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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:FNIP2-LRBA (FusionGDB2 ID:30969)

Fusion Gene Summary for FNIP2-LRBA

check button Fusion gene summary
Fusion gene informationFusion gene name: FNIP2-LRBA
Fusion gene ID: 30969
HgeneTgene
Gene symbol

FNIP2

LRBA

Gene ID

57600

987

Gene namefolliculin interacting protein 2LPS responsive beige-like anchor protein
SynonymsFNIPL|MAPO1BGL|CDC4L|CVID8|LAB300|LBA
Cytomap

4q32.1

4q31.3

Type of geneprotein-codingprotein-coding
Descriptionfolliculin-interacting protein 2FNIP1-like proteinO6-methylguanine-induced apoptosis 1 proteinlipopolysaccharide-responsive and beige-like anchor proteinCDC4-like proteinLPS-responsive vesicle trafficking, beach and anchor containingvesicle trafficking, beach and anchor containing
Modification date2020031320200320
UniProtAcc

Q9P278

P50851

Ensembl transtripts involved in fusion geneENST00000264433, ENST00000379346, 
ENST00000505445, 		ENST00000357115, 
ENST00000503716, ENST00000507224, 
ENST00000510413, ENST00000535741, 
Fusion gene scores* DoF score16 X 13 X 9=187225 X 25 X 10=6250
# samples 1827
** MAII scorelog2(18/1872*10)=-3.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(27/6250*10)=-4.53282487738598
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FNIP2 [Title/Abstract] AND LRBA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFNIP2(159690471)-LRBA(151242535), # samples:1
FNIP2(159690471)-LRBA(151242520), # samples:1
Anticipated loss of major functional domain due to fusion event.FNIP2-LRBA seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneFNIP2

GO:0000122

negative regulation of transcription by RNA polymerase II

21209915

HgeneFNIP2

GO:0001932

regulation of protein phosphorylation

18663353

HgeneFNIP2

GO:0006468

protein phosphorylation

18663353

HgeneFNIP2

GO:0031334

positive regulation of protein complex assembly

25126726

HgeneFNIP2

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19914239


check buttonFusion gene breakpoints across FNIP2 (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 LRBA (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-BH-A0H7-01AFNIP2chr4

159690471

-LRBAchr4

151242520

-
ChimerDB4BRCATCGA-BH-A0H7-01AFNIP2chr4

159690471

+LRBAchr4

151242535

-


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Fusion Gene ORF analysis for FNIP2-LRBA

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
5CDS-5UTRENST00000264433ENST00000357115FNIP2chr4

159690471

-LRBAchr4

151242520

-
5CDS-5UTRENST00000264433ENST00000503716FNIP2chr4

159690471

-LRBAchr4

151242520

-
5CDS-5UTRENST00000264433ENST00000503716FNIP2chr4

159690471

+LRBAchr4

151242535

-
5CDS-5UTRENST00000264433ENST00000507224FNIP2chr4

159690471

-LRBAchr4

151242520

-
5CDS-intronENST00000264433ENST00000357115FNIP2chr4

159690471

+LRBAchr4

151242535

-
5CDS-intronENST00000264433ENST00000507224FNIP2chr4

159690471

+LRBAchr4

151242535

-
5CDS-intronENST00000264433ENST00000510413FNIP2chr4

159690471

+LRBAchr4

151242535

-
5CDS-intronENST00000264433ENST00000535741FNIP2chr4

159690471

+LRBAchr4

151242535

-
Frame-shiftENST00000264433ENST00000510413FNIP2chr4

159690471

-LRBAchr4

151242520

-
Frame-shiftENST00000264433ENST00000535741FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-3CDSENST00000379346ENST00000510413FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-3CDSENST00000379346ENST00000535741FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-3CDSENST00000505445ENST00000510413FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-3CDSENST00000505445ENST00000535741FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-5UTRENST00000379346ENST00000357115FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-5UTRENST00000379346ENST00000503716FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-5UTRENST00000379346ENST00000503716FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-5UTRENST00000379346ENST00000507224FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-5UTRENST00000505445ENST00000357115FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-5UTRENST00000505445ENST00000503716FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-5UTRENST00000505445ENST00000503716FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-5UTRENST00000505445ENST00000507224FNIP2chr4

159690471

-LRBAchr4

151242520

-
intron-intronENST00000379346ENST00000357115FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-intronENST00000379346ENST00000507224FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-intronENST00000379346ENST00000510413FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-intronENST00000379346ENST00000535741FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-intronENST00000505445ENST00000357115FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-intronENST00000505445ENST00000507224FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-intronENST00000505445ENST00000510413FNIP2chr4

159690471

+LRBAchr4

151242535

-
intron-intronENST00000505445ENST00000535741FNIP2chr4

159690471

+LRBAchr4

151242535

-

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 FNIP2-LRBA


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 FNIP2-LRBA


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/:159690471/:151242535)
- 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
FNIP2

Q9P278

LRBA

P50851

FUNCTION: Binding partner of the GTPase-activating protein FLCN: involved in the cellular response to amino acid availability by regulating the mTORC1 signaling cascade controlling the MiT/TFE factors TFEB and TFE3 (PubMed:18663353, PubMed:31672913). In low-amino acid conditions, component of the lysosomal folliculin complex (LFC) on the membrane of lysosomes, which inhibits the GTPase-activating activity of FLCN, thereby inactivating mTORC1 and promoting nuclear translocation of TFEB and TFE3 (PubMed:31672913). Upon amino acid restimulation, disassembly of the LFC complex liberates the GTPase-activating activity of FLCN, leading to activation of mTORC1 and subsequent cytoplasmic retention of TFEB and TFE3 (PubMed:31672913). Together with FLCN, regulates autophagy: following phosphorylation by ULK1, interacts with GABARAP and promotes autophagy (PubMed:25126726). In addition to its role in mTORC1 signaling, also acts as a co-chaperone of HSP90AA1/Hsp90: inhibits the ATPase activity of HSP90AA1/Hsp90, leading to activate both kinase and non-kinase client proteins of HSP90AA1/Hsp90 (PubMed:18403135). Acts as a scaffold to load client protein FLCN onto HSP90AA1/Hsp90 (PubMed:18403135). Competes with the activating co-chaperone AHSA1 for binding to HSP90AA1, thereby providing a reciprocal regulatory mechanism for chaperoning of client proteins (PubMed:18403135). May play a role in the signal transduction pathway of apoptosis induced by O6-methylguanine-mispaired lesions (By similarity). {ECO:0000250|UniProtKB:Q80TD3, ECO:0000269|PubMed:18403135, ECO:0000269|PubMed:18663353, ECO:0000269|PubMed:25126726, ECO:0000269|PubMed:31672913}.FUNCTION: May be involved in coupling signal transduction and vesicle trafficking to enable polarized secretion and/or membrane deposition of immune effector molecules. {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 FNIP2-LRBA


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 FNIP2-LRBA


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 FNIP2-LRBA


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 FNIP2-LRBA


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