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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:TGFBRAP1-DPP10

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TGFBRAP1-DPP10
	FusionPDB ID: 90489
	FusionGDB2.0 ID: 90489
		Hgene	Tgene
	Gene symbol	TGFBRAP1	DPP10
	Gene ID	9392	57628
	Gene name	transforming growth factor beta receptor associated protein 1	dipeptidyl peptidase like 10
	Synonyms	TRAP-1\|TRAP1\|VPS3	DPL2\|DPPY\|DPRP-3\|DPRP3
	Cytomap	2q12.1-q12.2	2q14.1
	Type of gene	protein-coding	protein-coding
	Description	transforming growth factor-beta receptor-associated protein 1TGF-beta receptor-associated protein 1VPS3 CORVET complex subunit	inactive dipeptidyl peptidase 10DPP Xdipeptidyl peptidase 10dipeptidyl peptidase IV-related protein 3dipeptidyl peptidase Xdipeptidyl peptidase-like protein 2dipeptidyl-peptidase 10 (inactive)dipeptidyl-peptidase 10 (non-functional)
	Modification date	20200313	20200313
	UniProtAcc	.	Q8N608
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000258449, ENST00000393359,	ENST00000310323, ENST00000393147, ENST00000409163, ENST00000410059, ENST00000488208,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 6 X 5=240	12 X 13 X 3=468
	# samples	10	13
	** MAII score	log2(10/240*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/468*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: TGFBRAP1 [Title/Abstract] AND DPP10 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TGFBRAP1(105912813)-DPP10(115464694), # samples:2 TGFBRAP1(105912813)-DPP10(116066815), # samples:2
Anticipated loss of major functional domain due to fusion event.	TGFBRAP1-DPP10 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. TGFBRAP1-DPP10 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. TGFBRAP1-DPP10 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. TGFBRAP1-DPP10 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	TGFBRAP1	GO:0006355	regulation of transcription, DNA-templated	11278302
Hgene	TGFBRAP1	GO:0007165	signal transduction	11278302
Tgene	DPP10	GO:1903078	positive regulation of protein localization to plasma membrane	15671030

Fusion gene breakpoints across TGFBRAP1 (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 DPP10 (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	SARC	TCGA-DX-A8BU-01A	TGFBRAP1	chr2	105912813	-	DPP10	chr2	115464694	+
ChimerDB4	SARC	TCGA-DX-A8BU-01A	TGFBRAP1	chr2	105912813	-	DPP10	chr2	116066815	+
ChimerDB4	SARC	TCGA-DX-AB2J-01A	TGFBRAP1	chr2	105912813	-	DPP10	chr2	115464694	+
ChimerDB4	SARC	TCGA-DX-AB2J-01A	TGFBRAP1	chr2	105912813	-	DPP10	chr2	116066815	+

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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)

ENST00000393359

TGFBRAP1

chr2

105912813

ENST00000410059

DPP10

chr2

116066815

7203

1465

283

3795

1170

ENST00000258449

TGFBRAP1

chr2

105912813

ENST00000410059

DPP10

chr2

116066815

6796

1058

3388

1122

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
ENST00000393359	ENST00000410059	TGFBRAP1	chr2	105912813	-	DPP10	chr2	116066815	+	0.000289695	0.99971026
ENST00000258449	ENST00000410059	TGFBRAP1	chr2	105912813	-	DPP10	chr2	116066815	+	0.000177403	0.9998227

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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

>90489_90489_1_TGFBRAP1-DPP10_TGFBRAP1_chr2_105912813_ENST00000258449_DPP10_chr2_116066815_ENST00000410059_length(amino acids)=1122AA_BP=346
MMSIKAFTLVSAVERELLMGDKERVNIECVECCGRDLYVGTNDCFVYHFLLEERPVPAGPATFTATKQLQRHLGFKKPVNELRAASALNR
LLVLCDNSISLVNMLNLEPVPSGARIKGAATFALNENPVSGDPFCVEVCIISVKRRTIQMFLVYEDRVQIVKEVSTAEQPLAVAVDGHFL
CLALTTQYIIHNYSTGVSQDLFPYCSEERPPIVKRIGRQEFLLAGPGGLGMFATVAGISQRAPVHWSENVIGAAVSFPYVIALDDEFITV
HSMLDQQQKQTLPFKEGHILQDFEGRVIVATSKGVYILVPLPLEKQIQDLLASRRVEEALVLAKGARRNIPKEKFQELGSNSPPQRNWKG
IAIALLVILVVCSLITMSVILLTPDELTNSSETRLSLEDLFRKDFVLHDPEARWINDTDVVYKSENGHVIKLNIETNATTLLLENTTFVT
FKASRHSVSPDLKYVLLAYDVKQIFHYSYTASYVIYNIHTREVWELNPPEVEDSVLQYAAWGVQGQQLIYIFENNIYYQPDIKSSSLRLT
SSGKEEIIFNGIADWLYEEELLHSHIAHWWSPDGERLAFLMINDSLVPTMVIPRFTGALYPKGKQYPYPKAGQVNPTIKLYVVNLYGPTH
TLELMPPDSFKSREYYITMVKWVSNTKTVVRWLNRAQNISILTVCETTTGACSKKYEMTSDTWLSQQNEEPVFSRDGSKFFMTVPVKQGG
RGEFHHVAMFLIQSKSEQITVRHLTSGNWEVIKILAYDETTQKIYFLSTESSPRGRQLYSASTEGLLNRQCISCNFMKEQCTYFDASFSP
MNQHFLLFCEGPRVPVVSLHSTDNPAKYFILESNSMLKEAILKKKIGKPEIKILHIDDYELPLQLSLPKDFMDRNQYALLLIMDEEPGGQ
LVTDKFHIDWDSVLIDMDNVIVARFDGRGSGFQGLKILQEIHRRLGSVEVKDQITAVKFLLKLPYIDSKRLSIFGKGYGGYIASMILKSD
EKLFKCGSVVAPITDLKLYASAFSERYLGMPSKEESTYQAASVLHNVHGLKEENILIIHGTADTKVHFQHSAELIKHLIKAGVNYTMQVY

