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Gene Gene information from NCBI Gene database.
Entrez ID 1108
Gene name Chromodomain helicase DNA binding protein 4
Gene symbol CHD4
Synonyms (NCBI Gene)
CHD-4Mi-2bMi2-BETASIHIWES
Chromosome 12
Chromosome location 12p13.31
Summary The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional repression. Patients with dermatomyositis d
SNPs SNP information provided by dbSNP.
14 Show/Hide all (14)
SNP ID Visualize variation Clinical significance Consequence
rs886039915 C>T Pathogenic Coding sequence variant, missense variant
rs886039916 G>T Pathogenic Coding sequence variant, missense variant
rs886039917 C>T Pathogenic Coding sequence variant, missense variant
rs886039918 C>A Pathogenic Coding sequence variant, missense variant
rs886039919 C>A Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
664 Show/Hide all (664)
miRTarBase ID miRNA Experiments Reference
MIRT004656 hsa-miR-491-5p Luciferase reporter assay 20065103
MIRT016455 hsa-miR-193b-3p Proteomics 21512034
MIRT027771 hsa-miR-98-5p Microarray 19088304
MIRT032436 hsa-let-7b-5p Proteomics 18668040
MIRT032436 hsa-let-7b-5p CLASH 23622248
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
MBD2 Unknown 23071088
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
61 Show/Hide all (61)
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000166 Function Nucleotide binding IEA
GO:0000724 Process Double-strand break repair via homologous recombination IMP 25593309
GO:0000781 Component Chromosome, telomeric region IDA 25150861
GO:0000785 Component Chromatin HDA 16217013
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
603277 1919 ENSG00000111642
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q14839
Protein name Chromodomain-helicase-DNA-binding protein 4 (CHD-4) (EC 3.6.4.-) (ATP-dependent helicase CHD4) (Mi-2 autoantigen 218 kDa protein) (Mi2-beta)
Protein function ATP-dependent chromatin-remodeling factor that binds and distorts nucleosomal DNA (PubMed:28977666, PubMed:32543371). Acts as a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin (PubMed:16428440,
PDB 1MM2 , 1MM3 , 2EE1 , 2L5U , 2L75 , 2N5N , 4O9I , 6BGG , 6Q3M , 6RYR , 6RYU , 8D4Y
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00176 SNF2_N 699 → 1025 SNF2 family N-terminal domain Family
PF00271 Helicase_C 1050 → 1164 Helicase conserved C-terminal domain Family
PF00385 Chromo 622 → 674 Chromo (CHRromatin Organisation MOdifier) domain Domain
PF00628 PHD 372 → 417 PHD-finger Domain
PF00628 PHD 451 → 496 PHD-finger Domain
PF06461 DUF1086 1380 → 1521 Domain of Unknown Function (DUF1086) Domain
PF06465 DUF1087 1292 → 1352 Domain of Unknown Function (DUF1087) Domain
PF08073 CHDNT 164 → 217 CHDNT (NUC034) domain Domain
PF08074 CHDCT2 1725 → 1851 CHDCT2 (NUC038) domain Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:28977666}.
Sequence
MASGLGSPSPCSAGSEEEDMDALLNNSLPPPHPENEEDPEEDLSETETPKLKKKKKPKKP
RDPKIPKSKRQKKERMLLCRQLGDSSGEGPEFVEEEEEVALRSDSEGSDYTPGKKKKKKL
GPKKEKKSKSKRKEEEEEEDDDDDSKEPKSSAQLLEDWGMEDIDHVFSEEDYRTLTNYKA
FSQFVRPLIAAKNPKIAVSKMMMVLGAKWREFSTNNP
FKGSSGASVAAAAAAAVAVVESM
VTATEVAPPPPPVEVPIRKAKTKEGKGPNARRKPKGSPRVPDAKKPKPKKVAPLKIKLGG
FGSKRKRSSSEDDDLDVESDFDDASINSYSVSDGSTSRSSRSRKKLRTTKKKKKGEEEVT
AVDGYETDHQDYCEVCQQGGEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKEGIQ
WEAKEDNSEGEEILEEVGGDLEEEDDHHMEFCRVCKDGGELLCCDTCPSSYHIHCLNPPL
PEIPNGEWLCPRCTCP
ALKGKVQKILIWKWGQPPSPTPVPRPPDADPNTPSPKPLEGRPE
RQFFVKWQGMSYWHCSWVSELQLELHCQVMFRNYQRKNDMDEPPSGDFGGDEEKSRKRKN
KDPKFAEMEERFYRYGIKPEWMMIHRILNHSVDKKGHVHYLIKWRDLPYDQASWESEDVE
IQDYDLFKQSYWNH
RELMRGEEGRPGKKLKKVKLRKLERPPETPTVDPTVKYERQPEYLD
ATGGTLHPYQMEGLNWLRFSWAQGTDTILADEMGLGKTVQTAVFLYSLYKEGHSKGPFLV
SAPLSTIINWEREFEMWAPDMYVVTYVGDKDSRAIIRENEFSFEDNAIRGGKKASRMKKE
ASVKFHVLLTSYELITIDMAILGSIDWACLIVDEAHRLKNNQSKFFRVLNGYSLQHKLLL
TGTPLQNNLEELFHLLNFLTPERFHNLEGFLEEFADIAKEDQIKKLHDMLGPHMLRRLKA
DVFKNMPSKTELIVRVELSPMQKKYYKYILTRNFEALNARGGGNQVSLLNVVMDLKKCCN
HPYLF
PVAAMEAPKMPNGMYDGSALIRASGKLLLLQKMLKNLKEGGHRVLIFSQMTKMLD
LLEDFLEHEGYKYERIDGGITGNMRQEAIDRFNAPGAQQFCFLLSTRAGGLGINLATADT
VIIYDSDWNPHNDIQAFSRAHRIG
QNKKVMIYRFVTRASVEERITQVAKKKMMLTHLVVR
