Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
1107
Gene name Gene Name - the full gene name approved by the HGNC.
Chromodomain helicase DNA binding protein 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
CHD3
Synonyms (NCBI Gene) Gene synonyms aliases
Mi-2a, Mi2-ALPHA, SNIBCPS, ZFH
Disease Acronyms (UniProt) Disease acronyms from UniProt database
SNIBCPS
Chromosome Chromosome number
17
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
17p13.1
Summary Summary of gene provided in NCBI Entrez Gene.
This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase c
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs754919272 C>A,T Likely-pathogenic, pathogenic Coding sequence variant, synonymous variant, missense variant, genic downstream transcript variant, downstream transcript variant
rs1064795892 C>T Likely-pathogenic, not-provided Coding sequence variant, missense variant
rs1555611722 C>T Uncertain-significance, likely-pathogenic, pathogenic Coding sequence variant, missense variant
rs1555612691 GATGATGCTGAC>- Likely-pathogenic Downstream transcript variant, genic downstream transcript variant, inframe deletion, coding sequence variant
rs1567844992 G>T Likely-pathogenic Stop gained, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT032350 hsa-let-7b-5p Proteomics 18668040
MIRT032350 hsa-let-7b-5p CLASH 23622248
MIRT051081 hsa-miR-16-5p CLASH 23622248
MIRT036514 hsa-miR-1226-3p CLASH 23622248
MIRT036072 hsa-miR-1296-5p CLASH 23622248
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 27068747
GO:0000976 Function Transcription regulatory region sequence-specific DNA binding IDA 27068747
GO:0003677 Function DNA binding TAS 9326634
GO:0003678 Function DNA helicase activity TAS 9326634
GO:0003723 Function RNA binding HDA 22658674
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
602120 1918 ENSG00000170004
Protein
UniProt ID Q12873
Protein name Chromodomain-helicase-DNA-binding protein 3 (CHD-3) (EC 3.6.4.-) (ATP-dependent helicase CHD3) (Mi-2 autoantigen 240 kDa protein) (Mi2-alpha) (Zinc finger helicase) (hZFH)
Protein function ATP-dependent chromatin-remodeling factor that binds and distorts nucleosomal DNA (PubMed:28977666). Acts as a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin (PubMed:16428440, PubMed:28977666,
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF08073 CHDNT 148 201 CHDNT (NUC034) domain Domain
PF00628 PHD 381 426 PHD-finger Domain
PF00628 PHD 458 503 PHD-finger Domain
PF00385 Chromo 631 683 Chromo (CHRromatin Organisation MOdifier) domain Domain
PF00176 SNF2_N 739 1035 SNF2 family N-terminal domain Family
PF00271 Helicase_C 1060 1174 Helicase conserved C-terminal domain Family
PF06465 DUF1087 1295 1356 Domain of Unknown Function (DUF1087) Domain
PF06461 DUF1086 1376 1517 Domain of Unknown Function (DUF1086) Domain
PF08074 CHDCT2 1736 1862 CHDCT2 (NUC038) domain Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:28977666, ECO:0000269|PubMed:9688266}.
Sequence
MKAADTVILWARSKNDQLRISFPPGLCWGDRMPDKDDIRLLPSALGVKKRKRGPKKQKEN
KPGKPRKRKKRDSEEEFGSERDEYREKSESGGSEYGTGPGRKRRRKHREKKEKKTKRRKK
GEGDGGQKQVEQKSSATLLLTWGLEDVEHVFSEEDYHTLTNYKAFSQFMRPLIAKKNPKI
PMSKMMTILGAKWREFSANNP
FKGSAAAVAAAAAAAAAAVAEQVSAAVSSATPIAPSGPP
ALPPPPAADIQPPPIRRAKTKEGKGPGHKRRSKSPRVPDGRKKLRGKKMAPLKIKLGLLG
