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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:IL4I1-KCNQ2 (FusionGDB2 ID:39379)

Fusion Gene Summary for IL4I1-KCNQ2

check button Fusion gene summary
Fusion gene informationFusion gene name: IL4I1-KCNQ2
Fusion gene ID: 39379
HgeneTgene
Gene symbol

IL4I1

KCNQ2

Gene ID

259307

3785

Gene nameinterleukin 4 induced 1potassium voltage-gated channel subfamily Q member 2
SynonymsFIG1|LAAO|LAOBFNC|EBN|EBN1|ENB1|HNSPC|KCNA11|KV7.2
Cytomap

19q13.33

20q13.33

Type of geneprotein-codingprotein-coding
DescriptionL-amino-acid oxidaseFig-1 proteinIL4-induced protein 1interleukin four induced 1potassium 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 Kv7.2
Modification date2020031320200313
UniProtAcc

Q96RQ9

O43526

Ensembl transtripts involved in fusion geneENST00000391826, ENST00000595948, 
ENST00000341114, 		ENST00000359125, 
ENST00000357249, ENST00000359689, 
ENST00000354587, ENST00000360480, 
ENST00000370224, ENST00000344462, 
ENST00000482957, ENST00000344425, 
Fusion gene scores* DoF score14 X 9 X 10=12603 X 3 X 2=18
# samples 163
** MAII scorelog2(16/1260*10)=-2.97727992349992
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: IL4I1 [Title/Abstract] AND KCNQ2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointIL4I1(50430951)-KCNQ2(62076717), # samples:3
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
TgeneKCNQ2

GO:0071805

potassium ion transmembrane transport

9836639|27564677


check buttonFusion gene breakpoints across IL4I1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across KCNQ2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BRCATCGA-A2-A3XW-01AIL4I1chr19

50430951

-KCNQ2chr20

62076717

-
ChimerDB4BRCATCGA-A2-A3XW-01AIL4I1chr19

50430951

-KCNQ2chr20

62076717

-
ChimerDB4BRCATCGA-A2-A3XW-01AIL4I1chr19

50430951

-KCNQ2chr20

62076717

-


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Fusion Gene ORF analysis for IL4I1-KCNQ2

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-3CDSENST00000391826ENST00000359125IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
intron-3CDSENST00000391826ENST00000357249IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
intron-3CDSENST00000391826ENST00000359689IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
intron-3CDSENST00000391826ENST00000354587IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
intron-3CDSENST00000391826ENST00000360480IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
intron-3CDSENST00000391826ENST00000370224IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
intron-3CDSENST00000391826ENST00000344462IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
intron-intronENST00000391826ENST00000482957IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
intron-intronENST00000391826ENST00000344425IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000595948ENST00000359125IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000595948ENST00000357249IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000595948ENST00000359689IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000595948ENST00000354587IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000595948ENST00000360480IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000595948ENST00000370224IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000595948ENST00000344462IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-intronENST00000595948ENST00000482957IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-intronENST00000595948ENST00000344425IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000341114ENST00000359125IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000341114ENST00000357249IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000341114ENST00000359689IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000341114ENST00000354587IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000341114ENST00000360480IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000341114ENST00000370224IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-3CDSENST00000341114ENST00000344462IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-intronENST00000341114ENST00000482957IL4I1chr19

50430951

-KCNQ2chr20

62076717

-
5UTR-intronENST00000341114ENST00000344425IL4I1chr19

50430951

-KCNQ2chr20

62076717

-

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 IL4I1-KCNQ2


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for IL4I1-KCNQ2


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
IL4I1

Q96RQ9

KCNQ2

O43526

FUNCTION: Secreted L-amino-acid oxidase that acts as a key immunoregulator (PubMed:17356132, PubMed:32818467, PubMed:32866000). Has preference for L-aromatic amino acids: converts phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp) to phenylpyruvic acid (PP), hydroxyphenylpyruvic acid (HPP), and indole-3-pyruvic acid (I3P), respectively (PubMed:17356132, PubMed:32818467, PubMed:32866000). Also has weak L-arginine oxidase activity (PubMed:26673964). Acts as a negative regulator of anti-tumor immunity by mediating Trp degradation via an indole pyruvate pathway that activates the transcription factor AHR (PubMed:32818467, PubMed:32866000). IL4I1-mediated Trp catabolism generates I3P, giving rise to indole metabolites (indole-3-acetic acid (IAA) and indole-3-aldehyde (I3A)) and kynurenic acid, which act as ligands for AHR, a ligand-activated transcription factor that plays important roles in immunity and cancer (PubMed:32818467, PubMed:32866000). AHR activation by indoles following IL4I1-mediated Trp degradation enhances tumor progression by promoting cancer cell motility and suppressing adaptive immunity (PubMed:32818467). Also has an immunoregulatory function in some immune cells, probably by mediating Trp degradation and promoting downstream AHR activation: inhibits T-cell activation and proliferation, promotes the differentiation of naive CD4(+) T-cells into FOXP3(+) regulatory T-cells (Treg) and regulates the development and function of B-cells (PubMed:17356132, PubMed:25446972, PubMed:25778793, PubMed:28891065). Also regulates M2 macrophage polarization by inhibiting T-cell activation (By similarity). Also has antibacterial properties by inhibiting growth of Gram negative and Gram positive bacteria through the production of NH4(+) and H2O2 (PubMed:23355881). {ECO:0000250|UniProtKB:O09046, ECO:0000269|PubMed:17356132, ECO:0000269|PubMed:23355881, ECO:0000269|PubMed:25446972, ECO:0000269|PubMed:25778793, ECO:0000269|PubMed:26673964, ECO:0000269|PubMed:28891065, ECO:0000269|PubMed:32818467, ECO:0000269|PubMed:32866000}.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}.

