U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 26038, updated on 11-Apr-2024

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See CHD5 in Genome Data Viewer
Location:
1p36.31
Exon count:
42
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (6101787..6180321, complement)
RS_2023_10 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 H3K4me1 hESC enhancer GRCh37_chr1:5939868-5940372 Neighboring gene nephrocystin 4 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5956455-5957256 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5957257-5958056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5968773-5969298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5979954-5980454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5999651-6000151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6004026-6004526 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6009504-6009801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6027103-6027602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6031677-6032176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6051054-6051908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 70 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6059331-6060045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6060046-6060760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6062904-6063618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6068670-6069262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6070973-6071474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6072741-6073242 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6084854-6085618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 71 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6086382-6087145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 73 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 74 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6113495-6113995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6120127-6120627 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:6133526-6134725 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6143081-6143561 Neighboring gene uncharacterized LOC124903831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6162189-6162690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6162691-6163190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6186229-6187116 Neighboring gene Sharpr-MPRA regulatory region 11871 Neighboring gene MPRA-validated peak27 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6225727-6226227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6238637-6239138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6239139-6239638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 138 Neighboring gene Sharpr-MPRA regulatory region 5942 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6265555-6266374 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: C5676984 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

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
 
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 H3K27me3 modified histone binding IDA
Inferred from Direct Assay
more info
PubMed 
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 metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
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
 
involved_in chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cell population proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
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
 
part_of NuRD complex ISS
Inferred from Sequence or Structural Similarity
more info
 
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
part_of 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
 
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)

NEW Try the new Transcript table

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
    O75032, Q5TG89, Q7LGH2, 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: 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_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)