Human Gene CHD7 (ENST00000423902.7) from GENCODE V43
  Description: Homo sapiens chromodomain helicase DNA binding protein 7 (CHD7), transcript variant 1, mRNA. (from RefSeq NM_017780)
RefSeq Summary (NM_017780): 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].
Gencode Transcript: ENST00000423902.7
Gencode Gene: ENSG00000171316.14
Transcript (Including UTRs)
   Position: hg38 chr8:60,678,740-60,868,028 Size: 189,289 Total Exon Count: 38 Strand: +
Coding Region
   Position: hg38 chr8:60,741,433-60,865,933 Size: 124,501 Coding Exon Count: 37 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-02-17 13:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr8:60,678,740-60,868,028)mRNA (may differ from genome)Protein (2997 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 7; Short=CHD-7; EC=; AltName: Full=ATP-dependent helicase CHD7;
FUNCTION: Probable transcription regulator.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: May interact with CTCF. Interacts with CHD8.
INTERACTION: Q9HCK8-2:CHD8; NbExp=3; IntAct=EBI-3951683, EBI-4410319;
TISSUE SPECIFICITY: Widely expressed in fetal and adult tissues.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in CHD7 are a cause of CHARGE syndrome (CHARGES) [MIM:214800]. This syndrome, which is a common cause of congenital anomalies, is characterized by a non-random pattern of congenital anomalies including choanal atresia and malformations of the heart, inner ear, and retina.
DISEASE: Defects in CHD7 are a cause of susceptibility to idiopathic scoliosis type 3 (IS3) [MIM:608765]. Idiopathic scoliosis (IS) is the most common spinal deformity in children.
DISEASE: Defects in CHD7 are the cause of Kallmann syndrome type 5 (KAL5) [MIM:612370]. Kallmann syndrome is a disorder that associates hypogonadotropic hypogonadism and anosmia. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone- synthesizing neurons. In some patients other developmental anomalies can be present, which include renal agenesis, cleft lip and/or palate, selective tooth agenesis, and bimanual synkinesis. In some cases anosmia may be absent or inconspicuous.
DISEASE: Defects in CHD7 are a cause of idiopathic hypogonadotropic hypogonadism (IHH) [MIM:146110]. IHH is defined as a deficiency of the pituitary secretion of follicle-stimulating hormone and luteinizing hormone, which results in the impairment of pubertal maturation and of reproductive function.
SIMILARITY: Belongs to the SNF2/RAD54 helicase family.
SIMILARITY: Contains 2 chromo domains.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SEQUENCE CAUTION: Sequence=AAH14681.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH14681.1; Type=Miscellaneous discrepancy; Note=Potential poly-A sequence; Sequence=AAH53890.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH68000.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH80627.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH80627.1; Type=Miscellaneous discrepancy; Note=Potential poly-A sequence; Sequence=AAI10819.1; Type=Miscellaneous discrepancy; Note=Potential poly-A sequence; Sequence=BAA91113.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA91116.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
WEB RESOURCE: Name=GeneReviews; URL="";
WEB RESOURCE: Name=CHD7 database; URL="";

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: CHD7
Diseases sorted by gene-association score: charge syndrome* (1363), hypogonadotropic hypogonadism 5 with or without anosmia* (1231), chd7-related isolated gonadotropin-releasing hormone deficiency* (500), hypothyroidism* (400), kallmann syndrome 5* (400), scoliosis* (305), myopia* (235), myopia 6* (231), kallmann syndrome* (136), omenn syndrome* (118), normosmic congenital hypogonadotropic hypogonadism* (97), scoliosis, isolated 3* (50), idiopathic scoliosis (16), lichen nitidus (15), choanal atresia, posterior (14), hypogonadotropic hypogonadism (12), esophageal atresia (10), hypogonadism (10), osteogenesis imperfecta, type xiv (10), tinea favosa (9), coloboma (8), tracheoesophageal fistula (7), osgood-schlatter's disease (7), patent ductus arteriosus (6), ritscher-schinzel syndrome (6), hypoparathyroidism-deafness-renal disease syndrome (6), heart disease (5), nasal cavity disease (5), vertebrobasilar insufficiency (5), myopathy, tubular aggregate, 1 (5), duane-radial ray syndrome (5), nose disease (5), osteogenesis imperfecta, type ii (4), upper respiratory tract disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.45 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 157.68 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -217.70517-0.421 Picture PostScript Text
3' UTR -521.902095-0.249 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006576 - BRK_domain
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR001005 - SANT/Myb
IPR000330 - SNF2_N

Pfam Domains:
PF07533 - BRK domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF00271 - Helicase conserved C-terminal domain
PF00176 - SNF2 family N-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

ModBase Predicted Comparative 3D Structure on Q9P2D1
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl WormBase 
Protein SequenceProtein SequenceProtein Sequence Protein Sequence 
AlignmentAlignmentAlignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016817 hydrolase activity, acting on acid anhydrides
GO:1990841 promoter-specific chromatin binding

