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

Gene ID: 55636, updated on 3-Nov-2024

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
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Try the new Transcript table

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: HPA RNA-seq normal tissues 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
CHARGE syndrome
MedGen: C0265354 OMIM: 214800 GeneReviews: CHD7 Disorder
not available
Hypogonadotropic hypogonadism 5 with or without anosmia not available

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

Markers

Clone Names

  • FLJ20357, FLJ20361, KIAA1416

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 RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables chromatin binding TAS
Traceable Author Statement
more info
PubMed 
enables helicase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables promoter-specific chromatin 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 T cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in adult heart development IEA
Inferred from Electronic Annotation
more info
 
involved_in adult walking behavior IEA
Inferred from Electronic Annotation
more info
 
involved_in aorta morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in atrioventricular canal development IEA
Inferred from Electronic Annotation
more info
 
involved_in blood circulation IEA
Inferred from Electronic Annotation
more info
 
involved_in blood vessel remodeling IEA
Inferred from Electronic Annotation
more info
 
involved_in cardiac septum morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in central nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in chordate embryonic development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cognition IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cranial nerve development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cranial nerve development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in embryonic hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in epithelium development IEA
Inferred from Electronic Annotation
more info
 
involved_in face development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in female genitalia development IEA
Inferred from Electronic Annotation
more info
 
involved_in genitalia development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in heart morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in heart morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in in utero embryonic development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in inner ear morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in inner ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in innervation IEA
Inferred from Electronic Annotation
more info
 
involved_in limb development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nose development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in olfactory behavior IEA
Inferred from Electronic Annotation
more info
 
involved_in olfactory bulb development IEA
Inferred from Electronic Annotation
more info
 
involved_in olfactory nerve development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in rRNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of growth hormone secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of neurogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
involved_in response to bacterium IEA
Inferred from Electronic Annotation
more info
 
involved_in retina development in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in right ventricular compact myocardium morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in secondary palate development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in semicircular canal morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in sensory perception of sound IEA
Inferred from Electronic Annotation
more info
 
involved_in skeletal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in ventricular trabecula myocardium morphogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleolus 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 
located_in nucleus TAS
Traceable Author Statement
more info
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_001316690.1NP_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:593637
    BRK; domain in transcription and CHROMO domain helicases
    pfam15991
    Location:270418
    G_path_suppress; G-protein pathway suppressor
    cl25764
    Location:364587
    PAT1; Topoisomerase II-associated protein PAT1
  2. NM_017780.4NP_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:26422686
    BRK; domain in transcription and CHROMO domain helicases
    cd00024
    Location:801862
    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:9871136
    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:306423
    Forkhead_N; Forkhead N-terminal region
    pfam09606
    Location:202576
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00176
    Location:9711258
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:12901404
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:883935
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam07533
    Location:25642604
    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_011517553.3XP_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:26722716
    BRK; domain in transcription and CHROMO domain helicases
    cd00024
    Location:801862
    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:9871136
    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:306423
    Forkhead_N; Forkhead N-terminal region
    pfam09606
    Location:202576
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00176
    Location:9711258
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:12901404
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:883935
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam07533
    Location:25942634
    BRK; BRK domain
  2. XM_047421945.1XP_047277901.1  chromodomain-helicase-DNA-binding protein 7 isoform X4

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

    Conserved Domains (9) summary
    smart00592
    Location:26712715
    BRK; domain in transcription and CHROMO domain helicases
    cd00024
    Location:801862
    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:9871136
    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:306423
    Forkhead_N; Forkhead N-terminal region
    pfam09606
    Location:202576
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00176
    Location:9711258
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:12901404
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:883935
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam07533
    Location:25932633
    BRK; BRK domain
  4. XM_047421946.1XP_047277902.1  chromodomain-helicase-DNA-binding protein 7 isoform X5

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

    Conserved Domains (9) summary
    smart00592
    Location:26412685
    BRK; domain in transcription and CHROMO domain helicases
    cd00024
    Location:801862
    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:9871136
    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:306423
    Forkhead_N; Forkhead N-terminal region
    pfam09606
    Location:202576
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00176
    Location:9711258
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:12901404
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:883935
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam07533
    Location:25632603
    BRK; BRK domain
  6. XM_047421947.1XP_047277903.1  chromodomain-helicase-DNA-binding protein 7 isoform X6

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

    Conserved Domains (7) summary
    cd00024
    Location:801862
    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:9871136
    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:306423
    Forkhead_N; Forkhead N-terminal region
    pfam09606
    Location:187576
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00176
    Location:9711258
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:12901404
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:883935
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
  8. XM_011517554.4XP_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:26722716
    BRK; domain in transcription and CHROMO domain helicases
    cd00024
    Location:801862
    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:9871136
    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:306423
    Forkhead_N; Forkhead N-terminal region
    pfam09606
    Location:202576
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00176
    Location:9711258
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:12901404
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:883935
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam07533
    Location:25942634
    BRK; BRK domain
  9. XM_017013612.2XP_016869101.1  chromodomain-helicase-DNA-binding protein 7 isoform X1

    Conserved Domains (9) summary
    smart00592
    Location:26722716
    BRK; domain in transcription and CHROMO domain helicases
    cd00024
    Location:801862
    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:9871136
    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:306423
    Forkhead_N; Forkhead N-terminal region
    pfam09606
    Location:202576
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00176
    Location:9711258
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:12901404
    Helicase_C; Helicase conserved C-terminal domain
    pfam00385
    Location:883935
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam07533
    Location:25942634
    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_054360774.1XP_054216749.1  chromodomain-helicase-DNA-binding protein 7 isoform X1

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

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

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

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

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

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

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

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

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_017783.1: Suppressed sequence

    Description
    NM_017783.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.