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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:FOXN3-KCNQ1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FOXN3-KCNQ1
FusionPDB ID: 31143
FusionGDB2.0 ID: 31143
HgeneTgene
Gene symbol

FOXN3

KCNQ1

Gene ID

1112

3784

Gene nameforkhead box N3potassium voltage-gated channel subfamily Q member 1
SynonymsC14orf116|CHES1|PRO1635ATFB1|ATFB3|JLNS1|KCNA8|KCNA9|KVLQT1|Kv1.9|Kv7.1|LQT|LQT1|RWS|SQT2|WRS
Cytomap

14q31.3-q32.11

11p15.5-p15.4

Type of geneprotein-codingprotein-coding
Descriptionforkhead box protein N3checkpoint suppressor 1potassium voltage-gated channel subfamily KQT member 1IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1kidney and cardiac voltage dependend K+ channelpotassium channel, voltage gated KQT-like subfamily Q, member 1potassium voltag
Modification date2020031320200313
UniProtAcc

O00409

P51787

Ensembl transtripts involved in fusion geneENST idsENST00000261302, ENST00000345097, 
ENST00000555353, ENST00000557258, 
ENST00000555658, 
ENST00000526095, 
ENST00000155840, ENST00000335475, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score21 X 18 X 8=302410 X 10 X 5=500
# samples 2212
** MAII scorelog2(22/3024*10)=-3.78088271069641
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/500*10)=-2.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: FOXN3 [Title/Abstract] AND KCNQ1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FOXN3(89747294)-KCNQ1(2790074), # samples:2
Anticipated loss of major functional domain due to fusion event.FOXN3-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
FOXN3-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
FOXN3-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
FOXN3-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
FOXN3-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
FOXN3-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
FOXN3-KCNQ1 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
HgeneFOXN3

GO:0045892

negative regulation of transcription, DNA-templated

16102918

TgeneKCNQ1

GO:0035690

cellular response to drug

9108097

TgeneKCNQ1

GO:0060306

regulation of membrane repolarization

11299204

TgeneKCNQ1

GO:0071320

cellular response to cAMP

11299204|16002409

TgeneKCNQ1

GO:0071805

potassium ion transmembrane transport

9354802|11299204|16002409

TgeneKCNQ1

GO:0086011

membrane repolarization during action potential

8900283|11299204|19646991

TgeneKCNQ1

GO:0097623

potassium ion export across plasma membrane

8900283|10400998|17289006

TgeneKCNQ1

GO:1901381

positive regulation of potassium ion transmembrane transport

8900283


check buttonFusion gene breakpoints across FOXN3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across KCNQ1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4PRADTCGA-V1-A8MG-01AFOXN3chr14

89747294

-KCNQ1chr11

2790074

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000345097FOXN3chr1489747294-ENST00000155840KCNQ1chr112790074+24858621171124335
ENST00000345097FOXN3chr1489747294-ENST00000335475KCNQ1chr112790074+16148621171124335
ENST00000555353FOXN3chr1489747294-ENST00000155840KCNQ1chr112790074+25048811361143335
ENST00000555353FOXN3chr1489747294-ENST00000335475KCNQ1chr112790074+16338811361143335

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
ENST00000345097ENST00000155840FOXN3chr1489747294-KCNQ1chr112790074+0.275261580.7247384
ENST00000345097ENST00000335475FOXN3chr1489747294-KCNQ1chr112790074+0.23137710.76862293
ENST00000555353ENST00000155840FOXN3chr1489747294-KCNQ1chr112790074+0.27225260.72774744
ENST00000555353ENST00000335475FOXN3chr1489747294-KCNQ1chr112790074+0.213026580.7869734

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>31143_31143_1_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000345097_KCNQ1_chr11_2790074_ENST00000155840_length(amino acids)=335AA_BP=248
MGPVMPPSKKPESSGISVSSGLSQCYGGSGFSKALQEDDDLDFSLPDIRLEEGAMEDEELTNLNWLHESKNLLKSFGESVLRSVSPVQDL
DDDTPPSPAHSDMPYDARQNPNCKPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPTGWKNSVRHNLSLNKCFKKVDKERS
QSIGKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKRNGALLQGCGNTIGPPLRSFDACSTLWPR

--------------------------------------------------------------

>31143_31143_2_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000345097_KCNQ1_chr11_2790074_ENST00000335475_length(amino acids)=335AA_BP=248
MGPVMPPSKKPESSGISVSSGLSQCYGGSGFSKALQEDDDLDFSLPDIRLEEGAMEDEELTNLNWLHESKNLLKSFGESVLRSVSPVQDL
DDDTPPSPAHSDMPYDARQNPNCKPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPTGWKNSVRHNLSLNKCFKKVDKERS
QSIGKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKRNGALLQGCGNTIGPPLRSFDACSTLWPR

--------------------------------------------------------------

>31143_31143_3_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000555353_KCNQ1_chr11_2790074_ENST00000155840_length(amino acids)=335AA_BP=248
MGPVMPPSKKPESSGISVSSGLSQCYGGSGFSKALQEDDDLDFSLPDIRLEEGAMEDEELTNLNWLHESKNLLKSFGESVLRSVSPVQDL
DDDTPPSPAHSDMPYDARQNPNCKPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPTGWKNSVRHNLSLNKCFKKVDKERS
QSIGKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKRNGALLQGCGNTIGPPLRSFDACSTLWPR

