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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:GABRB3-DDX1 (FusionGDB2 ID:HG2562TG1653)

Fusion Gene Summary for GABRB3-DDX1

check button Fusion gene summary
Fusion gene informationFusion gene name: GABRB3-DDX1
Fusion gene ID: hg2562tg1653
HgeneTgene
Gene symbol

GABRB3

DDX1

Gene ID

2562

1653

Gene namegamma-aminobutyric acid type A receptor subunit beta3DEAD-box helicase 1
SynonymsECA5|EIEE43DBP-RB|UKVH5d
Cytomap('GABRB3')('DDX1')

15q12

2p24.3

Type of geneprotein-codingprotein-coding
Descriptiongamma-aminobutyric acid receptor subunit beta-3GABA-alpha receptor beta-2 subunitGABAA receptor beta-3 subunitgamma-aminobutyric acid (GABA) A receptor, beta 3gamma-aminobutyric acid A receptor beta 3gamma-aminobutyric acid type A receptor beta3 subuATP-dependent RNA helicase DDX1DEAD (Asp-Glu-Ala-Asp) box helicase 1DEAD (Asp-Glu-Ala-Asp) box polypeptide 1DEAD box polypeptide 1DEAD box protein 1DEAD box protein retinoblastomaDEAD box-1DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1DEAD/H-box h
Modification date2020032020200313
UniProtAcc

P28472

Q92499

Ensembl transtripts involved in fusion geneENST00000299267, ENST00000311550, 
ENST00000400188, ENST00000541819, 
ENST00000545868, ENST00000557641, 
Fusion gene scores* DoF score9 X 9 X 2=1624 X 5 X 3=60
# samples 95
** MAII scorelog2(9/162*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GABRB3 [Title/Abstract] AND DDX1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGABRB3(26790498)-DDX1(15768763), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneGABRB3

GO:0071420

cellular response to histamine

18281286

HgeneGABRB3

GO:1902476

chloride transmembrane transport

9039914

HgeneGABRB3

GO:1904862

inhibitory synapse assembly

25489750

TgeneDDX1

GO:0006302

double-strand break repair

18710941

TgeneDDX1

GO:0032508

DNA duplex unwinding

18710941

TgeneDDX1

GO:0090305

nucleic acid phosphodiester bond hydrolysis

18710941



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
ChiTaRS5.0N/ABG329765GABRB3chr15

26790498

-DDX1chr2

15768763

+


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Fusion Gene ORF analysis for GABRB3-DDX1

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
intron-3CDSENST00000299267ENST00000233084GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000299267ENST00000381341GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000311550ENST00000233084GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000311550ENST00000381341GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000400188ENST00000233084GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000400188ENST00000381341GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000541819ENST00000233084GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000541819ENST00000381341GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000545868ENST00000233084GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000545868ENST00000381341GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000557641ENST00000233084GABRB3chr15

26790498

-DDX1chr2

15768763

+
intron-3CDSENST00000557641ENST00000381341GABRB3chr15

26790498

-DDX1chr2

15768763

+

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 GABRB3-DDX1


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 GABRB3-DDX1


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/:26790498/:15768763)
- 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
GABRB3

P28472

DDX1

Q92499

FUNCTION: Ligand-gated chloride channel which is a component of the heteropentameric receptor for GABA, the major inhibitory neurotransmitter in the brain (PubMed:18514161, PubMed:22303015, PubMed:26950270, PubMed:22243422, PubMed:24909990). Plays an important role in the formation of functional inhibitory GABAergic synapses in addition to mediating synaptic inhibition as a GABA-gated ion channel (PubMed:25489750). The gamma2 subunit is necessary but not sufficient for a rapid formation of active synaptic contacts and the synaptogenic effect of this subunit is influenced by the type of alpha and beta subunits present in the receptor pentamer (By similarity). The alpha1/beta3/gamma2 receptor exhibits synaptogenic activity (PubMed:25489750). The alpha2/beta3/gamma2 receptor shows very little or no synaptogenic activity (By similarity). Functions also as histamine receptor and mediates cellular responses to histamine (PubMed:18281286). Plays an important role in somatosensation and in the production of antinociception (By similarity). {ECO:0000250|UniProtKB:P63080, ECO:0000269|PubMed:18281286, ECO:0000269|PubMed:18514161, ECO:0000269|PubMed:22243422, ECO:0000269|PubMed:22303015, ECO:0000269|PubMed:24909990, ECO:0000269|PubMed:25489750, ECO:0000269|PubMed:26950270}.FUNCTION: Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the NF-kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease (ZBTB8OS), acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation (PubMed:24870230). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of proinflammatory cytokines via the adapter molecule TICAM1. Specifically binds (via helicase ATP-binding domain) on both short and long poly(I:C) dsRNA (By similarity). {ECO:0000250|UniProtKB:Q91VR5, ECO:0000269|PubMed:12183465, ECO:0000269|PubMed:15567440, ECO:0000269|PubMed:18335541, ECO:0000269|PubMed:18710941, ECO:0000269|PubMed:20573827, ECO:0000269|PubMed:24870230}.; FUNCTION: (Microbial infection) Required for HIV-1 Rev function as well as for HIV-1 and coronavirus IBV replication. Binds to the RRE sequence of HIV-1 mRNAs. {ECO:0000269|PubMed:15567440}.; FUNCTION: (Microbial infection) Required for Coronavirus IBV replication. {ECO:0000269|PubMed:20573827}.