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

>90489_90489_2_TGFBRAP1-DPP10_TGFBRAP1_chr2_105912813_ENST00000393359_DPP10_chr2_116066815_ENST00000410059_length(amino acids)=1170AA_BP=394
MAAAPRDGKRRLRGRASPGAAGRSGAAGPQAAGRRGTAGAGAADQPVDMMSIKAFTLVSAVERELLMGDKERVNIECVECCGRDLYVGTN
DCFVYHFLLEERPVPAGPATFTATKQLQRHLGFKKPVNELRAASALNRLLVLCDNSISLVNMLNLEPVPSGARIKGAATFALNENPVSGD
PFCVEVCIISVKRRTIQMFLVYEDRVQIVKEVSTAEQPLAVAVDGHFLCLALTTQYIIHNYSTGVSQDLFPYCSEERPPIVKRIGRQEFL
LAGPGGLGMFATVAGISQRAPVHWSENVIGAAVSFPYVIALDDEFITVHSMLDQQQKQTLPFKEGHILQDFEGRVIVATSKGVYILVPLP
LEKQIQDLLASRRVEEALVLAKGARRNIPKEKFQELGSNSPPQRNWKGIAIALLVILVVCSLITMSVILLTPDELTNSSETRLSLEDLFR
KDFVLHDPEARWINDTDVVYKSENGHVIKLNIETNATTLLLENTTFVTFKASRHSVSPDLKYVLLAYDVKQIFHYSYTASYVIYNIHTRE
VWELNPPEVEDSVLQYAAWGVQGQQLIYIFENNIYYQPDIKSSSLRLTSSGKEEIIFNGIADWLYEEELLHSHIAHWWSPDGERLAFLMI
NDSLVPTMVIPRFTGALYPKGKQYPYPKAGQVNPTIKLYVVNLYGPTHTLELMPPDSFKSREYYITMVKWVSNTKTVVRWLNRAQNISIL
TVCETTTGACSKKYEMTSDTWLSQQNEEPVFSRDGSKFFMTVPVKQGGRGEFHHVAMFLIQSKSEQITVRHLTSGNWEVIKILAYDETTQ
KIYFLSTESSPRGRQLYSASTEGLLNRQCISCNFMKEQCTYFDASFSPMNQHFLLFCEGPRVPVVSLHSTDNPAKYFILESNSMLKEAIL
KKKIGKPEIKILHIDDYELPLQLSLPKDFMDRNQYALLLIMDEEPGGQLVTDKFHIDWDSVLIDMDNVIVARFDGRGSGFQGLKILQEIH
RRLGSVEVKDQITAVKFLLKLPYIDSKRLSIFGKGYGGYIASMILKSDEKLFKCGSVVAPITDLKLYASAFSERYLGMPSKEESTYQAAS
VLHNVHGLKEENILIIHGTADTKVHFQHSAELIKHLIKAGVNYTMQVYPDEGHNVSEKSKYHLYSTILKFFSDCLKEEISVLPQEPEEDE

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

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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/chr2:105912813/chr2:115464694)
- 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
.	DPP10 Q8N608
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: Promotes cell surface expression of the potassium channel KCND2 (PubMed:15454437). Modulates the activity and gating characteristics of the potassium channel KCND2 (PubMed:15454437). Has no dipeptidyl aminopeptidase activity (PubMed:12662155). {ECO:0000269\|PubMed:12662155, ECO:0000269\|PubMed:15454437, ECO:0000269\|PubMed:15671030}.