Biological Process:
GO:0001501 skeletal system development
GO:0001568 blood vessel development
GO:0001701 in utero embryonic development
GO:0001974 blood vessel remodeling
GO:0003007 heart morphogenesis
GO:0003222 ventricular trabecula myocardium morphogenesis
GO:0003226 right ventricular compact myocardium morphogenesis
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006364 rRNA processing
GO:0007417 central nervous system development
GO:0007512 adult heart development
GO:0007605 sensory perception of sound
GO:0007626 locomotory behavior
GO:0007628 adult walking behavior
GO:0008015 blood circulation
GO:0010880 regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
GO:0021545 cranial nerve development
GO:0021553 olfactory nerve development
GO:0021772 olfactory bulb development
GO:0030217 T cell differentiation
GO:0030540 female genitalia development
GO:0035116 embryonic hindlimb morphogenesis
GO:0035904 aorta development
GO:0035909 aorta morphogenesis
GO:0036302 atrioventricular canal development
GO:0040018 positive regulation of multicellular organism growth
GO:0042048 olfactory behavior
GO:0042471 ear morphogenesis
GO:0042472 inner ear morphogenesis
GO:0043010 camera-type eye development
GO:0043584 nose development
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048752 semicircular canal morphogenesis
GO:0048771 tissue remodeling
GO:0048806 genitalia development
GO:0048844 artery morphogenesis
GO:0050767 regulation of neurogenesis
GO:0050890 cognition
GO:0060021 palate development
GO:0060041 retina development in camera-type eye
GO:0060123 regulation of growth hormone secretion
GO:0060173 limb development
GO:0060324 face development
GO:0060384 innervation
GO:0060411 cardiac septum morphogenesis
GO:0060429 epithelium development

