Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	26038
Gene name	Chromodomain helicase DNA binding protein 5
Gene symbol	CHD5
Synonyms (NCBI Gene)	CHD-5PMNDS
Chromosome	1
Chromosome location	1p36.31
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

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Show/Hide all (116)

miRTarBase ID	miRNA	Experiments	Reference
MIRT040349	hsa-miR-615-3p	CLASH	23622248
MIRT037503	hsa-miR-744-5p	CLASH	23622248
MIRT889177	hsa-miR-1184	CLIP-seq
MIRT889178	hsa-miR-1197	CLIP-seq
MIRT889179	hsa-miR-1205	CLIP-seq
MIRT889180	hsa-miR-1207-5p	CLIP-seq
MIRT889181	hsa-miR-1224-5p	CLIP-seq
MIRT889182	hsa-miR-1254	CLIP-seq
MIRT889183	hsa-miR-1273e	CLIP-seq
MIRT889184	hsa-miR-1343	CLIP-seq
MIRT889185	hsa-miR-1909	CLIP-seq
MIRT889186	hsa-miR-2110	CLIP-seq
MIRT889187	hsa-miR-2467-5p	CLIP-seq
MIRT889188	hsa-miR-2861	CLIP-seq
MIRT889189	hsa-miR-298	CLIP-seq
MIRT889190	hsa-miR-3074-5p	CLIP-seq
MIRT889191	hsa-miR-3116	CLIP-seq
MIRT889192	hsa-miR-3124-3p	CLIP-seq
MIRT889193	hsa-miR-3150b-3p	CLIP-seq
MIRT889194	hsa-miR-3153	CLIP-seq
MIRT889195	hsa-miR-3158-5p	CLIP-seq
MIRT889196	hsa-miR-3194-3p	CLIP-seq
MIRT889197	hsa-miR-329	CLIP-seq
MIRT889198	hsa-miR-3607-5p	CLIP-seq
MIRT889199	hsa-miR-3612	CLIP-seq
MIRT889200	hsa-miR-362-3p	CLIP-seq
MIRT889201	hsa-miR-3663-3p	CLIP-seq
MIRT889202	hsa-miR-3691-3p	CLIP-seq
MIRT889203	hsa-miR-3915	CLIP-seq
MIRT889204	hsa-miR-4261	CLIP-seq
MIRT889205	hsa-miR-4271	CLIP-seq
MIRT889206	hsa-miR-4283	CLIP-seq
MIRT889207	hsa-miR-4435	CLIP-seq
MIRT889208	hsa-miR-4436a	CLIP-seq
MIRT889209	hsa-miR-4443	CLIP-seq
MIRT889210	hsa-miR-4489	CLIP-seq
MIRT889211	hsa-miR-4496	CLIP-seq
MIRT889212	hsa-miR-4667-5p	CLIP-seq
MIRT889213	hsa-miR-4675	CLIP-seq
MIRT889214	hsa-miR-4689	CLIP-seq
MIRT889215	hsa-miR-4691-5p	CLIP-seq
MIRT889216	hsa-miR-4700-5p	CLIP-seq
MIRT889217	hsa-miR-4716-5p	CLIP-seq
MIRT889218	hsa-miR-4725-3p	CLIP-seq
MIRT889219	hsa-miR-4736	CLIP-seq
MIRT889220	hsa-miR-4741	CLIP-seq
MIRT889221	hsa-miR-4755-3p	CLIP-seq
MIRT889222	hsa-miR-4763-3p	CLIP-seq
MIRT889223	hsa-miR-4784	CLIP-seq
MIRT889224	hsa-miR-550a	CLIP-seq
MIRT889225	hsa-miR-639	CLIP-seq
MIRT889226	hsa-miR-650	CLIP-seq
MIRT889227	hsa-miR-661	CLIP-seq
