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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:RPTOR-GAA

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RPTOR-GAA
FusionPDB ID: 78226
FusionGDB2.0 ID: 78226
HgeneTgene
Gene symbol

RPTOR

GAA

Gene ID

57521

2548

Gene nameregulatory associated protein of MTOR complex 1glucosidase alpha, acid
SynonymsKOG1|Mip1LYAG
Cytomap

17q25.3

17q25.3

Type of geneprotein-codingprotein-coding
Descriptionregulatory-associated protein of mTORp150 target of rapamycin (TOR)-scaffold protein containing WD-repeatsraptorlysosomal alpha-glucosidaseacid maltaseaglucosidase alfa
Modification date2020031320200315
UniProtAcc.

P10253

Main function of 5'-partner protein: FUNCTION: Essential for the degradation of glycogen in lysosomes (PubMed:1856189, PubMed:7717400, PubMed:14695532, PubMed:18429042). Has highest activity on alpha-1,4-linked glycosidic linkages, but can also hydrolyze alpha-1,6-linked glucans (PubMed:29061980). {ECO:0000269|PubMed:14695532, ECO:0000269|PubMed:18429042, ECO:0000269|PubMed:1856189, ECO:0000269|PubMed:29061980, ECO:0000269|PubMed:7717400}.
Ensembl transtripts involved in fusion geneENST idsENST00000575542, ENST00000306801, 
ENST00000537330, ENST00000544334, 
ENST00000570891, 		ENST00000302262, 
ENST00000390015, ENST00000574376, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score26 X 20 X 11=57203 X 4 X 4=48
# samples 274
** MAII scorelog2(27/5720*10)=-4.40498383461492
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

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

Fusion neoantigen context

PubMed: RPTOR [Title/Abstract] AND GAA [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RPTOR(78811797)-GAA(78078353), # samples:1
RPTOR(78519591)-GAA(78079548), # samples:1
Anticipated loss of major functional domain due to fusion event.RPTOR-GAA 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.
RPTOR-GAA 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.
* 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

TgeneGAA

GO:0005980

glycogen catabolic process

9505277|29061980



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/chr17:78811797/chr17:78078353)
- 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 buttonRetention analysis results 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, are available here.

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.
all structure

check buttonFusion gene breakpoints across GAA (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 Amino Acid Sequences


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)
ENST00000570891RPTORchr1778519591-ENST00000390015GAAchr1778079548+37749156993227842
ENST00000306801RPTORchr1778519591-ENST00000390015GAAchr1778079548+33835243082836842
ENST00000544334RPTORchr1778519591-ENST00000390015GAAchr1778079548+31833241082636842

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
ENST00000570891ENST00000390015RPTORchr1778519591-GAAchr1778079548+0.0030423880.99695766
ENST00000306801ENST00000390015RPTORchr1778519591-GAAchr1778079548+0.0027108980.9972892
ENST00000544334ENST00000390015RPTORchr1778519591-GAAchr1778079548+0.0027782820.9972217

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for RPTOR-GAA

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RPTORchr1778519591GAAchr177807954832472SKSLAQSWRMKDRIKDPANRRYEVPL
RPTORchr1778519591GAAchr177807954852472SKSLAQSWRMKDRIKDPANRRYEVPL
RPTORchr1778519591GAAchr177807954891572SKSLAQSWRMKDRIKDPANRRYEVPL

