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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:RPTOR-GAA

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RPTOR-GAA
	FusionPDB ID: 78226
	FusionGDB2.0 ID: 78226
		Hgene	Tgene
	Gene symbol	RPTOR	GAA
	Gene ID	57521	2548
	Gene name	regulatory associated protein of MTOR complex 1	glucosidase alpha, acid
	Synonyms	KOG1\|Mip1	LYAG
	Cytomap	17q25.3	17q25.3
	Type of gene	protein-coding	protein-coding
	Description	regulatory-associated protein of mTORp150 target of rapamycin (TOR)-scaffold protein containing WD-repeatsraptor	lysosomal alpha-glucosidaseacid maltaseaglucosidase alfa
	Modification date	20200313	20200315
	UniProtAcc	.	P10253
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000575542, ENST00000306801, ENST00000537330, ENST00000544334, ENST00000570891,	ENST00000302262, ENST00000390015, ENST00000574376,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	26 X 20 X 11=5720	3 X 4 X 4=48
	# samples	27	4
	** MAII score	log2(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
Context (manual curation of fusion genes in FusionPDB)	PubMed: RPTOR [Title/Abstract] AND GAA [Title/Abstract] AND fusion [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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	RPTOR	GO:0031929	TOR signaling	20381137
Hgene	RPTOR	GO:0032008	positive regulation of TOR signaling	12150926\|18439900
Hgene	RPTOR	GO:0071233	cellular response to leucine	22424946
Hgene	RPTOR	GO:0071902	positive regulation of protein serine/threonine kinase activity	12150926
Tgene	GAA	GO:0005980	glycogen catabolic process	9505277\|29061980

Fusion 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.

Fusion 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.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	OV	TCGA-09-1659	RPTOR	chr17	78811797	+	GAA	chr17	78078353	+
ChimerDB4	PRAD	TCGA-EJ-A46G-01A	RPTOR	chr17	78519591	-	GAA	chr17	78079548	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000570891	RPTOR	chr17	78519591	-	ENST00000390015	GAA	chr17	78079548	+	3774	915	699	3227	842
ENST00000306801	RPTOR	chr17	78519591	-	ENST00000390015	GAA	chr17	78079548	+	3383	524	308	2836	842
ENST00000544334	RPTOR	chr17	78519591	-	ENST00000390015	GAA	chr17	78079548	+	3183	324	108	2636	842

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000570891	ENST00000390015	RPTOR	chr17	78519591	-	GAA	chr17	78079548	+	0.003042388	0.99695766
ENST00000306801	ENST00000390015	RPTOR	chr17	78519591	-	GAA	chr17	78079548	+	0.002710898	0.9972892
ENST00000544334	ENST00000390015	RPTOR	chr17	78519591	-	GAA	chr17	78079548	+	0.002778282	0.9972217

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Fusion Amino Acid Sequences

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

>78226_78226_1_RPTOR-GAA_RPTOR_chr17_78519591_ENST00000306801_GAA_chr17_78079548_ENST00000390015_length(amino acids)=842AA_BP=72
MEVLERLLPRTPPPPPPLMESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLAQSWRMKDRIKDPANRRYEVPLETPHV
HSRAPSPLYSVEFSEEPFGVIVRRQLDGRVLLNTTVAPLFFADQFLQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGAN
LYGSHPFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYIFLGPEPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSS
TAITRQVVENMTRAHFPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMIVDPAISSSGPAGSYRPYDEGLRRGVFITN
ETGQPLIGKVWPGSTAFPDFTNPTALAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENPPYVPGVVGGTLQAATICAS
SHQFLSTHYNLHNLYGLTEAIASHRALVKARGTRPFVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPLVGADVCGFL
GNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPAQQAMRKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTV
DHQLLWGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPVEALGSLPPPPAAPREPAIHSEGQWVTLPAPLDTINVHLRAGYIIPLQGPG
LTTTESRQQPMALAVALTKGGEARGELFWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQKVTVLGVATAPQQVLSNG

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

>78226_78226_2_RPTOR-GAA_RPTOR_chr17_78519591_ENST00000544334_GAA_chr17_78079548_ENST00000390015_length(amino acids)=842AA_BP=72
MEVLERLLPRTPPPPPPLMESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLAQSWRMKDRIKDPANRRYEVPLETPHV
HSRAPSPLYSVEFSEEPFGVIVRRQLDGRVLLNTTVAPLFFADQFLQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGAN
LYGSHPFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYIFLGPEPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSS
TAITRQVVENMTRAHFPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMIVDPAISSSGPAGSYRPYDEGLRRGVFITN
ETGQPLIGKVWPGSTAFPDFTNPTALAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENPPYVPGVVGGTLQAATICAS
SHQFLSTHYNLHNLYGLTEAIASHRALVKARGTRPFVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPLVGADVCGFL
GNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPAQQAMRKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTV
DHQLLWGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPVEALGSLPPPPAAPREPAIHSEGQWVTLPAPLDTINVHLRAGYIIPLQGPG
LTTTESRQQPMALAVALTKGGEARGELFWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQKVTVLGVATAPQQVLSNG

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

>78226_78226_3_RPTOR-GAA_RPTOR_chr17_78519591_ENST00000570891_GAA_chr17_78079548_ENST00000390015_length(amino acids)=842AA_BP=72
MEVLERLLPRTPPPPPPLMESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLAQSWRMKDRIKDPANRRYEVPLETPHV
HSRAPSPLYSVEFSEEPFGVIVRRQLDGRVLLNTTVAPLFFADQFLQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGAN
LYGSHPFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYIFLGPEPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSS
TAITRQVVENMTRAHFPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMIVDPAISSSGPAGSYRPYDEGLRRGVFITN
ETGQPLIGKVWPGSTAFPDFTNPTALAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENPPYVPGVVGGTLQAATICAS
SHQFLSTHYNLHNLYGLTEAIASHRALVKARGTRPFVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPLVGADVCGFL
GNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPAQQAMRKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTV
DHQLLWGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPVEALGSLPPPPAAPREPAIHSEGQWVTLPAPLDTINVHLRAGYIIPLQGPG
LTTTESRQQPMALAVALTKGGEARGELFWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQKVTVLGVATAPQQVLSNG

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

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Fusion Protein Functional Features

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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	GAA P10253
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.	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}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000306801

881_887

54.0

1336.0

Compositional bias

Note=Poly-Ser

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000570891

881_887

54.0

380.0

Compositional bias

Note=Poly-Ser

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000306801

1020_1061

54.0

1336.0

Repeat

Note=WD 1

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000306801

1065_1106

54.0

1336.0

Repeat

Note=WD 2

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000306801

1121_1160

54.0

1336.0

Repeat

Note=WD 3

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000306801

1164_1203

54.0

1336.0

Repeat

Note=WD 4

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000306801

1209_1249

54.0

1336.0

Repeat

Note=WD 5

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000306801

1251_1291

54.0

1336.0

Repeat

Note=WD 6

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000306801

1299_1335

54.0

1336.0

Repeat

Note=WD 7

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000570891

1020_1061

54.0

380.0

Repeat

Note=WD 1

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000570891

1065_1106

54.0

380.0

Repeat

Note=WD 2

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000570891

1121_1160

54.0

380.0

Repeat

Note=WD 3

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000570891

1164_1203

54.0

380.0

Repeat

Note=WD 4

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000570891

1209_1249

54.0

380.0

Repeat

Note=WD 5

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000570891

1251_1291

54.0

380.0

Repeat

Note=WD 6

Hgene

RPTOR

chr17:78519591

chr17:78079548

ENST00000570891

1299_1335

54.0

380.0

Repeat

Note=WD 7

Tgene

GAA

chr17:78519591

chr17:78079548

ENST00000302262

80_131

182.0

953.0

Domain

P-type

Tgene

GAA

chr17:78519591

chr17:78079548

ENST00000390015

80_131

182.0

953.0

Domain

P-type

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
RPTOR
GAA

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to RPTOR-GAA

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to RPTOR-GAA

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

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source