GKRKKGGSYVFQSDEGPEPEAEESDLDSGSVHSASGRPDGPVRTKKLKRGRPGRKKKKVL
GCPAVAGEEEVDGYETDHQDYCEVCQQGGEIILCDTCPRAYHLVCLDPELDRAPEGKWSC
PHCEKE
GVQWEAKEEEEEYEEEGEEEGEKEEEDDHMEYCRVCKDGGELLCCDACISSYHI
HCLNPPLPDIPNGEWLCPRCTCP
VLKGRVQKILHWRWGEPPVAVPAPQQADGNPDVPPPR
PLQGRSEREFFVKWVGLSYWHCSWAKELQLEIFHLVMYRNYQRKNDMDEPPPLDYGSGED
DGKSDKRKVKDPHYAEMEEKYYRFGIKPEWMTVHRIINHSVDKKGNYHYLVKWRDLPYDQ
STWEEDEMNIPEYEEHKQSYWRH
RELIMGEDPAQPRKYKKKKKELQGDGPPSSPTNDPTV
KYETQPRFITATGGTLHMYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYK
EGHTKGPFLVSAPLSTIINWEREFQMWAPKFYVVTYTGDKDSRAIIRENEFSFEDNAIKG
GKKAFKMKREAQVKFHVLLTSYELITIDQAALGSIRWACLVVDEAHRLKNNQSKFFRVLN
GYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLL
GPHMLRRLKADVFKNMPAKTELIVRVELSPMQKKYYKYILTRNFEALNSRGGGNQVSLLN
IMMDLKKCCNHPYLF
PVAAMESPKLPSGAYEGGALIKSSGKLMLLQKMLRKLKEQGHRVL
IFSQMTKMLDLLEDFLDYEGYKYERIDGGITGALRQEAIDRFNAPGAQQFCFLLSTRAGG
LGINLATADTVIIFDSDWNPHNDIQAFSRAHRIG
QANKVMIYRFVTRASVEERITQVAKR
KMMLTHLVVRPGLGSKAGSMSKQELDDILKFGTEELFKDENEGENKEEDSSVIHYDNEAI
ARLLDRNQDATEDTDVQNMNEYLSSFKVAQYVVREEDKIEEIEREIIKQEENVDPDYWEK
LLRHHYEQQQEDLARNLGKGKRVRKQVNYNDAAQED
QDNQSEYSVGSEEEDEDFDERPEG
RRQSKRQLRNEKDKPLPPLLARVGGNIEVLGFNTRQRKAFLNAVMRWGMPPQDAFTTQWL
VRDLRGKTEKEFKAYVSLFMRHLCEPGADGSETFADGVPREGLSRQQVLTRIGVMSLVKK
KVQEFEHINGRWSMPEL
MPDPSADSKRSSRASSPTKTSPTTPEASATNSPCTSKPATPAP
SEKGEGIRTPLEKEEAENQEEKPEKNSRIGEKMETEADAPSPAPSLGERLEPRKIPLEDE
VPGVPGEMEPEPGYRGDREKSATESTPGERGEEKPLDGQEHRERPEGETGDLGKREDVKG
DRELRPGPRDEPRSNGRREEKTEKPRFMFNIADGGFTELHTLWQNEERAAISSGKLNEIW
HRRHDYWLLAGIVLHGYARWQDIQNDAQFAIINEPFKTEANKGNFLEMKNKFLARRFKLL
EQALVIEEQLRRAAYLNLSQEPAHPAMALHARFAEAECLAESHQHLSKESLAGNKPANAV
LH
KVLNQLEELLSDMKADVTRLPATLSRIPPIAARLQMSERSILSRLASKGTEPHPTPAY
PPGPYATPPGYGAAFSAAPVGALAAAGANYSQMPAGSFITAATNGPPVLVKKEKEMVGAL
VSDGLDRKEPRAGEVICIDD
Sequence length 2000
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG   Reactome
  ATP-dependent chromatin remodeling   HDACs deacetylate histones
SUMOylation of chromatin organization proteins
Regulation of TP53 Activity through Acetylation
RNA Polymerase I Transcription Initiation
Regulation of PTEN gene transcription
Associated diseases Disease information provided by ClinVar, GenCC, and GWAS databases.
Causal
Disease term Disease name dbSNP ID References
Apraxia Apraxia of Phonation rs121908377, rs121908378, rs1135401820, rs1178491246, rs1584969672
Developmental delay Global developmental delay rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291
View all (32 more)
29463886
Macrocephaly Macrocephaly rs786204854, rs764333096, rs1557739557 29463886
Mental retardation Intellectual Disability rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315
View all (1024 more)
29463886
Unknown
Disease term Disease name Evidence References Source
Ischemic stroke Ischemic stroke 26089329 ClinVar
Ischemic Stroke Ischemic Stroke GWAS
Associations from Text Mining
Disease Name Relationship Type References
Alzheimer Disease Associate 17489097, 34686734
Apraxias Associate 29463886, 30397230, 31949314
Arthritis Rheumatoid Associate 35479077
Ataxia Associate 39709005
Autism Spectrum Disorder Associate 37366052
Autistic Disorder Associate 33358638, 34535214, 39709005
Body Dysmorphic Disorders Associate 33358638
Breast Neoplasms Associate 28055972
Carcinoma Hepatocellular Associate 30043858
Carcinoma Hepatocellular Stimulate 39473409