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    CHD7 chromodomain helicase DNA binding protein 7 [ Homo sapiens (human) ]

    Gene ID: 55636, updated on 4-Jan-2025

    Summary

    Official Symbol
    CHD7provided by HGNC
    Official Full Name
    chromodomain helicase DNA binding protein 7provided by HGNC
    Primary source
    HGNC:HGNC:20626
    See related
    Ensembl:ENSG00000171316 MIM:608892; AllianceGenome:HGNC:20626
    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
    CRG; HH5; IS3; KAL5
    Summary
    This gene encodes a protein that contains several helicase family domains. Mutations in this gene have been found in some patients with the CHARGE syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
    Expression
    Ubiquitous expression in bone marrow (RPKM 6.4), brain (RPKM 4.0) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CHD7 in Genome Data Viewer
    Location:
    8q12.2
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (60678740..60868028)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (61102480..61291800)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (61591299..61780587)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:61428694-61429554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27423 Neighboring gene RAB2A, member RAS oncogene family Neighboring gene uncharacterized LOC124901950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19225 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:61563068-61563273 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:61564220-61564720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27425 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:61693034-61694233 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27427 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27428 Neighboring gene NANOG hESC enhancer GRCh37_chr8:61786284-61786806 Neighboring gene uncharacterized LOC124901951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27430 Neighboring gene IFITM3 pseudogene 8

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    BioGRID CRISPR Screen Phenotypes (47 hits/1303 screens)

    Associated conditions

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2023-04-11)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2023-04-11)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome-wide association study of lung function decline in adults with and without asthma.
    EBI GWAS Catalog
    Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Clone Names

    • FLJ20357, FLJ20361, KIAA1416

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding  
    enables ATP hydrolysis activity  
    enables ATP-dependent H2AZ histone chaperone activity  
    enables ATP-dependent H3-H4 histone complex chaperone activity  
    enables ATP-dependent chromatin remodeler activity  
    enables DNA binding  
    enables DNA clamp loader activity  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables chromatin binding  
    enables chromatin binding PubMed 
    enables chromatin extrusion motor activity  
    enables cohesin loader activity  
    enables double-stranded DNA helicase activity  
    enables forked DNA-dependent helicase activity  
    enables four-way junction helicase activity  
    enables histone binding  
    enables promoter-specific chromatin binding  
    enables protein binding PubMed 
    enables single-stranded 3'-5' DNA helicase activity  
    Items 1 - 25 of 50
    Process Evidence Code Pubs
    involved_in DNA duplex unwinding  
    involved_in T cell differentiation PubMed 
    involved_in adult heart development  
    involved_in adult walking behavior  
    involved_in aorta morphogenesis  
    involved_in atrioventricular canal development  
    involved_in blood circulation  
    involved_in blood vessel remodeling  
    involved_in cardiac septum morphogenesis  
    involved_in central nervous system development  
    involved_in central nervous system development PubMed 
    involved_in chordate embryonic development  
    involved_in chromatin looping  
    involved_in chromatin remodeling  
    involved_in cognition PubMed 
    involved_in cranial nerve development  
    involved_in cranial nerve development PubMed 
    involved_in embryonic hindlimb morphogenesis  
    involved_in epithelium development  
    involved_in face development PubMed 
    involved_in female genitalia development  
    involved_in genitalia development PubMed 
    involved_in heart morphogenesis  
    involved_in heart morphogenesis PubMed 
    involved_in in utero embryonic development PubMed 
    involved_in inner ear morphogenesis  
    involved_in inner ear morphogenesis PubMed 
    involved_in innervation  
    involved_in limb development PubMed 
    involved_in nose development PubMed 
    involved_in olfactory behavior  
    involved_in olfactory bulb development  
    involved_in olfactory nerve development  
    involved_in positive regulation of multicellular organism growth  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in rRNA processing  
    involved_in regulation of DNA-templated transcription PubMed 
    involved_in regulation of gene expression  
    involved_in regulation of growth hormone secretion PubMed 
    involved_in regulation of neurogenesis  
    involved_in regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum  
    involved_in response to bacterium  
    involved_in retina development in camera-type eye PubMed 
    involved_in right ventricular compact myocardium morphogenesis  
    involved_in secondary palate development PubMed 
    involved_in semicircular canal morphogenesis  
    involved_in sensory perception of sound  
    involved_in skeletal system development PubMed 
    involved_in transcription by RNA polymerase II  
    involved_in ventricular trabecula myocardium morphogenesis  
    Items 1 - 25 of 50
    Component Evidence Code Pubs
    located_in chromatin  
    located_in nucleolus  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus PubMed 
    located_in nucleus PubMed 

