD1 and SPOP synergistically protect prostate epithelial cells from DNA damage.
      Title: CHD1 and SPOP synergistically protect prostate epithelial cells from DNA damage.
    9. A regulatory role for CHD2 in myelopoiesis.
      Title: A regulatory role for CHD2 in myelopoiesis.
    10. CHD2-Related CNS Pathologies.
      Title: CHD2-Related CNS Pathologies.
    Submit: New GeneRIF Correction See all GeneRIFs (29)

    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)

    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 H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    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 DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    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 chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables four-way junction 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 
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin looping 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
    located_in 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_2024_08

    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.

    Chemical Information
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