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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:KCNQ2-GALR1 (FusionGDB2 ID:HG3785TG2587)

Fusion Gene Summary for KCNQ2-GALR1

check button Fusion gene summary
Fusion gene informationFusion gene name: KCNQ2-GALR1
Fusion gene ID: hg3785tg2587
HgeneTgene
Gene symbol

KCNQ2

GALR1

Gene ID

3785

2587

Gene namepotassium voltage-gated channel subfamily Q member 2galanin receptor 1
SynonymsBFNC|EBN|EBN1|ENB1|HNSPC|KCNA11|KV7.2GALNR|GALNR1
Cytomap('KCNQ2')('GALR1')

20q13.33

18q23

Type of geneprotein-codingprotein-coding
Descriptionpotassium voltage-gated channel subfamily KQT member 2neuroblastoma-specific potassium channel subunit alpha KvLQT2potassium channel, voltage gated KQT-like subfamily Q, member 2voltage-gated potassium channel subunit Kv7.2galanin receptor type 1GAL1-RGALR-1
Modification date2020031320200313
UniProtAcc

O43526

.
Ensembl transtripts involved in fusion geneENST00000344425, ENST00000344462, 
ENST00000354587, ENST00000357249, 
ENST00000359125, ENST00000359689, 
ENST00000360480, ENST00000370224, 
ENST00000482957, 
Fusion gene scores* DoF score2 X 2 X 1=41 X 1 X 1=1
# samples 21
** MAII scorelog2(2/4*10)=2.32192809488736log2(1/1*10)=3.32192809488736
Context

PubMed: KCNQ2 [Title/Abstract] AND GALR1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKCNQ2(62074948)-GALR1(74971575), # 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
HgeneKCNQ2

GO:0071805

potassium ion transmembrane transport

9836639|27564677

TgeneGALR1

GO:0045944

positive regulation of transcription by RNA polymerase II

24517231



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 KCNQ2-GALR1

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 KCNQ2-GALR1


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 KCNQ2-GALR1


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/:62074948/:74971575)
- 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
KCNQ2

O43526

.
FUNCTION: Associates with KCNQ3 to form a potassium channel with essentially identical properties to the channel underlying the native M-current, a slowly activating and deactivating potassium conductance which plays a critical role in determining the subthreshold electrical excitability of neurons as well as the responsiveness to synaptic inputs. Therefore, it is important in the regulation of neuronal excitability. KCNQ2/KCNQ3 current is blocked by linopirdine and XE991, and activated by the anticonvulsant retigabine (PubMed:9836639, PubMed:11572947, PubMed:14534157, PubMed:12742592, PubMed:17872363). As the native M-channel, the potassium channel composed of KCNQ2 and KCNQ3 is also suppressed by activation of the muscarinic acetylcholine receptor CHRM1 (PubMed:10684873). {ECO:0000269|PubMed:10684873, ECO:0000269|PubMed:11572947, ECO:0000269|PubMed:12742592, ECO:0000269|PubMed:14534157, ECO:0000269|PubMed:17872363, ECO:0000269|PubMed:25740509, ECO:0000269|PubMed:9836639}.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 KCNQ2-GALR1


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 KCNQ2-GALR1


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 KCNQ2-GALR1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneKCNQ2O43526DB00321AmitriptylineInhibitorSmall moleculeApproved
HgeneKCNQ2O43526DB04953EzogabineSmall moleculeApproved|Investigational
HgeneKCNQ2O43526DB00939Meclofenamic acidOtherSmall moleculeApproved|Vet_approved

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Related Diseases for KCNQ2-GALR1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKCNQ2C3149074SEIZURES, BENIGN FAMILIAL NEONATAL, 19CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneKCNQ2C3150986EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 79CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneKCNQ2C0220669Familial benign neonatal epilepsy4CTD_human;ORPHANET
HgeneKCNQ2C0008073Developmental Disabilities2CTD_human
HgeneKCNQ2C0014544Epilepsy2CTD_human
HgeneKCNQ2C0036341Schizophrenia2PSYGENET
HgeneKCNQ2C0085996Child Development Deviations2CTD_human
HgeneKCNQ2C0085997Child Development Disorders, Specific2CTD_human
HgeneKCNQ2C0086237Epilepsy, Cryptogenic2CTD_human
HgeneKCNQ2C0236018Aura2CTD_human
HgeneKCNQ2C0270851Benign neonatal epilepsy2CTD_human
HgeneKCNQ2C0393693Benign Neonatal Epilepsy, Nonfamilial2CTD_human
HgeneKCNQ2C0751111Awakening Epilepsy2CTD_human
HgeneKCNQ2C1843140SEIZURES, BENIGN FAMILIAL INFANTILE, 32CTD_human
HgeneKCNQ2C4551769Convulsions, Benign Familial Infantile, 12CTD_human
HgeneKCNQ2C0005586Bipolar Disorder1PSYGENET
HgeneKCNQ2C0006111Brain Diseases1CTD_human
HgeneKCNQ2C0022333Jacksonian Seizure1CTD_human
HgeneKCNQ2C0027765nervous system disorder1CTD_human
HgeneKCNQ2C0036572Seizures1CTD_human
HgeneKCNQ2C0085584Encephalopathies1CTD_human
HgeneKCNQ2C0149958Complex partial seizures1CTD_human
HgeneKCNQ2C0234533Generalized seizures1CTD_human
HgeneKCNQ2C0234535Clonic Seizures1CTD_human
HgeneKCNQ2C0270824Visual seizure1CTD_human
HgeneKCNQ2C0270844Tonic Seizures1CTD_human
HgeneKCNQ2C0270846Epileptic drop attack1CTD_human
HgeneKCNQ2C0422850Seizures, Somatosensory1CTD_human
HgeneKCNQ2C0422852Seizures, Auditory1CTD_human
HgeneKCNQ2C0422853Olfactory seizure1CTD_human
HgeneKCNQ2C0422854Gustatory seizure1CTD_human
HgeneKCNQ2C0422855Vertiginous seizure1CTD_human
HgeneKCNQ2C0494475Tonic - clonic seizures1CTD_human
HgeneKCNQ2C0751056Non-epileptic convulsion1CTD_human
HgeneKCNQ2C0751110Single Seizure1CTD_human
HgeneKCNQ2C0751123Atonic Absence Seizures1CTD_human
HgeneKCNQ2C0751494Convulsive Seizures1CTD_human
HgeneKCNQ2C0751495Seizures, Focal1CTD_human
HgeneKCNQ2C0751496Seizures, Sensory1CTD_human
HgeneKCNQ2C1535926Neurodevelopmental Disorders1CTD_human
HgeneKCNQ2C1839839MAJOR AFFECTIVE DISORDER 21PSYGENET
HgeneKCNQ2C3495874Nonepileptic Seizures1CTD_human
HgeneKCNQ2C4048158Convulsions1CTD_human
HgeneKCNQ2C4316903Absence Seizures1CTD_human
HgeneKCNQ2C4317109Epileptic Seizures1CTD_human
HgeneKCNQ2C4317123Myoclonic Seizures1CTD_human
HgeneKCNQ2C4505436Generalized Absence Seizures1CTD_human
TgeneC0011574Involutional Depression1CTD_human
TgeneC0600427Cocaine Dependence1PSYGENET
TgeneC1269683Major Depressive Disorder1CTD_human
TgeneC1571983Involutional paraphrenia1CTD_human
TgeneC1571984Psychosis, Involutional1CTD_human