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

Hgene

TGFBRAP1

chr2:105912813

chr2:116066815

ENST00000258449

24_297

346.0

861.0

Domain

CNH

Hgene

TGFBRAP1

chr2:105912813

chr2:116066815

ENST00000393359

24_297

346.0

861.0

Domain

CNH

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000409163

1_56

747.0

Region

Note=Mediates effects on KCND2

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000310323

56_796

13.0

790.0

Topological domain

Extracellular

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000393147

56_796

24.0

801.0

Topological domain

Extracellular

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000409163

1_34

747.0

Topological domain

Cytoplasmic

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000409163

56_796

747.0

Topological domain

Extracellular

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000410059

56_796

20.0

797.0

Topological domain

Extracellular

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000310323

35_55

13.0

790.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000393147

35_55

24.0

801.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000409163

35_55

747.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000410059

35_55

20.0

797.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

- 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

TGFBRAP1

chr2:105912813

chr2:116066815

ENST00000258449

564_728

346.0

861.0

Repeat

Note=CHCR

Hgene

TGFBRAP1

chr2:105912813

chr2:116066815

ENST00000393359

564_728

346.0

861.0

Repeat

Note=CHCR

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000310323

1_56

13.0

790.0

Region

Note=Mediates effects on KCND2

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000393147

1_56

24.0

801.0

Region

Note=Mediates effects on KCND2

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000410059

1_56

20.0

797.0

Region

Note=Mediates effects on KCND2

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000310323

1_34

13.0

790.0

Topological domain

Cytoplasmic

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000393147

1_34

24.0

801.0

Topological domain

Cytoplasmic

Tgene

DPP10

chr2:105912813

chr2:116066815

ENST00000410059

1_34

20.0

797.0

Topological domain

Cytoplasmic

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>1910_TGFBRAP1_105912813_DPP10_116066815_ranked_0.pdb	TGFBRAP1	105912813	105912813	ENST00000410059	DPP10	chr2	116066815	+	MAAAPRDGKRRLRGRASPGAAGRSGAAGPQAAGRRGTAGAGAADQPVDMMSIKAFTLVSAVERELLMGDKERVNIECVECCGRDLYVGTN DCFVYHFLLEERPVPAGPATFTATKQLQRHLGFKKPVNELRAASALNRLLVLCDNSISLVNMLNLEPVPSGARIKGAATFALNENPVSGD PFCVEVCIISVKRRTIQMFLVYEDRVQIVKEVSTAEQPLAVAVDGHFLCLALTTQYIIHNYSTGVSQDLFPYCSEERPPIVKRIGRQEFL LAGPGGLGMFATVAGISQRAPVHWSENVIGAAVSFPYVIALDDEFITVHSMLDQQQKQTLPFKEGHILQDFEGRVIVATSKGVYILVPLP LEKQIQDLLASRRVEEALVLAKGARRNIPKEKFQELGSNSPPQRNWKGIAIALLVILVVCSLITMSVILLTPDELTNSSETRLSLEDLFR KDFVLHDPEARWINDTDVVYKSENGHVIKLNIETNATTLLLENTTFVTFKASRHSVSPDLKYVLLAYDVKQIFHYSYTASYVIYNIHTRE VWELNPPEVEDSVLQYAAWGVQGQQLIYIFENNIYYQPDIKSSSLRLTSSGKEEIIFNGIADWLYEEELLHSHIAHWWSPDGERLAFLMI NDSLVPTMVIPRFTGALYPKGKQYPYPKAGQVNPTIKLYVVNLYGPTHTLELMPPDSFKSREYYITMVKWVSNTKTVVRWLNRAQNISIL TVCETTTGACSKKYEMTSDTWLSQQNEEPVFSRDGSKFFMTVPVKQGGRGEFHHVAMFLIQSKSEQITVRHLTSGNWEVIKILAYDETTQ KIYFLSTESSPRGRQLYSASTEGLLNRQCISCNFMKEQCTYFDASFSPMNQHFLLFCEGPRVPVVSLHSTDNPAKYFILESNSMLKEAIL KKKIGKPEIKILHIDDYELPLQLSLPKDFMDRNQYALLLIMDEEPGGQLVTDKFHIDWDSVLIDMDNVIVARFDGRGSGFQGLKILQEIH RRLGSVEVKDQITAVKFLLKLPYIDSKRLSIFGKGYGGYIASMILKSDEKLFKCGSVVAPITDLKLYASAFSERYLGMPSKEESTYQAAS VLHNVHGLKEENILIIHGTADTKVHFQHSAELIKHLIKAGVNYTMQVYPDEGHNVSEKSKYHLYSTILKFFSDCLKEEISVLPQEPEEDE	1170

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

TGFBRAP1_pLDDT.png

DPP10_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
TGFBRAP1
DPP10

- 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 TGFBRAP1-DPP10

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 TGFBRAP1-DPP10

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