MIRT889228	hsa-miR-760	CLIP-seq
MIRT889229	hsa-miR-939	CLIP-seq
MIRT1963525	hsa-miR-1206	CLIP-seq
MIRT889180	hsa-miR-1207-5p	CLIP-seq
MIRT1963526	hsa-miR-1587	CLIP-seq
MIRT1963527	hsa-miR-197	CLIP-seq
MIRT1963528	hsa-miR-2467-3p	CLIP-seq
MIRT889187	hsa-miR-2467-5p	CLIP-seq
MIRT1963529	hsa-miR-3065-3p	CLIP-seq
MIRT1963530	hsa-miR-3131	CLIP-seq
MIRT889195	hsa-miR-3158-5p	CLIP-seq
MIRT889197	hsa-miR-329	CLIP-seq
MIRT1963531	hsa-miR-3616-3p	CLIP-seq
MIRT889200	hsa-miR-362-3p	CLIP-seq
MIRT1963532	hsa-miR-3918	CLIP-seq
MIRT1963533	hsa-miR-3919	CLIP-seq
MIRT1963534	hsa-miR-4437	CLIP-seq
MIRT1963535	hsa-miR-4528	CLIP-seq
MIRT1963536	hsa-miR-4674	CLIP-seq
MIRT1963537	hsa-miR-4725-5p	CLIP-seq
MIRT1963538	hsa-miR-4751	CLIP-seq
MIRT1963539	hsa-miR-4756-3p	CLIP-seq
MIRT889222	hsa-miR-4763-3p	CLIP-seq
MIRT1963540	hsa-miR-4788	CLIP-seq
MIRT1963541	hsa-miR-504	CLIP-seq
MIRT1963542	hsa-miR-611	CLIP-seq
MIRT889180	hsa-miR-1207-5p	CLIP-seq
MIRT1963526	hsa-miR-1587	CLIP-seq
MIRT1963528	hsa-miR-2467-3p	CLIP-seq
MIRT2199939	hsa-miR-3125	CLIP-seq
MIRT2199940	hsa-miR-3127-5p	CLIP-seq
MIRT889197	hsa-miR-329	CLIP-seq
MIRT889200	hsa-miR-362-3p	CLIP-seq
MIRT2199941	hsa-miR-3714	CLIP-seq
MIRT2199942	hsa-miR-3916	CLIP-seq
MIRT1963532	hsa-miR-3918	CLIP-seq
MIRT1963533	hsa-miR-3919	CLIP-seq
MIRT2199943	hsa-miR-4324	CLIP-seq
MIRT2199944	hsa-miR-4436b-3p	CLIP-seq
MIRT2199945	hsa-miR-4476	CLIP-seq
MIRT2199946	hsa-miR-4492	CLIP-seq
MIRT889211	hsa-miR-4496	CLIP-seq
MIRT2199947	hsa-miR-4498	CLIP-seq
MIRT1963535	hsa-miR-4528	CLIP-seq
MIRT2199948	hsa-miR-4656	CLIP-seq
MIRT889213	hsa-miR-4675	CLIP-seq
MIRT889220	hsa-miR-4741	CLIP-seq
MIRT2199949	hsa-miR-4747-5p	CLIP-seq
MIRT1963539	hsa-miR-4756-3p	CLIP-seq
MIRT889222	hsa-miR-4763-3p	CLIP-seq
MIRT2199950	hsa-miR-4763-5p	CLIP-seq
MIRT2199951	hsa-miR-524-3p	CLIP-seq
MIRT2199952	hsa-miR-525-3p	CLIP-seq
MIRT2199953	hsa-miR-548aa	CLIP-seq
MIRT2199954	hsa-miR-596	CLIP-seq
MIRT2199955	hsa-miR-762	CLIP-seq
MIRT1963527	hsa-miR-197	CLIP-seq
MIRT2199944	hsa-miR-4436b-3p	CLIP-seq
MIRT2386006	hsa-miR-4685-5p	CLIP-seq
MIRT2446992	hsa-miR-4539	CLIP-seq
MIRT2446993	hsa-miR-4640-5p	CLIP-seq
MIRT2446994	hsa-miR-4680-5p	CLIP-seq
MIRT2446995	hsa-miR-4726-5p	CLIP-seq

