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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:RPTOR-CLN3 (FusionGDB2 ID:78222)

Fusion Gene Summary for RPTOR-CLN3

check button Fusion gene summary
Fusion gene informationFusion gene name: RPTOR-CLN3
Fusion gene ID: 78222
HgeneTgene
Gene symbol

RPTOR

CLN3

Gene ID

57521

1201

Gene nameregulatory associated protein of MTOR complex 1CLN3 lysosomal/endosomal transmembrane protein, battenin
SynonymsKOG1|Mip1BTN1|BTS|JNCL
Cytomap

17q25.3

16p12.1

Type of geneprotein-codingprotein-coding
Descriptionregulatory-associated protein of mTORp150 target of rapamycin (TOR)-scaffold protein containing WD-repeatsraptorbatteninCLN3, batteninbatten disease proteinceroid-lipofuscinosis, neuronal 3
Modification date2020031320200328
UniProtAcc.

Q13286

Ensembl transtripts involved in fusion geneENST00000306801, ENST00000537330, 
ENST00000544334, ENST00000570891, 
ENST00000575542, 		ENST00000333496, 
ENST00000354630, ENST00000355477, 
ENST00000357076, ENST00000357806, 
ENST00000357857, ENST00000359984, 
ENST00000360019, ENST00000395653, 
ENST00000535392, ENST00000565316, 
ENST00000567160, ENST00000567963, 
ENST00000568224, ENST00000569430, 
Fusion gene scores* DoF score26 X 20 X 11=57208 X 8 X 3=192
# samples 278
** MAII scorelog2(27/5720*10)=-4.40498383461492
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/192*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPTOR [Title/Abstract] AND CLN3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPTOR(78841581)-CLN3(28481290), # samples:2
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
HgeneRPTOR

GO:0031929

TOR signaling

20381137

HgeneRPTOR

GO:0032008

positive regulation of TOR signaling

12150926|18439900

HgeneRPTOR

GO:0071233

cellular response to leucine

22424946

HgeneRPTOR

GO:0071902

positive regulation of protein serine/threonine kinase activity

12150926

TgeneCLN3

GO:0015809

arginine transport

16251196

TgeneCLN3

GO:0035752

lysosomal lumen pH elevation

10924275

TgeneCLN3

GO:0042987

amyloid precursor protein catabolic process

10924275


check buttonFusion gene breakpoints across RPTOR (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 CLN3 (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/AAI732864RPTORchr17

78841581

+CLN3chr16

28481290

+
ChiTaRS5.0N/ADL060415RPTORchr17

78841581

+CLN3chr16

28481290

+


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Fusion Gene ORF analysis for RPTOR-CLN3

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-intronENST00000306801ENST00000333496RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000354630RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000355477RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000357076RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000357806RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000357857RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000359984RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000360019RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000395653RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000535392RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000565316RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000567160RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000567963RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000568224RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000306801ENST00000569430RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000333496RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000354630RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000355477RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000357076RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000357806RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000357857RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000359984RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000360019RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000395653RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000535392RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000565316RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000567160RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000567963RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000568224RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000537330ENST00000569430RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000333496RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000354630RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000355477RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000357076RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000357806RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000357857RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000359984RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000360019RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000395653RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000535392RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000565316RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000567160RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000567963RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000568224RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000544334ENST00000569430RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000333496RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000354630RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000355477RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000357076RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000357806RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000357857RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000359984RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000360019RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000395653RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000535392RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000565316RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000567160RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000567963RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000568224RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000570891ENST00000569430RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000333496RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000354630RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000355477RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000357076RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000357806RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000357857RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000359984RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000360019RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000395653RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000535392RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000565316RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000567160RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000567963RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000568224RPTORchr17

78841581

+CLN3chr16

28481290

+
intron-intronENST00000575542ENST00000569430RPTORchr17

78841581

+CLN3chr16

28481290

+

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 RPTOR-CLN3


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 RPTOR-CLN3


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/:78841581/:28481290)
- 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
.CLN3

Q13286

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}.FUNCTION: Mediates microtubule-dependent, anterograde transport connecting the Golgi network, endosomes, autophagosomes, lysosomes and plasma membrane, and participates in several cellular processes such as regulation of lysosomal pH, lysosome protein degradation, receptor-mediated endocytosis, autophagy, transport of proteins and lipids from the TGN, apoptosis and synaptic transmission (PubMed:10924275, PubMed:18817525, PubMed:18317235, PubMed:22261744, PubMed:15471887, PubMed:20850431). Facilitates the proteins transport from trans-Golgi network (TGN)-to other membrane compartments such as transport of microdomain-associated proteins to the plasma membrane, IGF2R transport to the lysosome where it regulates the CTSD release leading to regulation of CTSD maturation and thereby APP intracellular processing (PubMed:10924275, PubMed:18817525). Moreover regulates CTSD activity in response to osmotic stress (PubMed:23840424, PubMed:28390177). Also binds galactosylceramide and transports it from the trans Golgi to the rafts, which may have immediate and downstream effects on cell survival by modulating ceramide synthesis (PubMed:18317235). At the plasma membrane, regulates actin-dependent events including filopodia formation, cell migration, and pinocytosis through ARF1-CDC42 pathway and also the cytoskeleton organization through interaction with MYH10 and fodrin leading to the regulation of the plasma membrane association of Na+, K+ ATPase complex (PubMed:20850431). Regulates synaptic transmission in the amygdala, hippocampus, and cerebellum through regulation of synaptic vesicles density and their proximity to active zones leading to modulation of short-term plasticity and age-dependent anxious behavior, learning and memory (By similarity). Regulates autophagic vacuoles (AVs) maturation by modulating the trafficking between endocytic and autophagolysosomal/lysosomal compartments, which involves vesicle fusion leading to regulation of degradation process (By similarity). Participates also in cellular homeostasis of compounds such as, water, ions, amino acids, proteins and lipids in several tissue namely in brain and kidney through regulation of their transport and synthesis (PubMed:17482562). {ECO:0000250|UniProtKB:Q61124, ECO:0000269|PubMed:10924275, ECO:0000269|PubMed:15471887, ECO:0000269|PubMed:17482562, ECO:0000269|PubMed:18317235, ECO:0000269|PubMed:18817525, ECO:0000269|PubMed:20850431, ECO:0000269|PubMed:22261744, ECO:0000269|PubMed:23840424, ECO:0000269|PubMed:28390177}.

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 RPTOR-CLN3


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 RPTOR-CLN3


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 RPTOR-CLN3


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 RPTOR-CLN3


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