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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:GABRA4-KNOP1 (FusionGDB2 ID:HG2557TG400506)

Fusion Gene Summary for GABRA4-KNOP1

check button Fusion gene summary
Fusion gene informationFusion gene name: GABRA4-KNOP1
Fusion gene ID: hg2557tg400506
HgeneTgene
Gene symbol

GABRA4

KNOP1

Gene ID

2557

400506

Gene namegamma-aminobutyric acid type A receptor subunit alpha4lysine rich nucleolar protein 1
Synonyms-101F10.1|C16orf88|FAM191A|TSG118
Cytomap('GABRA4')('KNOP1')

4p12

16p12.3

Type of geneprotein-codingprotein-coding
Descriptiongamma-aminobutyric acid receptor subunit alpha-4GABA(A) receptor, alpha 4gamma-aminobutyric acid (GABA) A receptor, alpha 4gamma-aminobutyric acid A receptor alpha 4gamma-aminobutyric acid type A receptor alpha4 subunitlysine-rich nucleolar protein 1family with sequence similarity 191, member Aprotein C16orf88testis-specific gene 118 protein
Modification date2020031320200313
UniProtAcc

P48169

.
Ensembl transtripts involved in fusion geneENST00000264318, ENST00000509316, 
Fusion gene scores* DoF score1 X 1 X 1=13 X 3 X 2=18
# samples 13
** MAII scorelog2(1/1*10)=3.32192809488736log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: GABRA4 [Title/Abstract] AND KNOP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGABRA4(46963885)-KNOP1(19725485), # 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


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


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Fusion Gene ORF analysis for GABRA4-KNOP1

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

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 GABRA4-KNOP1


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 GABRA4-KNOP1


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/:46963885/:19725485)
- 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
GABRA4

P48169

.
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.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 GABRA4-KNOP1


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 GABRA4-KNOP1


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 GABRA4-KNOP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneGABRA4P48169DB00849MethylphenobarbitalPotentiatorSmall moleculeApproved
HgeneGABRA4P48169DB00898EthanolSmall moleculeApproved
HgeneGABRA4P48169DB00241ButalbitalPotentiatorSmall moleculeApproved|Illicit
HgeneGABRA4P48169DB00306TalbutalPotentiatorSmall moleculeApproved|Illicit
HgeneGABRA4P48169DB00371MeprobamateAgonistSmall moleculeApproved|Illicit
HgeneGABRA4P48169DB01351AmobarbitalPotentiatorSmall moleculeApproved|Illicit
HgeneGABRA4P48169DB01353ButobarbitalPotentiatorSmall moleculeApproved|Illicit
HgeneGABRA4P48169DB00312PentobarbitalPotentiatorSmall moleculeApproved|Investigational|Vet_approved
HgeneGABRA4P48169DB00418SecobarbitalPotentiatorSmall moleculeApproved|Vet_approved
HgeneGABRA4P48169DB00599ThiopentalPotentiatorSmall moleculeApproved|Vet_approved
HgeneGABRA4P48169DB00794PrimidonePotentiatorSmall moleculeApproved|Vet_approved

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Related Diseases for GABRA4-KNOP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGABRA4C0004352Autistic Disorder2CTD_human
HgeneGABRA4C0004134Ataxia1CTD_human
HgeneGABRA4C0036341Schizophrenia1PSYGENET
HgeneGABRA4C0240991Ataxia, Sensory1CTD_human
HgeneGABRA4C0270496Schizoaffective disorder, bipolar type1PSYGENET
HgeneGABRA4C0278161Ataxia, Motor1CTD_human
HgeneGABRA4C0427190Ataxia, Truncal1CTD_human
HgeneGABRA4C0520966Abnormal coordination1CTD_human
HgeneGABRA4C0750937Ataxia, Appendicular1CTD_human
HgeneGABRA4C0750940Tremor, Rubral1CTD_human