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus

-  Descriptions from all associated GenBank mRNAs
  GU060498 - Homo sapiens chromodomain helicase DNA binding protein 7 isoform CRA_e (CHD7) mRNA, complete cds, alternatively spliced.
BC172443 - Synthetic construct Homo sapiens clone IMAGE:100069137, MGC:199148 chromodomain helicase DNA binding protein 7 (CHD7) mRNA, encodes complete protein.
AB037837 - Homo sapiens mRNA for KIAA1416 protein, partial cds.
AK000368 - Homo sapiens cDNA FLJ20361 fis, clone HEP16789.
AK225354 - Homo sapiens mRNA for chromodomain helicase DNA binding protein 7 variant, clone: HEP16789.
BC068000 - Homo sapiens chromodomain helicase DNA binding protein 7, mRNA (cDNA clone IMAGE:6010918), partial cds.
BC053890 - Homo sapiens chromodomain helicase DNA binding protein 7, mRNA (cDNA clone IMAGE:6148161), partial cds.
BC110818 - Homo sapiens chromodomain helicase DNA binding protein 7, mRNA (cDNA clone IMAGE:5220216), partial cds.
BC033116 - Homo sapiens chromodomain helicase DNA binding protein 7, mRNA (cDNA clone IMAGE:3352674), partial cds.
BC041018 - Homo sapiens chromodomain helicase DNA binding protein 7, mRNA (cDNA clone IMAGE:3354323), partial cds.
BC014681 - Homo sapiens chromodomain helicase DNA binding protein 7, mRNA (cDNA clone IMAGE:3866722), partial cds.
JC506684 - Sequence 52 from Patent EP2733220.
JC737796 - Sequence 52 from Patent WO2014075939.
BC080627 - Homo sapiens chromodomain helicase DNA binding protein 7, mRNA (cDNA clone IMAGE:6340273), partial cds.
JD530237 - Sequence 511261 from Patent EP1572962.
JD338465 - Sequence 319489 from Patent EP1572962.
JD094672 - Sequence 75696 from Patent EP1572962.
JD039666 - Sequence 20690 from Patent EP1572962.
JD270711 - Sequence 251735 from Patent EP1572962.
JD168225 - Sequence 149249 from Patent EP1572962.
JD047979 - Sequence 29003 from Patent EP1572962.
JD381873 - Sequence 362897 from Patent EP1572962.
JD387217 - Sequence 368241 from Patent EP1572962.
AK123158 - Homo sapiens cDNA FLJ41163 fis, clone BRACE2039734.
JD115912 - Sequence 96936 from Patent EP1572962.
JD319121 - Sequence 300145 from Patent EP1572962.
JD323992 - Sequence 305016 from Patent EP1572962.
JD511126 - Sequence 492150 from Patent EP1572962.
JD354309 - Sequence 335333 from Patent EP1572962.
JD048719 - Sequence 29743 from Patent EP1572962.
JD047400 - Sequence 28424 from Patent EP1572962.
JD486873 - Sequence 467897 from Patent EP1572962.
JD094790 - Sequence 75814 from Patent EP1572962.
JD109626 - Sequence 90650 from Patent EP1572962.
JD292922 - Sequence 273946 from Patent EP1572962.
JD413149 - Sequence 394173 from Patent EP1572962.
JD115595 - Sequence 96619 from Patent EP1572962.
JD319682 - Sequence 300706 from Patent EP1572962.
JD301002 - Sequence 282026 from Patent EP1572962.
JD150465 - Sequence 131489 from Patent EP1572962.
JD173660 - Sequence 154684 from Patent EP1572962.
JD436142 - Sequence 417166 from Patent EP1572962.
JD298527 - Sequence 279551 from Patent EP1572962.
JD449151 - Sequence 430175 from Patent EP1572962.
JD088319 - Sequence 69343 from Patent EP1572962.
JD384956 - Sequence 365980 from Patent EP1572962.
AK295751 - Homo sapiens cDNA FLJ57840 complete cds, highly similar to Chromodomain-helicase-DNA-binding protein 7 (EC 3.6.1.-).
AK000364 - Homo sapiens cDNA FLJ20357 fis, clone HEP16545.
JD340161 - Sequence 321185 from Patent EP1572962.
AL833190 - Homo sapiens mRNA; cDNA DKFZp667M015 (from clone DKFZp667M015).
JD115361 - Sequence 96385 from Patent EP1572962.
JD434329 - Sequence 415353 from Patent EP1572962.
JD519003 - Sequence 500027 from Patent EP1572962.
JD512227 - Sequence 493251 from Patent EP1572962.
BC051264 - Homo sapiens chromodomain helicase DNA binding protein 7, mRNA (cDNA clone IMAGE:3636644), partial cds.
JD250614 - Sequence 231638 from Patent EP1572962.
JD037149 - Sequence 18173 from Patent EP1572962.
JD307357 - Sequence 288381 from Patent EP1572962.
JD089155 - Sequence 70179 from Patent EP1572962.
JD531126 - Sequence 512150 from Patent EP1572962.
JD557977 - Sequence 539001 from Patent EP1572962.
JD538237 - Sequence 519261 from Patent EP1572962.
JD559520 - Sequence 540544 from Patent EP1572962.
JD322408 - Sequence 303432 from Patent EP1572962.
JD449460 - Sequence 430484 from Patent EP1572962.
JD269898 - Sequence 250922 from Patent EP1572962.
JD553881 - Sequence 534905 from Patent EP1572962.
JD038891 - Sequence 19915 from Patent EP1572962.
JD339451 - Sequence 320475 from Patent EP1572962.
JD056703 - Sequence 37727 from Patent EP1572962.
JD174311 - Sequence 155335 from Patent EP1572962.
JD328079 - Sequence 309103 from Patent EP1572962.
JD428534 - Sequence 409558 from Patent EP1572962.
JD395687 - Sequence 376711 from Patent EP1572962.
JD477226 - Sequence 458250 from Patent EP1572962.
JD113881 - Sequence 94905 from Patent EP1572962.
JD339395 - Sequence 320419 from Patent EP1572962.
JD464112 - Sequence 445136 from Patent EP1572962.
JD404441 - Sequence 385465 from Patent EP1572962.
JD433997 - Sequence 415021 from Patent EP1572962.
JD204998 - Sequence 186022 from Patent EP1572962.
JD087383 - Sequence 68407 from Patent EP1572962.
JD305246 - Sequence 286270 from Patent EP1572962.
JD448981 - Sequence 430005 from Patent EP1572962.
JD294915 - Sequence 275939 from Patent EP1572962.
JD510357 - Sequence 491381 from Patent EP1572962.
JD086095 - Sequence 67119 from Patent EP1572962.
JD237695 - Sequence 218719 from Patent EP1572962.
JD474071 - Sequence 455095 from Patent EP1572962.
JD489491 - Sequence 470515 from Patent EP1572962.
JD554520 - Sequence 535544 from Patent EP1572962.
JD143943 - Sequence 124967 from Patent EP1572962.
JD504575 - Sequence 485599 from Patent EP1572962.
JD228623 - Sequence 209647 from Patent EP1572962.
JD506659 - Sequence 487683 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CHD7_HUMAN, ENST00000423902.1, ENST00000423902.2, ENST00000423902.3, ENST00000423902.4, ENST00000423902.5, ENST00000423902.6, KIAA1416, NM_017780, Q05DI5, Q2TAN4, Q66K35, Q7Z6C0, Q7Z7Q2, Q9NXA0, Q9NXA3, Q9P2D1, uc003xue.1, uc003xue.2, uc003xue.3, uc003xue.4, uc003xue.5
UCSC ID: ENST00000423902.7
RefSeq Accession: NM_017780
Protein: Q9P2D1 (aka CHD7_HUMAN)
CCDS: CCDS47865.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CHD7:
cdh-ov (Congenital Diaphragmatic Hernia Overview)
charge (CHD7 Disorder)
kms (Isolated Gonadotropin-Releasing Hormone (GnRH) Deficiency)
tef-ov (Esophageal Atresia/Tracheoesophageal Fistula Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.