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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:PCGF3-ACTR3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PCGF3-ACTR3
FusionPDB ID: 63287
FusionGDB2.0 ID: 63287
HgeneTgene
Gene symbol

PCGF3

ACTR3

Gene ID

10336

10096

Gene namepolycomb group ring finger 3actin related protein 3
SynonymsDONG1|RNF3|RNF3AARP3
Cytomap

4p16.3

2q14.1

Type of geneprotein-codingprotein-coding
Descriptionpolycomb group RING finger protein 3RING finger protein 3Aring finger protein 3actin-related protein 3ARP3 actin related protein 3 homologactin-like protein 3
Modification date2020031320200327
UniProtAcc.

Q9C0K3

Main function of 5'-partner protein: FUNCTION: May play a role in the suppression of metastatic potential in lung adenoma carcinoma cells. {ECO:0000269|PubMed:11162478}.
Ensembl transtripts involved in fusion geneENST idsENST00000362003, ENST00000470161, 
ENST00000505655, ENST00000521023, 
ENST00000400151, ENST00000482726, 
ENST00000263238, ENST00000535589, 
ENST00000536059, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 8 X 8=89616 X 13 X 7=1456
# samples 1817
** MAII scorelog2(18/896*10)=-2.31550182572793
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(17/1456*10)=-3.098403704061
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PCGF3 [Title/Abstract] AND ACTR3 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PCGF3 [Title/Abstract] AND ACTR3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PCGF3(738476)-ACTR3(114709056), # samples:1
Anticipated loss of major functional domain due to fusion event.PCGF3-ACTR3 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.
PCGF3-ACTR3 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.
PCGF3-ACTR3 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.
PCGF3-ACTR3 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
TgeneACTR3

GO:0034314

Arp2/3 complex-mediated actin nucleation

11741539|17220302

TgeneACTR3

GO:0045944

positive regulation of transcription by RNA polymerase II

17220302



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/chr4:738476/chr2:114709056)
- 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 PCGF3 (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 ACTR3 (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)
ENST00000362003PCGF3chr4738476+ENST00000263238ACTR3chr2114709056+63978573951255286
ENST00000362003PCGF3chr4738476+ENST00000536059ACTR3chr2114709056+13718573951255286
ENST00000362003PCGF3chr4738476+ENST00000535589ACTR3chr2114709056+13928573951255286
ENST00000470161PCGF3chr4738476+ENST00000263238ACTR3chr2114709056+63968563941254286
ENST00000470161PCGF3chr4738476+ENST00000536059ACTR3chr2114709056+13708563941254286
ENST00000470161PCGF3chr4738476+ENST00000535589ACTR3chr2114709056+13918563941254286
ENST00000521023PCGF3chr4738476+ENST00000263238ACTR3chr2114709056+7365182514622223253
ENST00000521023PCGF3chr4738476+ENST00000536059ACTR3chr2114709056+2339182514622223253
ENST00000521023PCGF3chr4738476+ENST00000535589ACTR3chr2114709056+2360182514622223253
ENST00000505655PCGF3chr4738476+ENST00000263238ACTR3chr2114709056+604650644904286
ENST00000505655PCGF3chr4738476+ENST00000536059ACTR3chr2114709056+102050644904286
ENST00000505655PCGF3chr4738476+ENST00000535589ACTR3chr2114709056+104150644904286