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Potential FusionNeoAntigen Information of RPTOR-GAA in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
RPTOR-GAA_78519591_78079548.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
RPTOR-GAAchr1778519591chr1778079548524HLA-A30:08RIKDPANRR0.99560.80771221
RPTOR-GAAchr1778519591chr1778079548524HLA-A74:03RIKDPANRR0.99420.74391221
RPTOR-GAAchr1778519591chr1778079548524HLA-A74:11RIKDPANRR0.99420.74391221
RPTOR-GAAchr1778519591chr1778079548524HLA-A74:09RIKDPANRR0.99420.74391221
RPTOR-GAAchr1778519591chr1778079548524HLA-A03:12RIKDPANRR0.97760.52661221
RPTOR-GAAchr1778519591chr1778079548524HLA-A03:25RIKDPANRR0.97690.50371221
RPTOR-GAAchr1778519591chr1778079548524HLA-A31:06RIKDPANRR0.96670.6821221
RPTOR-GAAchr1778519591chr1778079548524HLA-A31:02RIKDPANRR0.9290.76591221
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:01RIKDPANRRY0.99980.96271222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:25RIKDPANRRY0.99730.96541222
RPTOR-GAAchr1778519591chr1778079548524HLA-A33:01DRIKDPANRR0.79550.59021121
RPTOR-GAAchr1778519591chr1778079548524HLA-A33:05DRIKDPANRR0.79550.59021121
RPTOR-GAAchr1778519591chr1778079548524HLA-A68:03DRIKDPANRR0.43710.53371121
RPTOR-GAAchr1778519591chr1778079548524HLA-A31:02KDRIKDPANRR0.99460.76821021
RPTOR-GAAchr1778519591chr1778079548524HLA-A31:06KDRIKDPANRR0.96620.68331021
RPTOR-GAAchr1778519591chr1778079548524HLA-A31:01RIKDPANR0.99540.50511220
RPTOR-GAAchr1778519591chr1778079548524HLA-A31:01RIKDPANRR0.99460.71161221
RPTOR-GAAchr1778519591chr1778079548524HLA-A03:01RIKDPANRR0.97690.50371221
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:07RIKDPANRRY0.99930.82661222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:04RIKDPANRRY0.98760.97841222
RPTOR-GAAchr1778519591chr1778079548524HLA-A31:01KDRIKDPANRR0.99170.75891021
RPTOR-GAAchr1778519591chr1778079548524HLA-A30:01RIKDPANRR0.9960.88791221
RPTOR-GAAchr1778519591chr1778079548524HLA-A74:01RIKDPANRR0.99420.74391221
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:27RIKDPANRRY0.99980.96181222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:33RIKDPANRRY0.99980.96271222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:125RIKDPANRRY0.99980.96271222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:135RIKDPANRRY0.99980.96421222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:34RIKDPANRRY0.99980.96271222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:50RIKDPANRRY0.99970.9321222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:24RIKDPANRRY0.99950.97341222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:35RIKDPANRRY0.99940.96531222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:12RIKDPANRRY0.99920.92821222
RPTOR-GAAchr1778519591chr1778079548524HLA-B15:39RIKDPANRRY0.99710.93771222
RPTOR-GAAchr1778519591chr1778079548524HLA-A30:01RIKDPANRRY0.97580.85791222

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Potential FusionNeoAntigen Information of RPTOR-GAA in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
RPTOR-GAA_78519591_78079548.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
RPTOR-GAAchr1778519591chr1778079548524DRB1-0801AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0803AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0803LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0805AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0805LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0814AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0814LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0816AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0818AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0818LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0823AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0823LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0826AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0827AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0827LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0829AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0829LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0833AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0833LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0835AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0835LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0836AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0836LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0837AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0837LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0837SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-0837QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-0838AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0838LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-0839AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0840AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-0840LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1111AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1111LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1111QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1111SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1114AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1114LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1119AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1120AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1120LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1131AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1132AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1145AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1145LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1164AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1164LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1168AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1168LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1169AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1169LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1172AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1173AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1186AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1302AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1302LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1303AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1303LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-13101AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-13101LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-13101SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-13101QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1310AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1310LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1310SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1310QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1312AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1312LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1313AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1313LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1313SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1313QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1316AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1321AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1321LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1321SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1321QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1323AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1323LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1329AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1329LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1330AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1330LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1330SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1330QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1333AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1334AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1334LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1336AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1336LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1338AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1338LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1338SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1338QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1338KSLAQSWRMKDRIKD116
RPTOR-GAAchr1778519591chr1778079548524DRB1-1339AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1339LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1349AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1349LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1349SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1355AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1355LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1355SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1355QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1363AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1363LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1363QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1363SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1365AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1365LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1365SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1365QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1365KSLAQSWRMKDRIKD116
RPTOR-GAAchr1778519591chr1778079548524DRB1-1366AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1366LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1366SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1366QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1373AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1373LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1374AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1374LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1382AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1388AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1388LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1390AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1390LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1395AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1395LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1397AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1397LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1399AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1399LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1422AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1422LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1425AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1425LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1453AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1453LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1463AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1463LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1463SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1463QSWRMKDRIKDPANR520
RPTOR-GAAchr1778519591chr1778079548524DRB1-1485AQSWRMKDRIKDPAN419
RPTOR-GAAchr1778519591chr1778079548524DRB1-1485LAQSWRMKDRIKDPA318
RPTOR-GAAchr1778519591chr1778079548524DRB1-1485SLAQSWRMKDRIKDP217
RPTOR-GAAchr1778519591chr1778079548524DRB1-1485QSWRMKDRIKDPANR520