PGLGSKTGSMSKQELDDILKFGTEELFKDEATDGGGDNKEGEDSSVIHYDDKAIERLLDR
NQDETEDTELQGMNEYLSSFKVAQYVVREEEMGEEEEVEREIIKQEESVDPDYWEKLLRH
HYEQQQEDLARNLGKGKRIRKQVNYNDGSQED
RDWQDDQSDNQSDYSVASEEGDEDFDER
SEAPRRPSRKGLRNDKDKPLPPLLARVGGNIEVLGFNARQRKAFLNAIMRYGMPPQDAFT
TQWLVRDLRGKSEKEFKAYVSLFMRHLCEPGADGAETFADGVPREGLSRQHVLTRIGVMS
LIRKKVQEFEHVNGRWSMPEL
AEVEENKKMSQPGSPSPKTPTPSTPGDTQPNTPAPVPPA
EDGIKIEENSLKEEESIEGEKEVKSTAPETAIECTQAPAPASEDEKVVVEPPEGEEKVEK
AEVKERTEEPMETEPKGAADVEKVEEKSAIDLTPIVVEDKEEKKEEEEKKEVMLQNGETP
KDLNDEKQKKNIKQRFMFNIADGGFTELHSLWQNEERAATVTKKTYEIWHRRHDYWLLAG
IINHGYARWQDIQNDPRYAILNEPFKGEMNRGNFLEIKNKFLARRFKLLEQALVIEEQLR
RAAYLNMSEDPSHPSMALNTRFAEVECLAESHQHLSKESMAGNKPANAVLH
KVLKQLEEL
LSDMKADVTRLPATIARIPPVAVRLQMSERNILSRLANRAPEPTPQQVAQQQ
Sequence length 1912
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
KEGG Pathway Reactome Pathway
ATP-dependent chromatin remodeling HDACs deacetylate histones
Human papillomavirus infection Regulation of TP53 Activity through Acetylation
Viral carcinogenesis RNA Polymerase I Transcription Initiation
  Regulation of PTEN gene transcription
  NGF-stimulated transcription
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
30
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)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Show/Hide Causal Diseases (6)
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
CHD4-related disorder Likely pathogenic; Pathogenic rs2136213384, rs2540396222, rs2540391121, rs1555170507 RCV003978459
RCV003391665
RCV003898920
RCV004545782
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Moyamoya angiopathy with developmental delay Likely pathogenic rs1948532502, rs1229933151, rs1435884753, rs1948698590 RCV001261729
RCV001261730
RCV001261686
RCV001261727
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neonatal encephalopathy Likely pathogenic rs2540401004 RCV003154302
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ovarian serous cystadenocarcinoma Likely pathogenic rs2136221257 RCV005922502
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sifrim-Hitz-Weiss syndrome Likely pathogenic; Pathogenic rs1948326461, rs1948326612, rs1948327010, rs2136215102, rs751534948, rs2136209186, rs2540383458, rs1948436363, rs2540383441, rs2540395856, rs2540390261, rs886039915, rs886039916, rs886039917, rs886039918
View all (15 more)
RCV001331855
RCV001331854
RCV001331853
RCV001733839
RCV001780771
View all (26 more)
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
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.
Show/Hide Unknown Diseases (24)
Phenotype Name Clinical Significance Source Reference Evidence Score
Acute myeloid leukemia Likely benign ClinVar —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION — GWAS catalog 40645996
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER — CTD, Disgenet
CTD, Disgenet
30559488
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Likely benign ClinVar —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Show/Hide Text Mining Associations (101)
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute monocytic leukemia Monocytic Leukemia BEFREE 26265695
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 29667179
★★★★★
★☆☆☆☆
Found in Text Mining only
Adult Malignant Peripheral Nerve Sheath Tumor Malignant Peripheral Nerve Sheath Tumor BEFREE 28549031
★★★★★
★☆☆☆☆
Found in Text Mining only
Alveolar rhabdomyosarcoma Alveolar Rhabdomyosarcoma BEFREE 27760049
★★★★★
★☆☆☆☆
Found in Text Mining only
Ambiguous Genitalia Ambiguous Genitalia HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Apraxia of Phonation Apraxia BEFREE 31737996
★★★★★
★☆☆☆☆
Found in Text Mining only
Apraxias Apraxia Pubtator 31949314 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Arnold Chiari Malformation Arnold-Chiari malformation HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Arrhythmias Cardiac Cardiac arrhythmias Pubtator 34109749 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Arterial Occlusive Diseases Arterial occlusive disease Pubtator 31474762 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only