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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:GABRA5-SCN9A (FusionGDB2 ID:HG2558TG6335)

Fusion Gene Summary for GABRA5-SCN9A

check button Fusion gene summary
Fusion gene informationFusion gene name: GABRA5-SCN9A
Fusion gene ID: hg2558tg6335
HgeneTgene
Gene symbol

GABRA5

SCN9A

Gene ID

2558

6335

Gene namegamma-aminobutyric acid type A receptor subunit alpha5sodium voltage-gated channel alpha subunit 9
SynonymsEIEE79ETHA|FEB3B|GEFSP7|HSAN2D|NE-NA|NENA|Nav1.7|PN1|SFNP
Cytomap('GABRA5')('SCN9A')

15q12

2q24.3

Type of geneprotein-codingprotein-coding
Descriptiongamma-aminobutyric acid receptor subunit alpha-5GABA(A) receptor subunit alpha-5gamma-aminobutyric acid (GABA) A receptor, alpha 5gamma-aminobutyric acid type A receptor alpha5 subunitsodium channel protein type 9 subunit alphahNE-Naneuroendocrine sodium channelperipheral sodium channel 1sodium channel protein type IX subunit alphasodium channel, voltage-gated, type IX, alpha polypeptidesodium channel, voltage-gated, type IX, alp
Modification date2020031320200313
UniProtAcc

P31644

.
Ensembl transtripts involved in fusion geneENST00000335625, ENST00000355395, 
ENST00000400081, ENST00000557449, 
Fusion gene scores* DoF score2 X 3 X 2=125 X 4 X 4=80
# samples 25
** MAII scorelog2(2/12*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GABRA5 [Title/Abstract] AND SCN9A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGABRA5(27143092)-SCN9A(167221967), # 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
TgeneSCN9A

GO:0035725

sodium ion transmembrane transport

17145499



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 GABRA5-SCN9A

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 GABRA5-SCN9A


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 GABRA5-SCN9A


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/:27143092/:167221967)
- 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
GABRA5

P31644

.
FUNCTION: Ligand-gated chloride channel subunit which is a component of the heteropentameric receptor for GABA, the major inhibitory neurotransmitter in the brain (PubMed:29961870, PubMed:31056671). May be involved in GABA-A receptor assembly, and GABA-A receptor immobilization and accumulation by gephyrin at the synapse (PubMed:31056671). {ECO:0000269|PubMed:29961870, ECO:0000269|PubMed:31056671}.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 GABRA5-SCN9A


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 GABRA5-SCN9A


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 GABRA5-SCN9A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneGABRA5P31644DB00395CarisoprodolModulatorSmall moleculeApproved
HgeneGABRA5P31644DB00849MethylphenobarbitalPotentiatorSmall moleculeApproved
HgeneGABRA5P31644DB00898EthanolSmall moleculeApproved
HgeneGABRA5P31644DB01198ZopiclonePotentiatorSmall moleculeApproved
HgeneGABRA5P31644DB01205FlumazenilAntagonistSmall moleculeApproved
HgeneGABRA5P31644DB00241ButalbitalPotentiatorSmall moleculeApproved|Illicit
HgeneGABRA5P31644DB00306TalbutalPotentiatorSmall moleculeApproved|Illicit
HgeneGABRA5P31644DB00371MeprobamateAgonistSmall moleculeApproved|Illicit
HgeneGABRA5P31644DB01351AmobarbitalPotentiatorSmall moleculeApproved|Illicit
HgeneGABRA5P31644DB01353ButobarbitalPotentiatorSmall moleculeApproved|Illicit
HgeneGABRA5P31644DB00402EszopicloneAgonistSmall moleculeApproved|Investigational
HgeneGABRA5P31644DB00312PentobarbitalPotentiatorSmall moleculeApproved|Investigational|Vet_approved
HgeneGABRA5P31644DB00418SecobarbitalPotentiatorSmall moleculeApproved|Vet_approved
HgeneGABRA5P31644DB00599ThiopentalPotentiatorSmall moleculeApproved|Vet_approved
HgeneGABRA5P31644DB00794PrimidonePotentiatorSmall moleculeApproved|Vet_approved

