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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CHD6-CHRNB4 (FusionGDB2 ID:HG84181TG1143)

Fusion Gene Summary for CHD6-CHRNB4

check button Fusion gene summary
Fusion gene informationFusion gene name: CHD6-CHRNB4
Fusion gene ID: hg84181tg1143
HgeneTgene
Gene symbol

CHD6

CHRNB4

Gene ID

84181

1143

Gene namechromodomain helicase DNA binding protein 6cholinergic receptor nicotinic beta 4 subunit
SynonymsCHD-6|CHD5|RIGB-
Cytomap('CHD6')('CHRNB4')

20q12

15q25.1

Type of geneprotein-codingprotein-coding
Descriptionchromodomain-helicase-DNA-binding protein 6ATP-dependent helicase CHD6helicase C-terminal domain- and SNF2 N-terminal domain-containing proteinradiation-induced gene B proteinneuronal acetylcholine receptor subunit beta-4acetylcholine receptor, nicotinic, beta 4 (neuronal)cholinergic receptor, nicotinic, beta 4 (neuronal)cholinergic receptor, nicotinic, beta polypeptide 4neuronal nicotinic receptor beta 4 subunit
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000309279, ENST00000373222, 
ENST00000373233, ENST00000480022, 
Fusion gene scores* DoF score30 X 18 X 11=59402 X 2 X 2=8
# samples 352
** MAII scorelog2(35/5940*10)=-4.0850361038558
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: CHD6 [Title/Abstract] AND CHRNB4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHD6(40141485)-CHRNB4(78923674), # samples:1
Anticipated loss of major functional domain due to fusion event.CHD6-CHRNB4 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CHD6-CHRNB4 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CHD6-CHRNB4 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneCHRNB4

GO:0007165

signal transduction

8906617



check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4BRCATCGA-C8-A8HR-01ACHD6chr20

40141485

-CHRNB4chr15

78923674

-


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Fusion Gene ORF analysis for CHD6-CHRNB4

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-5UTRENST00000309279ENST00000560511CHD6chr20

40141485

-CHRNB4chr15

78923674

-
5CDS-5UTRENST00000373222ENST00000560511CHD6chr20

40141485

-CHRNB4chr15

78923674

-
5CDS-5UTRENST00000373233ENST00000560511CHD6chr20

40141485

-CHRNB4chr15

78923674

-
Frame-shiftENST00000309279ENST00000261751CHD6chr20

40141485

-CHRNB4chr15

78923674

-
Frame-shiftENST00000309279ENST00000412074CHD6chr20

40141485

-CHRNB4chr15

78923674

-
Frame-shiftENST00000373222ENST00000261751CHD6chr20

40141485

-CHRNB4chr15

78923674

-
Frame-shiftENST00000373222ENST00000412074CHD6chr20

40141485

-CHRNB4chr15

78923674

-
Frame-shiftENST00000373233ENST00000261751CHD6chr20

40141485

-CHRNB4chr15

78923674

-
Frame-shiftENST00000373233ENST00000412074CHD6chr20

40141485

-CHRNB4chr15

78923674

-
intron-3CDSENST00000480022ENST00000261751CHD6chr20

40141485

-CHRNB4chr15

78923674

-
intron-3CDSENST00000480022ENST00000412074CHD6chr20

40141485

-CHRNB4chr15

78923674

-
intron-5UTRENST00000480022ENST00000560511CHD6chr20

40141485

-CHRNB4chr15

78923674

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for CHD6-CHRNB4


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for CHD6-CHRNB4


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:40141485/:78923674)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for CHD6-CHRNB4


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CHD6-CHRNB4


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for CHD6-CHRNB4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CHD6-CHRNB4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCHD6C0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneCHD6C0005695Bladder Neoplasm1CTD_human
HgeneCHD6C0007138Carcinoma, Transitional Cell1CTD_human
HgeneCHD6C0027819Neuroblastoma1CTD_human
HgeneCHD6C0033578Prostatic Neoplasms1CTD_human
HgeneCHD6C0376358Malignant neoplasm of prostate1CTD_human
TgeneC0001973Alcoholic Intoxication, Chronic3PSYGENET
TgeneC0022333Jacksonian Seizure2CTD_human
TgeneC0036572Seizures2CTD_human
TgeneC0149958Complex partial seizures2CTD_human
TgeneC0234533Generalized seizures2CTD_human
TgeneC0234535Clonic Seizures2CTD_human
TgeneC0270824Visual seizure2CTD_human
TgeneC0270844Tonic Seizures2CTD_human
TgeneC0270846Epileptic drop attack2CTD_human
TgeneC0422850Seizures, Somatosensory2CTD_human
TgeneC0422852Seizures, Auditory2CTD_human
TgeneC0422853Olfactory seizure2CTD_human
TgeneC0422854Gustatory seizure2CTD_human
TgeneC0422855Vertiginous seizure2CTD_human
TgeneC0494475Tonic - clonic seizures2CTD_human
TgeneC0600427Cocaine Dependence2PSYGENET
TgeneC0751056Non-epileptic convulsion2CTD_human
TgeneC0751110Single Seizure2CTD_human
TgeneC0751123Atonic Absence Seizures2CTD_human
TgeneC0751494Convulsive Seizures2CTD_human
TgeneC0751495Seizures, Focal2CTD_human
TgeneC0751496Seizures, Sensory2CTD_human
TgeneC3495874Nonepileptic Seizures2CTD_human
TgeneC4048158Convulsions2CTD_human
TgeneC4316903Absence Seizures2CTD_human
TgeneC4317109Epileptic Seizures2CTD_human
TgeneC4317123Myoclonic Seizures2CTD_human
TgeneC4505436Generalized Absence Seizures2CTD_human
TgeneC0024121Lung Neoplasms1CTD_human
TgeneC0038587Substance Withdrawal Syndrome1CTD_human
TgeneC0086189Drug Withdrawal Symptoms1CTD_human
TgeneC0087169Withdrawal Symptoms1CTD_human
TgeneC0242379Malignant neoplasm of lung1CTD_human