--------------------------------------------------------------

>31143_31143_4_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000555353_KCNQ1_chr11_2790074_ENST00000335475_length(amino acids)=335AA_BP=248
MGPVMPPSKKPESSGISVSSGLSQCYGGSGFSKALQEDDDLDFSLPDIRLEEGAMEDEELTNLNWLHESKNLLKSFGESVLRSVSPVQDL
DDDTPPSPAHSDMPYDARQNPNCKPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPTGWKNSVRHNLSLNKCFKKVDKERS
QSIGKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKRNGALLQGCGNTIGPPLRSFDACSTLWPR

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr14:89747294/chr11:2790074)
- 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
FOXN3

O00409

KCNQ1

P51787

FUNCTION: Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints). {ECO:0000269|PubMed:16102918}.FUNCTION: Potassium channel that plays an important role in a number of tissues, including heart, inner ear, stomach and colon (PubMed:10646604, PubMed:25441029). Associates with KCNE beta subunits that modulates current kinetics (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505, PubMed:19687231). Induces a voltage-dependent current by rapidly activating and slowly deactivating potassium-selective outward current (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505, PubMed:25441029). Promotes also a delayed voltage activated potassium current showing outward rectification characteristic (By similarity). During beta-adrenergic receptor stimulation participates in cardiac repolarization by associating with KCNE1 to form the I(Ks) cardiac potassium current that increases the amplitude and slows down the activation kinetics of outward potassium current I(Ks) (By similarity) (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505). Muscarinic agonist oxotremorine-M strongly suppresses KCNQ1/KCNE1 current (PubMed:10713961). When associated with KCNE3, forms the potassium channel that is important for cyclic AMP-stimulated intestinal secretion of chloride ions (PubMed:10646604). This interaction with KCNE3 is reduced by 17beta-estradiol, resulting in the reduction of currents (By similarity). During conditions of increased substrate load, maintains the driving force for proximal tubular and intestinal sodium ions absorption, gastric acid secretion, and cAMP-induced jejunal chloride ions secretion (By similarity). Allows the provision of potassium ions to the luminal membrane of the secretory canaliculus in the resting state as well as during stimulated acid secretion (By similarity). When associated with KCNE2, forms a heterooligomer complex leading to currents with an apparently instantaneous activation, a rapid deactivation process and a linear current-voltage relationship and decreases the amplitude of the outward current (PubMed:11101505). When associated with KCNE4, inhibits voltage-gated potassium channel activity (PubMed:19687231). When associated with KCNE5, this complex only conducts current upon strong and continued depolarization (PubMed:12324418). Also forms a heterotetramer with KCNQ5; has a voltage-gated potassium channel activity (PubMed:24855057). Binds with phosphatidylinositol 4,5-bisphosphate (PubMed:25037568). {ECO:0000250|UniProtKB:P97414, ECO:0000250|UniProtKB:Q9Z0N7, ECO:0000269|PubMed:10646604, ECO:0000269|PubMed:10713961, ECO:0000269|PubMed:11101505, ECO:0000269|PubMed:12324418, ECO:0000269|PubMed:19687231, ECO:0000269|PubMed:24855057, ECO:0000269|PubMed:25037568, ECO:0000269|PubMed:8900283, ECO:0000269|PubMed:9108097, ECO:0000269|PubMed:9312006}.; FUNCTION: [Isoform 2]: Non-functional alone but modulatory when coexpressed with the full-length isoform 1. {ECO:0000269|PubMed:9305853}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneFOXN3chr14:89747294chr11:2790074ENST00000261302-36113_204248.33333333333334491.0DNA bindingFork-head
HgeneFOXN3chr14:89747294chr11:2790074ENST00000345097-47113_204248.33333333333334491.0DNA bindingFork-head
HgeneFOXN3chr14:89747294chr11:2790074ENST00000555353-46113_204248.33333333333334469.0DNA bindingFork-head
HgeneFOXN3chr14:89747294chr11:2790074ENST00000557258-46113_204248.33333333333334469.0DNA bindingFork-head
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016585_621504.6666666666667677.0Coiled coilOntology_term=ECO:0000269
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016585_621377.6666666666667550.0Coiled coilOntology_term=ECO:0000269
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016589_620504.6666666666667677.0RegionC-terminal assembly domain
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016589_620377.6666666666667550.0RegionC-terminal assembly domain

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016300_320504.6666666666667677.0IntramembranePore-forming%3B Name%3DSegment H5
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016300_320377.6666666666667550.0IntramembranePore-forming%3B Name%3DSegment H5
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016312_317504.6666666666667677.0MotifSelectivity filter
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016312_317377.6666666666667550.0MotifSelectivity filter
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016143_147504.6666666666667677.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016169_196504.6666666666667677.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST0000015584010161_121504.6666666666667677.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016218_225504.6666666666667677.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016249_261504.6666666666667677.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016283_299504.6666666666667677.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016321_327504.6666666666667677.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016349_676504.6666666666667677.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016143_147377.6666666666667550.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016169_196377.6666666666667550.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST0000033547510161_121377.6666666666667550.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016218_225377.6666666666667550.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016249_261377.6666666666667550.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016283_299377.6666666666667550.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016321_327377.6666666666667550.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016349_676377.6666666666667550.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016122_142504.6666666666667677.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016148_168504.6666666666667677.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016197_217504.6666666666667677.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016226_248504.6666666666667677.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016262_282504.6666666666667677.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016328_348504.6666666666667677.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016122_142377.6666666666667550.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016148_168377.6666666666667550.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016197_217377.6666666666667550.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016226_248377.6666666666667550.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016262_282377.6666666666667550.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016328_348377.6666666666667550.0TransmembraneHelical%3B Name%3DSegment S6


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
FOXN3
KCNQ1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016370_382504.6666666666667677.0CALM
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016370_382377.6666666666667550.0CALM


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Related Drugs to FOXN3-KCNQ1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to FOXN3-KCNQ1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource