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CHD5 chromodomain helicase DNA binding protein 5 [ Homo sapiens (human) ]

Gene ID: 26038, updated on 9-Oct-2022

Summary

Official Symbol
CHD5provided by HGNC
Official Full Name
chromodomain helicase DNA binding protein 5provided by HGNC
Primary source
HGNC:HGNC:16816
See related
Ensembl:ENSG00000116254 MIM:610771; AllianceGenome:HGNC:16816
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CHD-5; PMNDS
Summary
This gene encodes a member of the chromodomain helicase DNA-binding protein family. Members of this family are characterized by a chromodomain, a helicase ATP-binding domain and an additional functional domain. This gene encodes a neuron-specific protein that may function in chromatin remodeling and gene transcription. This gene is a potential tumor suppressor gene that may play a role in the development of neuroblastoma. [provided by RefSeq, Feb 2012]
Expression
Biased expression in brain (RPKM 14.5), testis (RPKM 9.9) and 1 other tissue See more
Orthologs
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Genomic context

See CHD5 in Genome Data Viewer
Location:
1p36.31
Exon count:
42
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (6101787..6180321, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (5627473..5705967, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (6161847..6240381, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nephrocystin 4 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene uncharacterized LOC124903831 Neighboring gene Sharpr-MPRA regulatory region 11871 Neighboring gene Sharpr-MPRA regulatory region 5942 Neighboring gene RNF207 antisense RNA 1 Neighboring gene ribosomal protein L22

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
Parenti-Mignot neurodevelopmental syndrome
MedGen: CN312032 OMIM: 619873 GeneReviews: Not available
not available

Copy number response

Description
Copy number response
Triplosensitivity

Not yet evaluated (Last evaluated 2022-09-27)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2022-09-27)

ClinGen Genome Curation PagePubMed

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: RPL22

Homology

Clone Names

  • KIAA0444, DKFZp434N231

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
PubMed 
enables ATP-dependent chromatin remodeler activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables DNA helicase activity IEA
Inferred from Electronic Annotation
more info
 
enables H3K27me3 modified histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
 
involved_in cerebral cortex neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in histone H3-K27 trimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in histone H4 acetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of cell population proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of signal transduction by p53 class mediator ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sperm DNA condensation ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
part_of NuRD complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of NuRD complex ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in membrane HDA PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
chromodomain-helicase-DNA-binding protein 5
Names
ATP-dependent helicase CHD5
NP_056372.1

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.

mRNA and Protein(s)

  1. NM_015557.3NP_056372.1  chromodomain-helicase-DNA-binding protein 5

    See identical proteins and their annotated locations for NP_056372.1

    Status: VALIDATED

    Source sequence(s)
    AF425231, AL031847, AL035406, AW005809
    Consensus CDS
    CCDS57.1
    UniProtKB/Swiss-Prot
    Q8TDI0, Q9UFR9
    Related
    ENSP00000262450.3, ENST00000262450.8
    Conserved Domains (10) summary
    smart00298
    Location:592625
    CHROMO; Chromatin organization modifier domain
    cd00046
    Location:720878
    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:345387
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:418460
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam00176
    Location:703999
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:10231138
    Helicase_C; Helicase conserved C-terminal domain
    pfam06461
    Location:13881529
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:12981358
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam08073
    Location:150199
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:17321903
    CHDCT2; CHDCT2 (NUC038) domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    6101787..6180321 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    5627473..5705967 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)