Show/Hide all (38)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000785	Component	Chromatin	IBA
GO:0000792	Component	Heterochromatin	ISS
GO:0003677	Function	DNA binding	IBA
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IBA
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	21931736
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005694	Component	Chromosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IBA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006338	Process	Chromatin remodeling	IMP	23948251
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IMP	23948251
GO:0007283	Process	Spermatogenesis	IEA
GO:0007399	Process	Nervous system development	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	ISS
GO:0016020	Component	Membrane	HDA	19946888
GO:0016581	Component	NuRD complex	IBA
GO:0016581	Component	NuRD complex	ISS
GO:0016607	Component	Nuclear speck	IDA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IBA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0021895	Process	Cerebral cortex neuron differentiation	ISS
GO:0030154	Process	Cell differentiation	IEA
GO:0035092	Process	Sperm DNA condensation	ISS
GO:0042393	Function	Histone binding	IBA
GO:0046872	Function	Metal ion binding	IEA
GO:0061628	Function	Histone H3K27me3 reader activity	IDA	23948251
GO:0140658	Function	ATP-dependent chromatin remodeler activity	IBA
GO:1901798	Process	Positive regulation of signal transduction by p53 class mediator	ISS

MIM	HGNC	e!Ensembl
610771	16816	ENSG00000116254

Q8TDI0

Protein name

Chromodomain-helicase-DNA-binding protein 5 (CHD-5) (EC 3.6.4.-) (ATP-dependent helicase CHD5)

Protein function

ATP-dependent chromatin-remodeling factor that binds DNA through histones and regulates gene transcription. May specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3. Acts as a component of th

PDB

6GUU

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08073	CHDNT	147 → 200	CHDNT (NUC034) domain	Domain
PF00628	PHD	345 → 390	PHD-finger	Domain
PF00628	PHD	418 → 463	PHD-finger	Domain
PF00385	Chromo	592 → 644	Chromo (CHRromatin Organisation MOdifier) domain	Domain
PF00176	SNF2_N	685 → 999	SNF2 family N-terminal domain	Family
PF00271	Helicase_C	1024 → 1138	Helicase conserved C-terminal domain	Family
PF06465	DUF1087	1297 → 1358	Domain of Unknown Function (DUF1087)	Domain
PF06461	DUF1086	1388 → 1529	Domain of Unknown Function (DUF1086)	Domain
PF08074	CHDCT2	1732 → 1858	CHDCT2 (NUC038) domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Preferentially expressed in total brain, fetal brain, and cerebellum. It is also moderately expressed in the adrenal gland and detected in testis. {ECO:0000269|PubMed:12592387, ECO:0000269|PubMed:21931736}.

