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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:TRIO-PPP2R5E

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TRIO-PPP2R5E
FusionPDB ID: 94214
FusionGDB2.0 ID: 94214
HgeneTgene
Gene symbol

TRIO

PPP2R5E

Gene ID

7204

5529

Gene nametrio Rho guanine nucleotide exchange factorprotein phosphatase 2 regulatory subunit B'epsilon
SynonymsARHGEF23|MEBAS|MRD44|tgatB56E|B56epsilon
Cytomap

5p15.2

14q23.2

Type of geneprotein-codingprotein-coding
Descriptiontriple functional domain proteinPTPRF-interacting proteintriple functional domain (PTPRF interacting)serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoformPP2A, B subunit, B' epsilonPP2A, B subunit, B56 epsilonPP2A, B subunit, PR61 epsilonPP2A, B subunit, R5 epsilonepsilon isoform of regulatory subunit B56, protein phospha
Modification date2020031320200320
UniProtAcc

TPI1

.
Ensembl transtripts involved in fusion geneENST idsENST00000344204, ENST00000509967, 
ENST00000537187, ENST00000344135, 
ENST00000515710, 
ENST00000553266, 
ENST00000337537, ENST00000422769, 
ENST00000555899, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score34 X 28 X 12=1142416 X 15 X 5=1200
# samples 3516
** MAII scorelog2(35/11424*10)=-5.02856915219677
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(16/1200*10)=-2.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: TRIO [Title/Abstract] AND PPP2R5E [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TRIO(14280545)-PPP2R5E(63848875), # samples:5
Anticipated loss of major functional domain due to fusion event.TRIO-PPP2R5E 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.
TRIO-PPP2R5E 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

check buttonFusion gene breakpoints across TRIO (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 PPP2R5E (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 Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4HNSCTCGA-BA-5153-01ATRIOchr5

14280545

-PPP2R5Echr14

63848875

-
ChimerDB4HNSCTCGA-BA-5153-01ATRIOchr5

14280545

+PPP2R5Echr14

63848875

-
ChimerDB4HNSCTCGA-BA-5153TRIOchr5

14280545

+PPP2R5Echr14

63848875

-


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Fusion ORF Analysis


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)
ENST00000344204TRIOchr514280545+ENST00000337537PPP2R5Echr1463848875-522537124572182
ENST00000344204TRIOchr514280545+ENST00000555899PPP2R5Echr1463848875-80637124557177
ENST00000344204TRIOchr514280545+ENST00000422769PPP2R5Echr1463848875-72937124572182
ENST00000537187TRIOchr514280545+ENST00000337537PPP2R5Echr1463848875-52073536554182
ENST00000537187TRIOchr514280545+ENST00000555899PPP2R5Echr1463848875-7883536539177
ENST00000537187TRIOchr514280545+ENST00000422769PPP2R5Echr1463848875-7113536554182
ENST00000509967TRIOchr514280545+ENST00000337537PPP2R5Echr1463848875-5206352152553133
ENST00000509967TRIOchr514280545+ENST00000555899PPP2R5Echr1463848875-787352152538128
ENST00000509967TRIOchr514280545+ENST00000422769PPP2R5Echr1463848875-710352152553133

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
ENST00000344204ENST00000337537TRIOchr514280545+PPP2R5Echr1463848875-0.0004323950.99956757
ENST00000344204ENST00000555899TRIOchr514280545+PPP2R5Echr1463848875-0.0010694950.9989305
ENST00000344204ENST00000422769TRIOchr514280545+PPP2R5Echr1463848875-0.0013426580.99865735
ENST00000537187ENST00000337537TRIOchr514280545+PPP2R5Echr1463848875-0.0004433570.9995566
ENST00000537187ENST00000555899TRIOchr514280545+PPP2R5Echr1463848875-0.0008924550.99910754
ENST00000537187ENST00000422769TRIOchr514280545+PPP2R5Echr1463848875-0.0011912740.99880874
ENST00000509967ENST00000337537TRIOchr514280545+PPP2R5Echr1463848875-0.0056864030.9943136
ENST00000509967ENST00000555899TRIOchr514280545+PPP2R5Echr1463848875-0.0126828880.98731714
ENST00000509967ENST00000422769TRIOchr514280545+PPP2R5Echr1463848875-0.0288499910.97115

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Fusion Amino Acid Sequences


check button 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

>94214_94214_1_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000344204_PPP2R5E_chr14_63848875_ENST00000337537_length(amino acids)=182AA_BP=115
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF
PARSNHDRIRQEDLRRLISYLACIPRAIVALVYNVLKAFMEMNSTMFDELTATYKSDRQREKKKEKEREELWKKLEDLELKRGLRRDGII

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

>94214_94214_2_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000344204_PPP2R5E_chr14_63848875_ENST00000422769_length(amino acids)=182AA_BP=115
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF
PARSNHDRIRQEDLRRLISYLACIPRAIVALVYNVLKAFMEMNSTMFDELTATYKSDRQREKKKEKEREELWKKLEDLELKRGLRRDGII

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

>94214_94214_3_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000344204_PPP2R5E_chr14_63848875_ENST00000555899_length(amino acids)=177AA_BP=115
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF

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

>94214_94214_4_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000509967_PPP2R5E_chr14_63848875_ENST00000337537_length(amino acids)=133AA_BP=66
MAEGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTFPARSNHDRIRQEDLRRLISYLACIPRAIVALVYNVLKAFMEMNSTMFDE

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

>94214_94214_5_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000509967_PPP2R5E_chr14_63848875_ENST00000422769_length(amino acids)=133AA_BP=66
MAEGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTFPARSNHDRIRQEDLRRLISYLACIPRAIVALVYNVLKAFMEMNSTMFDE

