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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:C21orf90-GABRA3 (FusionGDB2 ID:HG114043TG2556)

Fusion Gene Summary for C21orf90-GABRA3

check button Fusion gene summary
Fusion gene informationFusion gene name: C21orf90-GABRA3
Fusion gene ID: hg114043tg2556
HgeneTgene
Gene symbol

C21orf90

GABRA3

Gene ID

114043

2556

Gene nameTSPEAR antisense RNA 2gamma-aminobutyric acid type A receptor subunit alpha3
SynonymsC21orf90-
Cytomap('C21orf90')('GABRA3')

21q22.3

Xq28

Type of genencRNAprotein-coding
Description-gamma-aminobutyric acid receptor subunit alpha-3GABA(A) receptor subunit alpha-3GABA(A) receptor, alpha 3gamma-aminobutyric acid (GABA) A receptor, alpha 3gamma-aminobutyric acid type A receptor alpha3 subunitgamma-animobutyric acid (GABA) A receptor
Modification date2020031320200313
UniProtAcc.

P34903

Ensembl transtripts involved in fusion geneENST00000465978, ENST00000330490, 
ENST00000354333, 
Fusion gene scores* DoF score3 X 1 X 3=98 X 6 X 6=288
# samples 37
** MAII scorelog2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(7/288*10)=-2.04064198449735
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: C21orf90 [Title/Abstract] AND GABRA3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC21orf90(45937718)-GABRA3(151453207), # samples:2
Anticipated loss of major functional domain due to fusion event.C21orf90-GABRA3 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


check button Fusion gene information
* 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
ChimerDB4KIRCTCGA-CJ-5681-01AC21orf90chr21

45937718

-GABRA3chrX

151453207

-
ChimerDB4KIRCTCGA-CJ-5681-01AC21orf90chr21

45937718

+GABRA3chrX

151453207

-


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Fusion Gene ORF analysis for C21orf90-GABRA3

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
3UTR-3CDSENST00000465978ENST00000370314C21orf90chr21

45937718

+GABRA3chrX

151453207

-
3UTR-3CDSENST00000465978ENST00000535043C21orf90chr21

45937718

+GABRA3chrX

151453207

-
3UTR-intronENST00000465978ENST00000497894C21orf90chr21

45937718

+GABRA3chrX

151453207

-
5CDS-intronENST00000330490ENST00000497894C21orf90chr21

45937718

+GABRA3chrX

151453207

-
5CDS-intronENST00000354333ENST00000497894C21orf90chr21

45937718

+GABRA3chrX

151453207

-
Frame-shiftENST00000330490ENST00000370314C21orf90chr21

45937718

+GABRA3chrX

151453207

-
Frame-shiftENST00000330490ENST00000535043C21orf90chr21

45937718

+GABRA3chrX

151453207

-
Frame-shiftENST00000354333ENST00000370314C21orf90chr21

45937718

+GABRA3chrX

151453207

-
Frame-shiftENST00000354333ENST00000535043C21orf90chr21

45937718

+GABRA3chrX

151453207

-

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 C21orf90-GABRA3


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 C21orf90-GABRA3


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/:45937718/:151453207)
- 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
.GABRA3

P34903

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: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel.

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 C21orf90-GABRA3


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 C21orf90-GABRA3


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 C21orf90-GABRA3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneGABRA3P34903DB00395CarisoprodolModulatorSmall moleculeApproved
TgeneGABRA3P34903DB00425ZolpidemAgonistSmall moleculeApproved
TgeneGABRA3P34903DB00849MethylphenobarbitalPotentiatorSmall moleculeApproved
TgeneGABRA3P34903DB00898EthanolSmall moleculeApproved
TgeneGABRA3P34903DB01198ZopiclonePotentiatorSmall moleculeApproved
TgeneGABRA3P34903DB00241ButalbitalPotentiatorSmall moleculeApproved|Illicit
TgeneGABRA3P34903DB00306TalbutalPotentiatorSmall moleculeApproved|Illicit
TgeneGABRA3P34903DB00371MeprobamateAgonistSmall moleculeApproved|Illicit
TgeneGABRA3P34903DB01351AmobarbitalPotentiatorSmall moleculeApproved|Illicit
TgeneGABRA3P34903DB01353ButobarbitalPotentiatorSmall moleculeApproved|Illicit
TgeneGABRA3P34903DB00402EszopicloneAgonistSmall moleculeApproved|Investigational
TgeneGABRA3P34903DB00312PentobarbitalPotentiatorSmall moleculeApproved|Investigational|Vet_approved
TgeneGABRA3P34903DB00418SecobarbitalPotentiatorSmall moleculeApproved|Vet_approved
TgeneGABRA3P34903DB00599ThiopentalPotentiatorSmall moleculeApproved|Vet_approved
TgeneGABRA3P34903DB00794PrimidonePotentiatorSmall moleculeApproved|Vet_approved

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Related Diseases for C21orf90-GABRA3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0005586Bipolar Disorder5PSYGENET
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0011570Mental Depression1PSYGENET
TgeneC0011581Depressive disorder1PSYGENET
TgeneC0268446Thyrotoxic periodic paralysis1ORPHANET