    General protein information

    Preferred Names
    chromodomain-helicase-DNA-binding protein 7
    Names
    ATP-dependent helicase CHD7
    CHARGE association
    NP_001303619.1
    NP_060250.2
    XP_011515855.1
    XP_011515856.1
    XP_011515857.1
    XP_011515862.1
    XP_016869101.1
    XP_016869102.1
    XP_047277901.1
    XP_047277902.1
    XP_047277903.1
    XP_054216749.1
    XP_054216750.1
    XP_054216751.1
    XP_054216752.1
    XP_054216753.1
    XP_054216754.1
    XP_054216755.1
    XP_054216756.1
    XP_054216757.1

    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.

    Genomic

    1. NG_007009.1 RefSeqGene

      Range
      4986..194249
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_176

    mRNA and Protein(s)

    1. NM_001316690.1 → NP_001303619.1  chromodomain-helicase-DNA-binding protein 7 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as CRA_e) lacks most of the internal exons compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is significantly shorter compared to isoform 1. This isoform, described in PMID:20925924, may negatively regulate the activity of isoform 1.
      Source sequence(s)
      AC113143, BC068000, BI039198, GU060498, W78145
      Consensus CDS
      CCDS83299.1
      UniProtKB/Swiss-Prot
      Q9P2D1
      Related
      ENSP00000437061.1, ENST00000524602.5
      Conserved Domains (3) summary
      smart00592
      Location:593 → 637
      BRK; domain in transcription and CHROMO domain helicases
      pfam15991
      Location:270 → 418
      G_path_suppress; G-protein pathway suppressor
      cl25764
      Location:364 → 587
      PAT1; Topoisomerase II-associated protein PAT1
    2. NM_017780.4 → NP_060250.2  chromodomain-helicase-DNA-binding protein 7 isoform 1

      See identical proteins and their annotated locations for NP_060250.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB037837, AC023102, AC113143, AK123158, BC033116, BC051264, BC068000, BI039198, W78145
      Consensus CDS
      CCDS47865.1
      UniProtKB/Swiss-Prot
      D0VBA5, E9PNZ2, Q05DI5, Q2TAN4, Q66K35, Q7Z6C0, Q7Z7Q2, Q9NXA0, Q9NXA3, Q9P2D1
      Related
      ENSP00000392028.1, ENST00000423902.7
      Conserved Domains (9) summary
      smart00592
      Location:2642 → 2686
      BRK; domain in transcription and CHROMO domain helicases
      cd00024
      Location:801 → 862
      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:987 → 1136
      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.
      pfam08430
      Location:306 → 423
      Forkhead_N; Forkhead N-terminal region
      pfam09606
      Location:202 → 576
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam00176
      Location:971 → 1258
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1290 → 1404
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:883 → 935
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam07533
      Location:2564 → 2604
      BRK; BRK domain

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      60678740..60868028
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011517553.3 → XP_011515855.1  chromodomain-helicase-DNA-binding protein 7 isoform X1

      See identical proteins and their annotated locations for XP_011515855.1

      Conserved Domains (9) summary
      smart00592
      Location:2672 → 2716
      BRK; domain in transcription and CHROMO domain helicases
      cd00024
      Location:801 → 862
      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:987 → 1136
      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.
      pfam08430
      Location:306 → 423
      Forkhead_N; Forkhead N-terminal region
      pfam09606
      Location:202 → 576
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam00176
      Location:971 → 1258
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1290 → 1404
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:883 → 935
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam07533
      Location:2594 → 2634
      BRK; BRK domain
    2. XM_047421945.1 → XP_047277901.1  chromodomain-helicase-DNA-binding protein 7 isoform X4

