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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:AHCY-PIGU

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: AHCY-PIGU
FusionPDB ID: 3071
FusionGDB2.0 ID: 3071
HgeneTgene
Gene symbol

AHCY

PIGU

Gene ID

191

128869

Gene nameadenosylhomocysteinasephosphatidylinositol glycan anchor biosynthesis class U
SynonymsSAHH|adoHcyaseCDC91L1|GAB1|GPIBD21
Cytomap

20q11.22

20q11.22

Type of geneprotein-codingprotein-coding
DescriptionadenosylhomocysteinaseS-adenosyl-L-homocysteine hydrolaseS-adenosylhomocysteine hydrolaseepididymis secretory sperm binding proteinphosphatidylinositol glycan anchor biosynthesis class U proteinCDC91 (cell division cycle 91, S. cerevisiae, homolog)-like 1GPI transamidase component PIG-UGPI transamidase subunitcell division cycle 91-like 1 proteincell division cycle protein 91-li
Modification date2020032020200322
UniProtAcc

Q96HN2

Main function of 5'-partner protein: FUNCTION: May regulate the electrogenic sodium/bicarbonate cotransporter SLC4A4 activity and Mg(2+)-sensitivity. On the contrary of its homolog AHCYL1, does not regulate ITPR1 sensitivity to inositol 1,4,5-trisphosphate (PubMed:19220705). {ECO:0000250|UniProtKB:A6QLP2, ECO:0000269|PubMed:19220705}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000217426, ENST00000538132, 
ENST00000468908, 
ENST00000480175, 
ENST00000374820, ENST00000452740, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score9 X 9 X 4=32419 X 15 X 11=3135
# samples 921
** MAII scorelog2(9/324*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(21/3135*10)=-3.90000421002328
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: AHCY [Title/Abstract] AND PIGU [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: AHCY [Title/Abstract] AND PIGU [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)AHCY(32881886)-PIGU(33245048), # samples:1
PIGU(33203846)-AHCY(32873440), # samples:1
Anticipated loss of major functional domain due to fusion event.AHCY-PIGU 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.
AHCY-PIGU 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.
PIGU-AHCY 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.
PIGU-AHCY 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.
AHCY-PIGU seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
AHCY-PIGU seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AHCY-PIGU seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
AHCY-PIGU seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
AHCY-PIGU seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PIGU-AHCY seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PIGU-AHCY seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PIGU-AHCY seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PIGU-AHCY seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PIGU-AHCY seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted 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
TgenePIGU

GO:0006506

GPI anchor biosynthetic process

15034568

TgenePIGU

GO:0046425

regulation of JAK-STAT cascade

15034568



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/chr20:32881886/chr20:33245048)
- 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 AHCY (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 PIGU (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)
ENST00000538132AHCYchr2032881886-ENST00000452740PIGUchr2033245048-19375982461739497
ENST00000217426AHCYchr2032881886-ENST00000374820PIGUchr2033245048-1814373781490470

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
ENST00000538132ENST00000452740AHCYchr2032881886-PIGUchr2033245048-0.0212811940.9787188
ENST00000217426ENST00000374820AHCYchr2032881886-PIGUchr2033245048-0.0074740410.99252594

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 AHCY-PIGU

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
AHCYchr2032881886PIGUchr203324504837398DHAAAAIAKAGIPVVEGLSLLDLGVS
AHCYchr2032881886PIGUchr2033245048598117DHAAAAIAKAGIPVVEGLSLLDLGVS