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Fusion breakpoint peptide structures of RPTOR-GAA

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
9188SWRMKDRIKDPANRRPTORGAAchr1778519591chr1778079548524

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RPTOR-GAA

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN9188SWRMKDRIKDPANR-5.97758-6.09098
HLA-B14:023BVN9188SWRMKDRIKDPANR-5.15013-6.18543
HLA-B52:013W399188SWRMKDRIKDPANR-6.29935-6.41275
HLA-B52:013W399188SWRMKDRIKDPANR-6.07479-7.11009
HLA-A24:025HGA9188SWRMKDRIKDPANR-7.25246-8.28776
HLA-A24:025HGA9188SWRMKDRIKDPANR-6.23064-6.34404
HLA-B44:053DX89188SWRMKDRIKDPANR-4.66421-5.69951
HLA-B44:053DX89188SWRMKDRIKDPANR-4.52141-4.63481
HLA-A02:016TDR9188SWRMKDRIKDPANR-7.72945-7.84285

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Vaccine Design for the FusionNeoAntigens of RPTOR-GAA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
RPTOR-GAAchr1778519591chr17780795481021KDRIKDPANRRAAGGATCGGATCAAAGATCCAGCTAACAGGCGC
RPTOR-GAAchr1778519591chr17780795481121DRIKDPANRRGATCGGATCAAAGATCCAGCTAACAGGCGC
RPTOR-GAAchr1778519591chr17780795481220RIKDPANRCGGATCAAAGATCCAGCTAACAGG
RPTOR-GAAchr1778519591chr17780795481221RIKDPANRRCGGATCAAAGATCCAGCTAACAGGCGC
RPTOR-GAAchr1778519591chr17780795481222RIKDPANRRYCGGATCAAAGATCCAGCTAACAGGCGCTAC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
RPTOR-GAAchr1778519591chr1778079548116KSLAQSWRMKDRIKDAAATCCTTAGCTCAGAGCTGGAGGATGAAGGATCGGATCAAAGAT
RPTOR-GAAchr1778519591chr1778079548217SLAQSWRMKDRIKDPTCCTTAGCTCAGAGCTGGAGGATGAAGGATCGGATCAAAGATCCA
RPTOR-GAAchr1778519591chr1778079548318LAQSWRMKDRIKDPATTAGCTCAGAGCTGGAGGATGAAGGATCGGATCAAAGATCCAGCT
RPTOR-GAAchr1778519591chr1778079548419AQSWRMKDRIKDPANGCTCAGAGCTGGAGGATGAAGGATCGGATCAAAGATCCAGCTAAC
RPTOR-GAAchr1778519591chr1778079548520QSWRMKDRIKDPANRCAGAGCTGGAGGATGAAGGATCGGATCAAAGATCCAGCTAACAGG

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Information of the samples that have these potential fusion neoantigens of RPTOR-GAA

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample
PRADRPTOR-GAAchr1778519591ENST00000306801chr1778079548ENST00000390015TCGA-EJ-A46G-01A

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Potential target of CAR-T therapy development for RPTOR-GAA

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to RPTOR-GAA

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 RPTOR-GAA

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