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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:IFT46-FXYD3 (FusionGDB2 ID:38422)

Fusion Gene Summary for IFT46-FXYD3

check button Fusion gene summary
Fusion gene informationFusion gene name: IFT46-FXYD3
Fusion gene ID: 38422
HgeneTgene
Gene symbol

IFT46

FXYD3

Gene ID

56912

5349

Gene nameintraflagellar transport 46FXYD domain containing ion transport regulator 3
SynonymsC11orf2|C11orf60|CFAP32MAT8|PLML
Cytomap

11q23.3

19q13.12

Type of geneprotein-codingprotein-coding
Descriptionintraflagellar transport protein 46 homologUPF0360cilia and flagella associated protein 32intraflagellar transport 46 homologintraflagellar transport protein IFT46FXYD domain-containing ion transport regulator 3chloride conductance inducer protein Mat-8mammary tumor 8 kDa proteinphospholemman-like proteinsodium/potassium-transporting ATPase subunit FXYD3
Modification date2020031320200313
UniProtAcc

Q9NQC8

Q14802

Ensembl transtripts involved in fusion geneENST00000264020, ENST00000264021, 
ENST00000527868, ENST00000530872, 
ENST00000344013, ENST00000346446, 
ENST00000435734, ENST00000604404, 
ENST00000406242, ENST00000406988, 
ENST00000454903, ENST00000535103, 
ENST00000603181, ENST00000603449, 
ENST00000603524, ENST00000604255, 
ENST00000604621, ENST00000604804, 
ENST00000605550, ENST00000605552, 
ENST00000605677, 
Fusion gene scores* DoF score9 X 4 X 2=729 X 10 X 8=720
# samples 911
** MAII scorelog2(9/72*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(11/720*10)=-2.71049338280502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: IFT46 [Title/Abstract] AND FXYD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointIFT46(118419107)-FXYD3(35614558), # 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 buttonFusion gene breakpoints across IFT46 (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 FXYD3 (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
ChiTaRS5.0N/ABG231278IFT46chr11

118419107

+FXYD3chr19

35614558

-


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Fusion Gene ORF analysis for IFT46-FXYD3

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-3UTRENST00000264020ENST00000344013IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000264020ENST00000346446IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000264020ENST00000435734IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000264020ENST00000604404IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000264021ENST00000344013IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000264021ENST00000346446IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000264021ENST00000435734IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000264021ENST00000604404IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000527868ENST00000344013IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000527868ENST00000346446IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000527868ENST00000435734IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000527868ENST00000604404IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000530872ENST00000344013IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000530872ENST00000346446IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000530872ENST00000435734IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-3UTRENST00000530872ENST00000604404IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000406242IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000406988IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000454903IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000535103IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000603181IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000603449IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000603524IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000604255IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000604621IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000604804IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000605550IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000605552IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264020ENST00000605677IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000406242IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000406988IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000454903IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000535103IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000603181IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000603449IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000603524IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000604255IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000604621IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000604804IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000605550IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000605552IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000264021ENST00000605677IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000406242IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000406988IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000454903IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000535103IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000603181IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000603449IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000603524IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000604255IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000604621IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000604804IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000605550IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000605552IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000527868ENST00000605677IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000406242IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000406988IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000454903IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000535103IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000603181IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000603449IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000603524IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000604255IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000604621IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000604804IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000605550IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000605552IFT46chr11

118419107

+FXYD3chr19

35614558

-
intron-intronENST00000530872ENST00000605677IFT46chr11

118419107

+FXYD3chr19

35614558

-

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 IFT46-FXYD3


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 IFT46-FXYD3


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/:118419107/:35614558)
- 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
IFT46

Q9NQC8

FXYD3

Q14802

FUNCTION: Forms part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia. May play a role in chondrocyte maturation and skeletogenesis (By similarity). {ECO:0000250}.FUNCTION: Associates with and regulates the activity of the sodium/potassium-transporting ATPase (NKA) which transports Na(+) out of the cell and K(+) into the cell (PubMed:17077088). Reduces glutathionylation of the NKA beta-1 subunit ATP1B1, thus reversing glutathionylation-mediated inhibition of ATP1B1 (PubMed:21454534). Induces a hyperpolarization-activated chloride current when expressed in Xenopus oocytes (PubMed:7836447). {ECO:0000269|PubMed:17077088, ECO:0000269|PubMed:21454534, ECO:0000269|PubMed:7836447}.; FUNCTION: [Isoform 1]: Decreases the apparent K+ and Na+ affinity of the sodium/potassium-transporting ATPase over a large range of membrane potentials. {ECO:0000269|PubMed:17077088}.; FUNCTION: [Isoform 2]: Decreases the apparent K+ affinity of the sodium/potassium-transporting ATPase only at slightly negative and positive membrane potentials and increases the apparent Na+ affinity over a large range of membrane potentials. {ECO:0000269|PubMed:17077088}.

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 IFT46-FXYD3


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 IFT46-FXYD3


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 IFT46-FXYD3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for IFT46-FXYD3


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