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Potential FusionNeoAntigen Information of AHCY-PIGU 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.
AHCY-PIGU_32881886_33245048.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)
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:02IAKAGIPVV0.99450.6293615
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:01IAKAGIPVV0.99170.8087615
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:03IPVVEGLSL0.99140.91681120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:01IPVVEGLSL0.99120.92181120
AHCY-PIGUchr2032881886chr2033245048373HLA-B52:01IAKAGIPVV0.99020.9896615
AHCY-PIGUchr2032881886chr2033245048373HLA-A02:38AIAKAGIPV0.9890.7066514
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:08IPVVEGLSL0.97780.86531120
AHCY-PIGUchr2032881886chr2033245048373HLA-B08:09IAKAGIPVV0.95730.6958615
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:05IPVVEGLSL0.93840.62311120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:04IPVVEGLSL0.93710.96741120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:02IPVVEGLSL0.93710.96741120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:03IPVVEGLSLL0.96360.88161121
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:02IPVVEGLSLL0.8780.94461121
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:04IPVVEGLSLL0.8780.94461121
AHCY-PIGUchr2032881886chr2033245048373HLA-B48:01AKAGIPVVEGL0.99210.8861718
AHCY-PIGUchr2032881886chr2033245048373HLA-C15:06IAKAGIPVV0.99820.842615
AHCY-PIGUchr2032881886chr2033245048373HLA-C03:19IAKAGIPVV0.99620.9895615
AHCY-PIGUchr2032881886chr2033245048373HLA-B78:01IAKAGIPVV0.99530.9086615
AHCY-PIGUchr2032881886chr2033245048373HLA-C12:04IAKAGIPVV0.99230.995615
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:07IAKAGIPVV0.99140.9789615
AHCY-PIGUchr2032881886chr2033245048373HLA-C06:03IAKAGIPVV0.99140.9943615
AHCY-PIGUchr2032881886chr2033245048373HLA-C12:12IAKAGIPVV0.98250.9644615
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:08IAKAGIPVV0.96590.5505615
AHCY-PIGUchr2032881886chr2033245048373HLA-C03:08IAKAGIPVV0.96120.7902615
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:12IPVVEGLSL0.93710.96741120
AHCY-PIGUchr2032881886chr2033245048373HLA-B07:12IPVVEGLSL0.87650.50751120
AHCY-PIGUchr2032881886chr2033245048373HLA-B39:10IPVVEGLSL0.81390.93941120
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:07IPVVEGLSL0.79590.78091120
AHCY-PIGUchr2032881886chr2033245048373HLA-C02:06IAKAGIPVV0.79390.9746615
AHCY-PIGUchr2032881886chr2033245048373HLA-B42:02IPVVEGLSL0.61050.7311120
AHCY-PIGUchr2032881886chr2033245048373HLA-B42:01IPVVEGLSL0.54640.73221120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:12IPVVEGLSLL0.8780.94461121
AHCY-PIGUchr2032881886chr2033245048373HLA-B39:10IPVVEGLSLL0.70460.91421121
AHCY-PIGUchr2032881886chr2033245048373HLA-B07:12AGIPVVEGLSL0.99250.6369920
AHCY-PIGUchr2032881886chr2033245048373HLA-C15:02IAKAGIPVV0.99880.866615
AHCY-PIGUchr2032881886chr2033245048373HLA-C15:05IAKAGIPVV0.99860.9305615
AHCY-PIGUchr2032881886chr2033245048373HLA-C03:17IAKAGIPVV0.99740.9592615
AHCY-PIGUchr2032881886chr2033245048373HLA-C03:05IAKAGIPVV0.99720.8911615
AHCY-PIGUchr2032881886chr2033245048373HLA-B56:05IAKAGIPVV0.99570.7501615
AHCY-PIGUchr2032881886chr2033245048373HLA-B78:02IAKAGIPVV0.99390.9696615
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:23IPVVEGLSL0.99220.91621120
AHCY-PIGUchr2032881886chr2033245048373HLA-C12:03IAKAGIPVV0.99170.9888615
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:13IAKAGIPVV0.99160.7096615
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:77IPVVEGLSL0.99120.92181120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:13IPVVEGLSL0.990.92081120
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:21IAKAGIPVV0.98930.6059615
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:14IAKAGIPVV0.98910.6988615
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:09IAKAGIPVV0.98030.739615
AHCY-PIGUchr2032881886chr2033245048373HLA-C16:04IAKAGIPVV0.97850.9848615
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:24IPVVEGLSL0.96490.90831120
AHCY-PIGUchr2032881886chr2033245048373HLA-C12:02IAKAGIPVV0.96310.9719615
AHCY-PIGUchr2032881886chr2033245048373HLA-C16:02IAKAGIPVV0.95590.9919615
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:30IPVVEGLSL0.94140.78231120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:17IPVVEGLSL0.94140.78231120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:09IPVVEGLSL0.93710.96741120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:11IPVVEGLSL0.93320.86291120
AHCY-PIGUchr2032881886chr2033245048373HLA-B59:01IAKAGIPVV0.90090.5692615
AHCY-PIGUchr2032881886chr2033245048373HLA-B67:01IPVVEGLSL0.80430.83871120
AHCY-PIGUchr2032881886chr2033245048373HLA-C16:01IAKAGIPVV0.74870.9848615
AHCY-PIGUchr2032881886chr2033245048373HLA-B51:29IAKAGIPVV0.74090.6489615
AHCY-PIGUchr2032881886chr2033245048373HLA-C02:02IAKAGIPVV0.52190.9746615
AHCY-PIGUchr2032881886chr2033245048373HLA-C02:10IAKAGIPVV0.52190.9746615
AHCY-PIGUchr2032881886chr2033245048373HLA-B18:07IPVVEGLSL0.15030.83991120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:43IPVVEGLSL0.02790.77741120
AHCY-PIGUchr2032881886chr2033245048373HLA-B15:08IPVVEGLSL0.020.77961120
AHCY-PIGUchr2032881886chr2033245048373HLA-B15:11IPVVEGLSL0.01940.79221120
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:13IPVVEGLSLL0.96040.88561121
AHCY-PIGUchr2032881886chr2033245048373HLA-B35:09IPVVEGLSLL0.8780.94461121
AHCY-PIGUchr2032881886chr2033245048373HLA-B67:01IPVVEGLSLL0.71990.79061121
AHCY-PIGUchr2032881886chr2033245048373HLA-B67:01AGIPVVEGLSL0.97820.9202920