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Related Diseases for GABRA5-SCN9A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGABRA5C0005586Bipolar Disorder5PSYGENET
HgeneGABRA5C0001973Alcoholic Intoxication, Chronic1PSYGENET
HgeneGABRA5C0004352Autistic Disorder1CTD_human
HgeneGABRA5C0022333Jacksonian Seizure1CTD_human
HgeneGABRA5C0025261Memory Disorders1CTD_human
HgeneGABRA5C0036341Schizophrenia1PSYGENET
HgeneGABRA5C0036572Seizures1CTD_human
HgeneGABRA5C0149958Complex partial seizures1CTD_human
HgeneGABRA5C0150080Social Communication Disorder1CTD_human
HgeneGABRA5C0233794Memory impairment1CTD_human
HgeneGABRA5C0234533Generalized seizures1CTD_human
HgeneGABRA5C0234535Clonic Seizures1CTD_human
HgeneGABRA5C0270824Visual seizure1CTD_human
HgeneGABRA5C0270844Tonic Seizures1CTD_human
HgeneGABRA5C0270846Epileptic drop attack1CTD_human
HgeneGABRA5C0422850Seizures, Somatosensory1CTD_human
HgeneGABRA5C0422852Seizures, Auditory1CTD_human
HgeneGABRA5C0422853Olfactory seizure1CTD_human
HgeneGABRA5C0422854Gustatory seizure1CTD_human
HgeneGABRA5C0422855Vertiginous seizure1CTD_human
HgeneGABRA5C0424605Developmental delay (disorder)1GENOMICS_ENGLAND
HgeneGABRA5C0494475Tonic - clonic seizures1CTD_human
HgeneGABRA5C0525045Mood Disorders1PSYGENET
HgeneGABRA5C0557874Global developmental delay1GENOMICS_ENGLAND
HgeneGABRA5C0751056Non-epileptic convulsion1CTD_human
HgeneGABRA5C0751110Single Seizure1CTD_human
HgeneGABRA5C0751123Atonic Absence Seizures1CTD_human
HgeneGABRA5C0751292Age-Related Memory Disorders1CTD_human
HgeneGABRA5C0751293Memory Disorder, Semantic1CTD_human
HgeneGABRA5C0751294Memory Disorder, Spatial1CTD_human
HgeneGABRA5C0751295Memory Loss1CTD_human
HgeneGABRA5C0751494Convulsive Seizures1CTD_human
HgeneGABRA5C0751495Seizures, Focal1CTD_human
HgeneGABRA5C0751496Seizures, Sensory1CTD_human
HgeneGABRA5C1510586Autism Spectrum Disorders1CTD_human
HgeneGABRA5C3495874Nonepileptic Seizures1CTD_human
HgeneGABRA5C3711376Isodicentric Chromosome 15 Syndrome1CTD_human
HgeneGABRA5C4048158Convulsions1CTD_human
HgeneGABRA5C4316903Absence Seizures1CTD_human
HgeneGABRA5C4317109Epileptic Seizures1CTD_human
HgeneGABRA5C4317123Myoclonic Seizures1CTD_human
HgeneGABRA5C4505436Generalized Absence Seizures1CTD_human
TgeneC0014805Primary Erythermalgia15CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0014544Epilepsy6CLINGEN
TgeneC1833661PAROXYSMAL EXTREME PAIN DISORDER5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0751122Infantile Severe Myoclonic Epilepsy4CTD_human;ORPHANET
TgeneC1855739Indifference to Pain, Congenital, Autosomal Recessive4CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0014804Erythromelalgia3CTD_human
TgeneC2751778Generalized Epilepsy With Febrile Seizures Plus, 73CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0002768Congenital Pain Insensitivity2GENOMICS_ENGLAND;ORPHANET
TgeneC0019372Herpesviridae Infections1CTD_human
TgeneC0020072Hereditary Sensory Autonomic Neuropathy, Type 21ORPHANET
TgeneC0020075Hereditary Sensory Autonomic Neuropathy, Type 51ORPHANET
TgeneC0027796Neuralgia1CTD_human
TgeneC0032768Postherpetic neuralgia1CTD_human
TgeneC0033774Pruritus1CTD_human
TgeneC0037140B Virus Infection1CTD_human
TgeneC0038870Neuralgia, Supraorbital1CTD_human
TgeneC0042656Neuralgia, Vidian1CTD_human
TgeneC0150055Chronic pain1CTD_human
TgeneC0234247Neuralgia, Atypical1CTD_human
TgeneC0234249Neuralgia, Stump1CTD_human
TgeneC0270914Hereditary Motor and Sensory-Neuropathy Type II1ORPHANET
TgeneC0423711Neuralgia, Perineal1CTD_human
TgeneC0423712Neuralgia, Iliohypogastric Nerve1CTD_human
TgeneC0432262Dysosteosclerosis1GENOMICS_ENGLAND
TgeneC0598589Inherited neuropathies1GENOMICS_ENGLAND
TgeneC0699739Sensory Neuropathy, Hereditary1GENOMICS_ENGLAND
TgeneC0751371Neuralgia, Ilioinguinal1CTD_human
TgeneC0751372Nerve Pain1CTD_human
TgeneC0751373Paroxysmal Nerve Pain1CTD_human
TgeneC3178789Widespread Chronic Pain1CTD_human
TgeneC4551549Early Infantile Epileptic Encephalopathy 61GENOMICS_ENGLAND