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CHD4 chromodomain helicase DNA binding protein 4 [ Homo sapiens (human) ]

Gene ID: 1108, updated on 9-Feb-2020

Summary

Official Symbol
CHD4provided by HGNC
Official Full Name
chromodomain helicase DNA binding protein 4provided by HGNC
Primary source
HGNC:HGNC:1919
See related
Ensembl:ENSG00000111642 MIM:603277
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
CHD-4; Mi-2b; SIHIWES; Mi2-BETA
Summary
The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional repression. Patients with dermatomyositis develop antibodies against this protein. Somatic mutations in this gene are associated with serous endometrial tumors. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in thyroid (RPKM 37.2), endometrium (RPKM 27.5) and 25 other tissues See more
Orthologs

Genomic context

See CHD4 in Genome Data Viewer
Location:
12p13.31
Exon count:
40
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (6570082..6607379, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6679248..6716551, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene intermediate filament family orphan 1 Neighboring gene NOP2 nucleolar protein Neighboring gene Sharpr-MPRA regulatory region 3501 Neighboring gene small Cajal body-specific RNA 11 Neighboring gene CRISPRi-validated cis-regulatory element chr12.325 Neighboring gene uncharacterized LOC105369631 Neighboring gene lysophosphatidic acid receptor 5

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Sifrim-Hitz-Weiss syndrome
MedGen: C4310688 OMIM: 617159 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686E06161

Gene Ontology Provided by GOA

Component Evidence Code Pubs
NuRD complex IDA
Inferred from Direct Assay
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
membrane HDA PubMed 
nuclear chromatin HDA PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
protein-containing complex HDA PubMed 

General protein information

Preferred Names
chromodomain-helicase-DNA-binding protein 4
Names
ATP-dependent helicase CHD4
Mi-2 autoantigen 218 kDa protein
NP_001264.2
NP_001284482.1
NP_001350535.1

NCBI Reference Sequences (RefSeq)

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_052823.1 RefSeqGene

    Range
    5061..42358
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001273.5NP_001264.2  chromodomain-helicase-DNA-binding protein 4 isoform 1

    See identical proteins and their annotated locations for NP_001264.2

    Status: REVIEWED

    Source sequence(s)
    AC006064, BC038596, BP234473, X86691
    Consensus CDS
    CCDS8552.1
    UniProtKB/Swiss-Prot
    Q14839
    Related
    ENSP00000440542.2, ENST00000544040.6
    Conserved Domains (12) summary
    smart00298
    Location:622676
    CHROMO; Chromatin organization modifier domain
    cd00024
    Location:540577
    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:746904
    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.
    cd15531
    Location:372414
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:451493
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam00176
    Location:7291025
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:10681164
    Helicase_C; Helicase conserved C-terminal domain
    pfam06461
    Location:13851521
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:13021352
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam06614
    Location:15171649
    Neuromodulin; Neuromodulin
    pfam08073
    Location:164216
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:17261896
    CHDCT2; CHDCT2 (NUC038) domain
  2. NM_001297553.2NP_001284482.1  chromodomain-helicase-DNA-binding protein 4 isoform 2

    See identical proteins and their annotated locations for NP_001284482.1

    Status: REVIEWED

    Source sequence(s)
    AC006064, BC038596, CR936680, X86691
    Consensus CDS
    CCDS76510.1
    UniProtKB/Swiss-Prot
    Q14839
    UniProtKB/TrEMBL
    F5GWX5
    Related
    ENSP00000496163.1, ENST00000645022.1
    Conserved Domains (12) summary
    smart00298
    Location:615669
    CHROMO; Chromatin organization modifier domain
    cd00024
    Location:533570
    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:739897
    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.
    cd15531
    Location:365407
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:444486
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam00176
    Location:7221018
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:10611157
    Helicase_C; Helicase conserved C-terminal domain
    pfam06461
    Location:13781514
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:12951345
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam06614
    Location:15101642
    Neuromodulin; Neuromodulin
    pfam08073
    Location:157209
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:17191889
    CHDCT2; CHDCT2 (NUC038) domain
  3. NM_001363606.2NP_001350535.1  chromodomain-helicase-DNA-binding protein 4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC006064
    Consensus CDS
    CCDS86267.1
    Related
    ENSP00000349508.3, ENST00000357008.7
    Conserved Domains (10) summary
    smart00298
    Location:609663
    CHROMO; Chromatin organization modifier domain
    cd00024
    Location:527564
    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 ...
    cd15531
    Location:359401
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:438480
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam06461
    Location:13721508
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:12891339
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam08073
    Location:164217
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:17151886
    CHDCT2; CHDCT2 (NUC038) domain
    cl25758
    Location:14981633
    DUF4775; Domain of unknown function (DUF4775)
    cl26465
    Location:7111268
    SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    6570082..6607379 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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