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

101

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
CHD5-related disorder	Likely pathogenic	rs760743983	RCV004751954
Global developmental delay	Likely pathogenic; Pathogenic	rs781200968, rs2100842233, rs371488822, rs2100843382, rs1162494442, rs2100847449, rs1474624774, rs2100860639, rs2100863089, rs2100868745, rs1571164162	RCV001376669 RCV001376668 RCV001376667 RCV001376666 RCV001376663 RCV001376662 RCV001376660 RCV001376659 RCV001376658 RCV001376656 RCV001376654
Intellectual disability	Likely pathogenic; Pathogenic	rs781200968, rs2100842233, rs371488822, rs2100843382, rs2100847449, rs1474624774	RCV001376669 RCV001376668 RCV001376667 RCV001376666 RCV001376662 RCV001376660
Neurodevelopmental delay	Likely pathogenic	rs2100843382	RCV002274327
Neurodevelopmental disorder	Likely pathogenic	rs2100843378	RCV001780067
Parenti-mignot neurodevelopmental syndrome	Likely pathogenic	rs2525363379, rs2525395003, rs2525372237, rs2525387042, rs2525311581, rs2100843382, rs2100846484, rs2100868745	RCV003153207 RCV003444187 RCV003493357 RCV003883482 RCV004586390 RCV002246282 RCV002246281 RCV002246279
Seizure	Likely pathogenic; Pathogenic	rs781200968, rs2100842233, rs371488822, rs2100846484, rs1162494442, rs2100847449, rs760743983, rs2100868745	RCV001376669 RCV001376668 RCV001376667 RCV001376664 RCV001376663 RCV001376662 RCV001376661 RCV001376656

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
CHD5-associated Neurodevelopmental disorder	Uncertain significance	rs2100851117	RCV002266728
CHD5-related Neurodevelopmental disorder	Uncertain significance	rs775681121	RCV001839272
Gastric cancer	Benign	rs115664978	RCV005913118
Harel-Yoon syndrome	Uncertain significance	rs1666868736	RCV001839169
See cases	Uncertain significance	rs149780291	RCV003232925

Show/Hide Text Mining Associations (37)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenoma	Associate	24243398
Azoospermia	Associate	33621950
Breast Neoplasms	Inhibit	18698156, 22569290
Carcinogenesis	Associate	24243398
Carcinoma Hepatocellular	Associate	26517514, 29907144, 30043858
Carcinoma Hepatocellular	Inhibit	35808817
Carcinoma Renal Cell	Associate	26943038
Colorectal Neoplasms	Associate	19750230
Colorectal Neoplasms	Inhibit	24243398
Craniosynostoses	Associate	33944996
Developmental Disabilities	Associate	33944996, 35468861
Epilepsy	Associate	33944996
Glioblastoma	Associate	35955624
Glioma	Associate	18698156, 35955624
Hypersensitivity Delayed	Associate	33944996
Intellectual Disability	Associate	33944996
Language Development Disorders	Associate	33944996
Language Disorders	Associate	33944996
Learning Disabilities	Associate	33944996
Leukemia	Inhibit	24454811
Lymphatic Metastasis	Inhibit	22569290
Lymphoma	Associate	30043858
Lymphoma Non Hodgkin	Associate	35955624
Machado Joseph Disease	Associate	34871736
Mental Disorders	Associate	33944996
Neoplasm Metastasis	Inhibit	26517514
Neoplasms	Associate	18698156, 30043858, 31792669, 35768791
Neoplasms	Inhibit	18953434, 20950435, 22294723, 22569290, 22834704, 24243398, 24454811, 25247294, 25825869, 26245651, 26517514, 26895110, 26943038, 29907144, 33915956, 35768791, 35808817, 35955624 View all (3 more)
Neuroblastoma	Inhibit	20950435, 25825869
Neuroblastoma	Associate	22294723, 22328561, 25247294, 26245651, 26895110, 33915956, 35768791, 35955624
Ovarian Diseases	Associate	31792669
Ovarian Neoplasms	Associate	18953434
Prostatic Neoplasms	Associate	21147910
Seizures	Associate	33944996
Spasms Infantile	Associate	33944996
Stomach Neoplasms	Inhibit	19840376
Stomach Neoplasms	Associate	30043858

CHD5 (chromodomain helicase DNA binding protein 5)