    3. XM_011517555.3 → XP_011515857.1  chromodomain-helicase-DNA-binding protein 7 isoform X2

      Conserved Domains (9) summary
      smart00592
      Location:2671 → 2715
      BRK; domain in transcription and CHROMO domain helicases
      cd00024
      Location:801 → 862
      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:987 → 1136
      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.
      pfam08430
      Location:306 → 423
      Forkhead_N; Forkhead N-terminal region
      pfam09606
      Location:202 → 576
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam00176
      Location:971 → 1258
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1290 → 1404
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:883 → 935
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam07533
      Location:2593 → 2633
      BRK; BRK domain
    4. XM_047421946.1 → XP_047277902.1  chromodomain-helicase-DNA-binding protein 7 isoform X5

    5. XM_017013613.2 → XP_016869102.1  chromodomain-helicase-DNA-binding protein 7 isoform X3

      Conserved Domains (9) summary
      smart00592
      Location:2641 → 2685
      BRK; domain in transcription and CHROMO domain helicases
      cd00024
      Location:801 → 862
      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:987 → 1136
      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.
      pfam08430
      Location:306 → 423
      Forkhead_N; Forkhead N-terminal region
      pfam09606
      Location:202 → 576
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam00176
      Location:971 → 1258
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1290 → 1404
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:883 → 935
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam07533
      Location:2563 → 2603
      BRK; BRK domain
    6. XM_047421947.1 → XP_047277903.1  chromodomain-helicase-DNA-binding protein 7 isoform X6

    7. XM_011517560.3 → XP_011515862.1  chromodomain-helicase-DNA-binding protein 7 isoform X7

      Conserved Domains (7) summary
      cd00024
      Location:801 → 862
      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:987 → 1136
      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.
      pfam08430
      Location:306 → 423
      Forkhead_N; Forkhead N-terminal region
      pfam09606
      Location:187 → 576
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam00176
      Location:971 → 1258
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1290 → 1404
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:883 → 935
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
    8. XM_011517554.4 → XP_011515856.1  chromodomain-helicase-DNA-binding protein 7 isoform X1

      See identical proteins and their annotated locations for XP_011515856.1

      Conserved Domains (9) summary
      smart00592
      Location:2672 → 2716
      BRK; domain in transcription and CHROMO domain helicases
      cd00024
      Location:801 → 862
      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:987 → 1136
      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.
      pfam08430
      Location:306 → 423
      Forkhead_N; Forkhead N-terminal region
      pfam09606
      Location:202 → 576
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam00176
      Location:971 → 1258
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1290 → 1404
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:883 → 935
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam07533
      Location:2594 → 2634
      BRK; BRK domain
    9. XM_017013612.2 → XP_016869101.1  chromodomain-helicase-DNA-binding protein 7 isoform X1

      Conserved Domains (9) summary
      smart00592
      Location:2672 → 2716
      BRK; domain in transcription and CHROMO domain helicases
      cd00024
      Location:801 → 862
      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:987 → 1136
      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.
      pfam08430
      Location:306 → 423
      Forkhead_N; Forkhead N-terminal region
      pfam09606
      Location:202 → 576
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam00176
      Location:971 → 1258
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1290 → 1404
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:883 → 935
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam07533
      Location:2594 → 2634
      BRK; BRK domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      61102480..61291800
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360774.1 → XP_054216749.1  chromodomain-helicase-DNA-binding protein 7 isoform X1

    2. XM_054360779.1 → XP_054216754.1  chromodomain-helicase-DNA-binding protein 7 isoform X4

    3. XM_054360777.1 → XP_054216752.1  chromodomain-helicase-DNA-binding protein 7 isoform X2

    4. XM_054360780.1 → XP_054216755.1  chromodomain-helicase-DNA-binding protein 7 isoform X5

    5. XM_054360778.1 → XP_054216753.1  chromodomain-helicase-DNA-binding protein 7 isoform X3

    6. XM_054360781.1 → XP_054216756.1  chromodomain-helicase-DNA-binding protein 7 isoform X6

    7. XM_054360782.1 → XP_054216757.1  chromodomain-helicase-DNA-binding protein 7 isoform X7

    8. XM_054360776.1 → XP_054216751.1  chromodomain-helicase-DNA-binding protein 7 isoform X1

    9. XM_054360775.1 → XP_054216750.1  chromodomain-helicase-DNA-binding protein 7 isoform X1

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