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 GABRB3-DDX1


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 GABRB3-DDX1


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 GABRB3-DDX1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneGABRB3P28472DB00898EthanolSmall moleculeApproved
HgeneGABRB3P28472DB06716FospropofolPotentiatorSmall moleculeApproved|Illicit|Investigational
HgeneGABRB3P28472DB00602IvermectinAgonistSmall moleculeApproved|Investigational|Vet_approved
HgeneGABRB3P28472DB00818PropofolPotentiatorSmall moleculeApproved|Investigational|Vet_approved
HgeneGABRB3P28472DB00592PiperazineAgonistSmall moleculeApproved|Vet_approved
HgeneGABRB3P28472DB00431LindaneSmall moleculeApproved|Withdrawn

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Related Diseases for GABRB3-DDX1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGABRB3C4310712EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 436CTD_human;UNIPROT
HgeneGABRB3C0011570Mental Depression5PSYGENET
HgeneGABRB3C0011581Depressive disorder5PSYGENET
HgeneGABRB3C0001973Alcoholic Intoxication, Chronic4PSYGENET
HgeneGABRB3C2677087EPILEPSY, CHILDHOOD ABSENCE, SUSCEPTIBILITY TO, 53GENOMICS_ENGLAND;UNIPROT
HgeneGABRB3C0004352Autistic Disorder2CTD_human
HgeneGABRB3C0005586Bipolar Disorder2PSYGENET
HgeneGABRB3C0014544Epilepsy2CTD_human
HgeneGABRB3C0036341Schizophrenia2PSYGENET
HgeneGABRB3C0086237Epilepsy, Cryptogenic2CTD_human
HgeneGABRB3C0236018Aura2CTD_human
HgeneGABRB3C0238111Lennox-Gastaut syndrome2ORPHANET
HgeneGABRB3C0751111Awakening Epilepsy2CTD_human
HgeneGABRB3C0001890Akinetic Petit Mal1CTD_human
HgeneGABRB3C0014553Absence Epilepsy1CTD_human
HgeneGABRB3C0021603Sleep Initiation and Maintenance Disorders1CTD_human
HgeneGABRB3C0033139Primary Insomnia1CTD_human
HgeneGABRB3C0162635Angelman Syndrome1CTD_human
HgeneGABRB3C0270541Rebound Insomnia1CTD_human
HgeneGABRB3C0349255Nonorganic Insomnia1CTD_human
HgeneGABRB3C0376634Craniofacial Abnormalities1CTD_human
HgeneGABRB3C0393759Transient Insomnia1CTD_human
HgeneGABRB3C0541798Early Awakening1CTD_human
HgeneGABRB3C0751124Epilepsy, Absence, Atypical1CTD_human
HgeneGABRB3C0751249Chronic Insomnia1CTD_human
HgeneGABRB3C0751250Psychophysiological Insomnia1CTD_human
HgeneGABRB3C0751251Secondary Insomnia1CTD_human
HgeneGABRB3C0751252Sleep Initiation Dysfunction1CTD_human
HgeneGABRB3C0917801Sleeplessness1CTD_human
HgeneGABRB3C1510586Autism Spectrum Disorders1CTD_human
HgeneGABRB3C1535926Neurodevelopmental Disorders1CTD_human
HgeneGABRB3C1838604EPILEPSY, CHILDHOOD ABSENCE, 11ORPHANET
HgeneGABRB3C3711376Isodicentric Chromosome 15 Syndrome1CTD_human
HgeneGABRB3C4281785Childhood Absence Epilepsy1CTD_human
HgeneGABRB3C4317339Juvenile Absence Epilepsy1CTD_human
HgeneGABRB3C4552765Epilepsy, Minor1CTD_human
HgeneGABRB3C4553705Absence Seizure Disorder1CTD_human
TgeneC0013146Drug abuse1CTD_human
TgeneC0013170Drug habituation1CTD_human
TgeneC0013222Drug Use Disorders1CTD_human
TgeneC0014173Endometrial Hyperplasia1CTD_human
TgeneC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgeneC0038580Substance Dependence1CTD_human
TgeneC0038586Substance Use Disorders1CTD_human
TgeneC0236969Substance-Related Disorders1CTD_human
TgeneC0349578Complex Endometrial Hyperplasia1CTD_human
TgeneC0349579Atypical Endometrial Hyperplasia1CTD_human
TgeneC0456483Simple Endometrial Hyperplasia1CTD_human
TgeneC0740858Substance abuse problem1CTD_human
TgeneC1510472Drug Dependence1CTD_human
TgeneC4316881Prescription Drug Abuse1CTD_human