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
ENST00000362003ENST00000263238PCGF3chr4738476+ACTR3chr2114709056+0.0001279310.9998721
ENST00000362003ENST00000536059PCGF3chr4738476+ACTR3chr2114709056+0.0023725260.99762744
ENST00000362003ENST00000535589PCGF3chr4738476+ACTR3chr2114709056+0.002184410.9978156
ENST00000470161ENST00000263238PCGF3chr4738476+ACTR3chr2114709056+0.0001264820.9998735
ENST00000470161ENST00000536059PCGF3chr4738476+ACTR3chr2114709056+0.0023869680.9976131
ENST00000470161ENST00000535589PCGF3chr4738476+ACTR3chr2114709056+0.0022079690.997792
ENST00000521023ENST00000263238PCGF3chr4738476+ACTR3chr2114709056+0.0004973740.99950266
ENST00000521023ENST00000536059PCGF3chr4738476+ACTR3chr2114709056+0.0029774860.99702245
ENST00000521023ENST00000535589PCGF3chr4738476+ACTR3chr2114709056+0.0028204540.9971795
ENST00000505655ENST00000263238PCGF3chr4738476+ACTR3chr2114709056+0.0001132620.99988675
ENST00000505655ENST00000536059PCGF3chr4738476+ACTR3chr2114709056+0.0018721140.9981279
ENST00000505655ENST00000535589PCGF3chr4738476+ACTR3chr2114709056+0.0018033780.99819666

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 PCGF3-ACTR3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PCGF3chr4738476ACTR3chr21147090561825120KPEEDNDYHRSDEQFANPDFTQPISE
PCGF3chr4738476ACTR3chr2114709056506153KPEEDNDYHRSDEQFANPDFTQPISE
PCGF3chr4738476ACTR3chr2114709056856153KPEEDNDYHRSDEQFANPDFTQPISE
PCGF3chr4738476ACTR3chr2114709056857153KPEEDNDYHRSDEQFANPDFTQPISE

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Potential FusionNeoAntigen Information of PCGF3-ACTR3 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.
PCGF3-ACTR3_738476_114709056.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)
PCGF3-ACTR3chr4738476chr2114709056857HLA-B15:18YHRSDEQF0.95650.7547715
PCGF3-ACTR3chr4738476chr2114709056857HLA-B38:02YHRSDEQF0.92080.922715
PCGF3-ACTR3chr4738476chr2114709056857HLA-B15:10YHRSDEQF0.9190.5975715
PCGF3-ACTR3chr4738476chr2114709056857HLA-B38:01YHRSDEQF0.910.9242715
PCGF3-ACTR3chr4738476chr2114709056857HLA-B15:37YHRSDEQF0.84910.7337715
PCGF3-ACTR3chr4738476chr2114709056857HLA-B18:01DEQFANPDF0.98740.88051120
PCGF3-ACTR3chr4738476chr2114709056857HLA-B39:06YHRSDEQFA0.98040.7055716
PCGF3-ACTR3chr4738476chr2114709056857HLA-B73:01HRSDEQFANP0.96590.7192818
PCGF3-ACTR3chr4738476chr2114709056857HLA-B38:05YHRSDEQF0.910.9242715
PCGF3-ACTR3chr4738476chr2114709056857HLA-B18:04DEQFANPDF0.99130.89891120
PCGF3-ACTR3chr4738476chr2114709056857HLA-B18:07DEQFANPDF0.98980.85031120
PCGF3-ACTR3chr4738476chr2114709056857HLA-B18:05DEQFANPDF0.98740.88051120
PCGF3-ACTR3chr4738476chr2114709056857HLA-B18:08DEQFANPDF0.98620.83841120
PCGF3-ACTR3chr4738476chr2114709056857HLA-B18:06DEQFANPDF0.98270.88211120
PCGF3-ACTR3chr4738476chr2114709056857HLA-B18:03DEQFANPDF0.98110.87221120
PCGF3-ACTR3chr4738476chr2114709056857HLA-B18:11DEQFANPDF0.74230.74311120
PCGF3-ACTR3chr4738476chr2114709056857HLA-B57:02RSDEQFANPDF0.99820.8938920