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

>94214_94214_6_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000509967_PPP2R5E_chr14_63848875_ENST00000555899_length(amino acids)=128AA_BP=66
MAEGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTFPARSNHDRIRQEDLRRLISYLACIPRAIVALVYNVLKAFMEMNSTMFDE

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

>94214_94214_7_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000537187_PPP2R5E_chr14_63848875_ENST00000337537_length(amino acids)=182AA_BP=115
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF
PARSNHDRIRQEDLRRLISYLACIPRAIVALVYNVLKAFMEMNSTMFDELTATYKSDRQREKKKEKEREELWKKLEDLELKRGLRRDGII

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

>94214_94214_8_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000537187_PPP2R5E_chr14_63848875_ENST00000422769_length(amino acids)=182AA_BP=115
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF
PARSNHDRIRQEDLRRLISYLACIPRAIVALVYNVLKAFMEMNSTMFDELTATYKSDRQREKKKEKEREELWKKLEDLELKRGLRRDGII

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

>94214_94214_9_TRIO-PPP2R5E_TRIO_chr5_14280545_ENST00000537187_PPP2R5E_chr14_63848875_ENST00000555899_length(amino acids)=177AA_BP=115
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF

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

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Fusion Protein Functional Features


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/chr5:14280545/chr14:63848875)
- 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
TRIO

TPI1

.
249FUNCTION: 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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1101845_18500597.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1102292_23120597.0Compositional biasNote=Poly-Gly
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1102545_25510597.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+110715_7180597.0Compositional biasNote=Poly-Gln
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3571845_1850115.666666666666673098.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3572292_2312115.666666666666673098.0Compositional biasNote=Poly-Gly
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3572545_2551115.666666666666673098.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+357715_718115.666666666666673098.0Compositional biasNote=Poly-Gln
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3581845_1850115.666666666666672922.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3582292_2312115.666666666666672922.0Compositional biasNote=Poly-Gly
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3582545_2551115.666666666666672922.0Compositional biasNote=Poly-Ser
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+358715_718115.666666666666672922.0Compositional biasNote=Poly-Gln
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1101292_14670597.0DomainDH 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1101480_15910597.0DomainPH 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1101656_17210597.0DomainSH3 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1101969_21450597.0DomainDH 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1102157_22710597.0DomainPH 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1102551_26160597.0DomainSH3 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1102685_27750597.0DomainNote=Ig-like C2-type
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1102796_30520597.0DomainProtein kinase
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+11065_2100597.0DomainCRAL-TRIO
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3571292_1467115.666666666666673098.0DomainDH 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3571480_1591115.666666666666673098.0DomainPH 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3571656_1721115.666666666666673098.0DomainSH3 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3571969_2145115.666666666666673098.0DomainDH 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3572157_2271115.666666666666673098.0DomainPH 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3572551_2616115.666666666666673098.0DomainSH3 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3572685_2775115.666666666666673098.0DomainNote=Ig-like C2-type
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3572796_3052115.666666666666673098.0DomainProtein kinase
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+35765_210115.666666666666673098.0DomainCRAL-TRIO
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3581292_1467115.666666666666672922.0DomainDH 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3581480_1591115.666666666666672922.0DomainPH 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3581656_1721115.666666666666672922.0DomainSH3 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3581969_2145115.666666666666672922.0DomainDH 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3582157_2271115.666666666666672922.0DomainPH 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3582551_2616115.666666666666672922.0DomainSH3 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3582685_2775115.666666666666672922.0DomainNote=Ig-like C2-type
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3582796_3052115.666666666666672922.0DomainProtein kinase
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+35865_210115.666666666666672922.0DomainCRAL-TRIO
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1102802_28100597.0Nucleotide bindingATP
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3572802_2810115.666666666666673098.0Nucleotide bindingATP
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3582802_2810115.666666666666672922.0Nucleotide bindingATP
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+1101109_12160597.0RepeatNote=Spectrin 4
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+110311_4180597.0RepeatNote=Spectrin 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+110538_6440597.0RepeatNote=Spectrin 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000344135+110878_9840597.0RepeatNote=Spectrin 3
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+3571109_1216115.666666666666673098.0RepeatNote=Spectrin 4
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+357311_418115.666666666666673098.0RepeatNote=Spectrin 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+357538_644115.666666666666673098.0RepeatNote=Spectrin 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000344204+357878_984115.666666666666673098.0RepeatNote=Spectrin 3
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+3581109_1216115.666666666666672922.0RepeatNote=Spectrin 4
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+358311_418115.666666666666672922.0RepeatNote=Spectrin 1
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+358538_644115.666666666666672922.0RepeatNote=Spectrin 2
HgeneTRIOchr5:14280545chr14:63848875ENST00000537187+358878_984115.666666666666672922.0RepeatNote=Spectrin 3


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Fusion Protein Structures

check button 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)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>211_TRIO_14280545_PPP2R5E_63848875_ranked_0.pdbTRIO1428054514280545ENST00000422769PPP2R5Echr1463848875-
MSGSSGGAAAPAASSGPAAAASAAGSGCGGGAGEGAEEAAKDLADIAAFFRSGFRKNDEMKAMDVLPILKEKVAYLSGGRDKRGGPILTF
PARSNHDRIRQEDLRRLISYLACIPRAIVALVYNVLKAFMEMNSTMFDELTATYKSDRQREKKKEKEREELWKKLEDLELKRGLRRDGII
182


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pLDDT score distribution

check button 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.
TRIO_pLDDT.png
all structure
all structure
PPP2R5E_pLDDT.png
all structure
all structure

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


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Ramachandran Plot of Fusion Protein Structure


check button 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


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
TRIO
PPP2R5E


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to TRIO-PPP2R5E


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 TRIO-PPP2R5E


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