Sequence

MRGPVGTEEELPRLFAEEMENEDEMSEEEDGGLEAFDDFFPVEPVSLPKKKKPKKLKENK
CKGKRKKKEGSNDELSENEEDLEEKSESEGSDYSPNKKKKKKLKDKKEKKAKRKKKDEDE
DDNDDGCLKEPKSSGQLMAEWGLDDVDYLFSEEDYHTLTNYKAFSQFLRPLIAKKNPKIP
MSKMMTVLGAKWREFSANNPFKGSSAAAAAAAVAAAVETVTISPPLAVSPPQVPQPVPIR
KAKTKEGKGPGVRKKIKGSKDGKKKGKGKKTAGLKFRFGGISNKRKKGSSSEEDEREESD
FDSASIHSASVRSECSAALGKKSKRRRKKKRIDDGDGYETDHQDYCEVCQQGGEIILCDT
CPRAYHLVCLDPELEKAPEGKWSCPHCEKEGIQWEPKDDDDEEEEGGCEEEEDDHMEFCR
VCKDGGELLCCDACPSSYHLHCLNPPLPEIPNGEWLCPRCTCPPLKGKVQRILHWRWTEP
PAPFMVGLPGPDVEPSLPPPKPLEGIPEREFFVKWAGLSYWHCSWVKELQLELYHTVMYR
NYQRKNDMDEPPPFDYGSGDEDGKSEKRKNKDPLYAKMEERFYRYGIKPEWMMIHRILNH
SFDKKGDVHYLIKWKDLPYDQCTWEIDDIDIPYYDNLKQAYWGHRELMLGEDTRLPKRLL
KKGKKLRDDKQEKPPDTPIVDPTVKFDKQPWYIDSTGGTLHPYQLEGLNWLRFSWAQGTD
TILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVTY
TGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFHVLLTSYELITIDQAILGSIE
WACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNN
LEGFLEEFADISKEDQIKKLHDLLGPHMLRRLKADVFKNMPAKTELIVRVELSQMQKKYY
KFILTRNFEALNSKGGGNQVSLLNIMMDLKKCCNHPYLFPVAAVEAPVLPNGSYDGSSLV
KSSGKLMLLQKMLKKLRDEGHRVLIFSQMTKMLDLLEDFLEYEGYKYERIDGGITGGLRQ
EAIDRFNAPGAQQFCFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQN
KKVMIYRFVTRASVEERITQVAKRKMMLTHLVVRPGLGSKSGSMTKQELDDILKFGTEEL
FKDDVEGMMSQGQRPVTPIPDVQSSKGGNLAASAKKKHGSTPPGDNKDVEDSSVIHYDDA
AISKLLDRNQDATDDTELQNMNEYLSSFKVAQYVVREEDGVEEVEREIIKQEENVDPDYW
EKLLRHHYEQQQEDLARNLGKGKRIRKQVNYNDASQEDQEWQDELSDNQSEYSIGSEDED
EDFEERPEGQSGRRQSRRQLKSDRDKPLPPLLARVGGNIEVLGFNARQRKAFLNAIMRWG
MPPQDAFNSHWLVRDLRGKSEKEFRAYVSLFMRHLCEPGADGAETFADGVPREGLSRQHV
LTRIGVMSLVRKKVQEFEHVNGKYSTPDLIPEGPEGKKSGEVISSDPNTPVPASPAHLLP
APLGLPDKMEAQLGYMDEKDPGAQKPRQPLEVQALPAALDRVESEDKHESPASKERAREE
RPEETEKAPPSPEQLPREEVLPEKEKILDKLELSLIHSRGDSSELRPDDTKAEEKEPIET
QQNGDKEEDDEGKKEDKKGKFKFMFNIADGGFTELHTLWQNEERAAVSSGKIYDIWHRRH
DYWLLAGIVTHGYARWQDIQNDPRYMILNEPFKSEVHKGNYLEMKNKFLARRFKLLEQAL
VIEEQLRRAAYLNMTQDPNHPAMALNARLAEVECLAESHQHLSKESLAGNKPANAVLHKV
LNQLEELLSDMKADVTRLPSMLSRIPPVAARLQMSERSILSRLTNRAGDPTIQQGAFGSS
QMYSNNFGPNFRGPGPGGIVNYNQMPLGPYVTDI

Sequence length

1954

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
CHD5-related disorder	Likely pathogenic	rs760743983	RCV004751954	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic; Pathogenic	rs781200968, rs2100842233, rs371488822, rs2100843382, rs1162494442, rs2100847449, rs1474624774, rs2100860639, rs2100863089, rs2100868745, rs1571164162	RCV001376669 RCV001376668 RCV001376667 RCV001376666 RCV001376663 View all (6 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Intellectual disability	Likely pathogenic; Pathogenic	rs781200968, rs2100842233, rs371488822, rs2100843382, rs2100847449, rs1474624774	RCV001376669 RCV001376668 RCV001376667 RCV001376666 RCV001376662 RCV001376660 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental delay	Likely pathogenic	rs2100843382	RCV002274327	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Likely pathogenic	rs2100843378	RCV001780067	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Parenti-mignot neurodevelopmental syndrome	Likely pathogenic	rs2525363379, rs2525395003, rs2525372237, rs2525387042, rs2525311581, rs2100843382, rs2100846484, rs2100868745	RCV003153207 RCV003444187 RCV003493357 RCV003883482 RCV004586390 RCV002246282 RCV002246281 RCV002246279 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Seizure	Likely pathogenic; Pathogenic	rs781200968, rs2100842233, rs371488822, rs2100846484, rs1162494442, rs2100847449, rs760743983, rs2100868745	RCV001376669 RCV001376668 RCV001376667 RCV001376664 RCV001376663 RCV001376662 RCV001376661 RCV001376656 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHD5-associated Neurodevelopmental disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHD5-related Neurodevelopmental disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Harel-Yoon syndrome	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROBLASTOMA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR ANOMALIES, AXONAL NEUROPATHY, DEVELOPMENTAL DELAY SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

CHD5 (chromodomain helicase DNA binding protein 5)