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Potential FusionNeoAntigen Information of PCGF3-ACTR3 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.
PCGF3-ACTR3_738476_114709056.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)
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0901DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0901EDNDYHRSDEQFANP318
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0901EEDNDYHRSDEQFAN217
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0901NDYHRSDEQFANPDF520
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0902DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0902EDNDYHRSDEQFANP318
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0903DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0903EDNDYHRSDEQFANP318
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0903EEDNDYHRSDEQFAN217
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0904DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0904EDNDYHRSDEQFANP318
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0904EEDNDYHRSDEQFAN217
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0905DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0905EDNDYHRSDEQFANP318
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0907DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0907EDNDYHRSDEQFANP318
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0907EEDNDYHRSDEQFAN217
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0907NDYHRSDEQFANPDF520
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0908DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0908EDNDYHRSDEQFANP318
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0908EEDNDYHRSDEQFAN217
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0908NDYHRSDEQFANPDF520
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0909DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0909EDNDYHRSDEQFANP318
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0909EEDNDYHRSDEQFAN217
PCGF3-ACTR3chr4738476chr2114709056857DRB1-0909NDYHRSDEQFANPDF520
PCGF3-ACTR3chr4738476chr2114709056857DRB5-0112DNDYHRSDEQFANPD419
PCGF3-ACTR3chr4738476chr2114709056857DRB5-0112EDNDYHRSDEQFANP318

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Fusion breakpoint peptide structures of PCGF3-ACTR3

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
1492DYHRSDEQFANPDFPCGF3ACTR3chr4738476chr2114709056857

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PCGF3-ACTR3

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-B14:023BVN1492DYHRSDEQFANPDF-7.15543-7.26883
HLA-B14:023BVN1492DYHRSDEQFANPDF-4.77435-5.80965
HLA-B52:013W391492DYHRSDEQFANPDF-6.80875-6.92215
HLA-B52:013W391492DYHRSDEQFANPDF-4.20386-5.23916
HLA-A11:014UQ21492DYHRSDEQFANPDF-7.5194-8.5547
HLA-A11:014UQ21492DYHRSDEQFANPDF-6.9601-7.0735
HLA-A24:025HGA1492DYHRSDEQFANPDF-7.52403-7.63743
HLA-A24:025HGA1492DYHRSDEQFANPDF-5.82433-6.85963
HLA-B27:056PYJ1492DYHRSDEQFANPDF-3.28285-4.31815
HLA-B44:053DX81492DYHRSDEQFANPDF-5.91172-6.94702
HLA-B44:053DX81492DYHRSDEQFANPDF-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of PCGF3-ACTR3

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
PCGF3-ACTR3chr4738476chr21147090561120DEQFANPDFGAGCAGTTTGCTAATCCAGACTTTACA
PCGF3-ACTR3chr4738476chr2114709056715YHRSDEQFCACCGCAGCGACGAGCAGTTTGCT
PCGF3-ACTR3chr4738476chr2114709056716YHRSDEQFACACCGCAGCGACGAGCAGTTTGCTAAT
PCGF3-ACTR3chr4738476chr2114709056818HRSDEQFANPCGCAGCGACGAGCAGTTTGCTAATCCAGAC
PCGF3-ACTR3chr4738476chr2114709056920RSDEQFANPDFAGCGACGAGCAGTTTGCTAATCCAGACTTTACA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PCGF3-ACTR3chr4738476chr2114709056217EEDNDYHRSDEQFANGAGGACAACGACTACCACCGCAGCGACGAGCAGTTTGCTAATCCA
PCGF3-ACTR3chr4738476chr2114709056318EDNDYHRSDEQFANPGACAACGACTACCACCGCAGCGACGAGCAGTTTGCTAATCCAGAC
PCGF3-ACTR3chr4738476chr2114709056419DNDYHRSDEQFANPDAACGACTACCACCGCAGCGACGAGCAGTTTGCTAATCCAGACTTT
PCGF3-ACTR3chr4738476chr2114709056520NDYHRSDEQFANPDFGACTACCACCGCAGCGACGAGCAGTTTGCTAATCCAGACTTTACA

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Information of the samples that have these potential fusion neoantigens of PCGF3-ACTR3

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
STADPCGF3-ACTR3chr4738476ENST00000362003chr2114709056ENST00000263238TCGA-BR-A4J5-01A

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Potential target of CAR-T therapy development for PCGF3-ACTR3

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 PCGF3-ACTR3

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 PCGF3-ACTR3

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