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 IL4I1-KCNQ2


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 IL4I1-KCNQ2


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 IL4I1-KCNQ2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneIL4I1Q96RQ9DB03147Flavin adenine dinucleotideSmall moleculeApproved
HgeneIL4I1Q96RQ9DB03147Flavin adenine dinucleotideSmall moleculeApproved
HgeneIL4I1Q96RQ9DB03147Flavin adenine dinucleotideSmall moleculeApproved
HgeneIL4I1Q96RQ9DB04272Citric acidSmall moleculeApproved|Nutraceutical|Vet_approved
HgeneIL4I1Q96RQ9DB04272Citric acidSmall moleculeApproved|Nutraceutical|Vet_approved
HgeneIL4I1Q96RQ9DB04272Citric acidSmall moleculeApproved|Nutraceutical|Vet_approved
TgeneKCNQ2O43526DB00321AmitriptylineInhibitorSmall moleculeApproved
TgeneKCNQ2O43526DB04953EzogabineSmall moleculeApproved|Investigational
TgeneKCNQ2O43526DB00939Meclofenamic acidOtherSmall moleculeApproved|Vet_approved

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Related Diseases for IL4I1-KCNQ2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneKCNQ2C3149074SEIZURES, BENIGN FAMILIAL NEONATAL, 19CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneKCNQ2C3150986EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 79CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneKCNQ2C0220669Familial benign neonatal epilepsy4CTD_human;ORPHANET
TgeneKCNQ2C0008073Developmental Disabilities2CTD_human
TgeneKCNQ2C0014544Epilepsy2CTD_human
TgeneKCNQ2C0036341Schizophrenia2PSYGENET
TgeneKCNQ2C0085996Child Development Deviations2CTD_human
TgeneKCNQ2C0085997Child Development Disorders, Specific2CTD_human
TgeneKCNQ2C0086237Epilepsy, Cryptogenic2CTD_human
TgeneKCNQ2C0236018Aura2CTD_human
TgeneKCNQ2C0270851Benign neonatal epilepsy2CTD_human
TgeneKCNQ2C0393693Benign Neonatal Epilepsy, Nonfamilial2CTD_human
TgeneKCNQ2C0751111Awakening Epilepsy2CTD_human
TgeneKCNQ2C1843140SEIZURES, BENIGN FAMILIAL INFANTILE, 32CTD_human
TgeneKCNQ2C4551769Convulsions, Benign Familial Infantile, 12CTD_human
TgeneKCNQ2C0005586Bipolar Disorder1PSYGENET
TgeneKCNQ2C0006111Brain Diseases1CTD_human
TgeneKCNQ2C0022333Jacksonian Seizure1CTD_human
TgeneKCNQ2C0027765nervous system disorder1CTD_human
TgeneKCNQ2C0036572Seizures1CTD_human
TgeneKCNQ2C0085584Encephalopathies1CTD_human
TgeneKCNQ2C0149958Complex partial seizures1CTD_human
TgeneKCNQ2C0234533Generalized seizures1CTD_human
TgeneKCNQ2C0234535Clonic Seizures1CTD_human
TgeneKCNQ2C0270824Visual seizure1CTD_human
TgeneKCNQ2C0270844Tonic Seizures1CTD_human
TgeneKCNQ2C0270846Epileptic drop attack1CTD_human
TgeneKCNQ2C0422850Seizures, Somatosensory1CTD_human
TgeneKCNQ2C0422852Seizures, Auditory1CTD_human
TgeneKCNQ2C0422853Olfactory seizure1CTD_human
TgeneKCNQ2C0422854Gustatory seizure1CTD_human
TgeneKCNQ2C0422855Vertiginous seizure1CTD_human
TgeneKCNQ2C0494475Tonic - clonic seizures1CTD_human
TgeneKCNQ2C0751056Non-epileptic convulsion1CTD_human
TgeneKCNQ2C0751110Single Seizure1CTD_human
TgeneKCNQ2C0751123Atonic Absence Seizures1CTD_human
TgeneKCNQ2C0751494Convulsive Seizures1CTD_human
TgeneKCNQ2C0751495Seizures, Focal1CTD_human
TgeneKCNQ2C0751496Seizures, Sensory1CTD_human
TgeneKCNQ2C1535926Neurodevelopmental Disorders1CTD_human
TgeneKCNQ2C1839839MAJOR AFFECTIVE DISORDER 21PSYGENET
TgeneKCNQ2C3495874Nonepileptic Seizures1CTD_human
TgeneKCNQ2C4048158Convulsions1CTD_human
TgeneKCNQ2C4316903Absence Seizures1CTD_human
TgeneKCNQ2C4317109Epileptic Seizures1CTD_human
TgeneKCNQ2C4317123Myoclonic Seizures1CTD_human
TgeneKCNQ2C4505436Generalized Absence Seizures1CTD_human