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

    Gene ID: 26038, updated on 5-May-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
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    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)