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Potential FusionNeoAntigen Information of AHCY-PIGU 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.

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)

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Fusion breakpoint peptide structures of AHCY-PIGU

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
3585IAKAGIPVVEGLSLAHCYPIGUchr2032881886chr2033245048373

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AHCY-PIGU

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-B14:023BVN3585IAKAGIPVVEGLSL-5.45575-5.46295
HLA-B52:013W393585IAKAGIPVVEGLSL-5.51835-5.52555
HLA-A24:025HGA3585IAKAGIPVVEGLSL-7.37668-7.38388
HLA-B44:053DX83585IAKAGIPVVEGLSL-4.22448-4.23168

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Vaccine Design for the FusionNeoAntigens of AHCY-PIGU

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
AHCY-PIGUchr2032881886chr20332450481120IPVVEGLSLTTCCGGTGGTTGAAGGCCTTTCACTGT
AHCY-PIGUchr2032881886chr20332450481121IPVVEGLSLLTTCCGGTGGTTGAAGGCCTTTCACTGTTGG
AHCY-PIGUchr2032881886chr2033245048514AIAKAGIPVCCATTGCCAAGGCTGGCATTCCGGTGG
AHCY-PIGUchr2032881886chr2033245048615IAKAGIPVVTTGCCAAGGCTGGCATTCCGGTGGTTG
AHCY-PIGUchr2032881886chr2033245048718AKAGIPVVEGLCCAAGGCTGGCATTCCGGTGGTTGAAGGCCTTT
AHCY-PIGUchr2032881886chr2033245048920AGIPVVEGLSLCTGGCATTCCGGTGGTTGAAGGCCTTTCACTGT

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

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Information of the samples that have these potential fusion neoantigens of AHCY-PIGU

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
STADAHCY-PIGUchr2032881886ENST00000217426chr2033245048ENST00000374820TCGA-HU-A4GX

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Potential target of CAR-T therapy development for AHCY-PIGU

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
TgenePIGUchr20:32881886chr20:33245048ENST00000374820011166_1860416.0TransmembraneHelical
TgenePIGUchr20:32881886chr20:33245048ENST00000374820011188_2080416.0TransmembraneHelical
TgenePIGUchr20:32881886chr20:33245048ENST00000374820011237_2570416.0TransmembraneHelical
TgenePIGUchr20:32881886chr20:33245048ENST00000374820011259_2790416.0TransmembraneHelical
TgenePIGUchr20:32881886chr20:33245048ENST00000374820011286_3060416.0TransmembraneHelical
TgenePIGUchr20:32881886chr20:33245048ENST00000374820011313_3330416.0TransmembraneHelical
TgenePIGUchr20:32881886chr20:33245048ENST00000374820011355_3750416.0TransmembraneHelical
TgenePIGUchr20:32881886chr20:33245048ENST00000374820011386_4060416.0TransmembraneHelical
TgenePIGUchr20:32881886chr20:33245048ENST0000037482001166_860416.0TransmembraneHelical

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 AHCY-PIGU

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 AHCY-PIGU

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