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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:MGST3-SPOP

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MGST3-SPOP
FusionPDB ID: 53454
FusionGDB2.0 ID: 53454
HgeneTgene
Gene symbol

MGST3

SPOP

Gene ID

4259

8405

Gene namemicrosomal glutathione S-transferase 3speckle type BTB/POZ protein
SynonymsGST-IIIBTBD32|TEF2
Cytomap

1q24.1

17q21.33

Type of geneprotein-codingprotein-coding
Descriptionmicrosomal glutathione S-transferase 3LTC4 synthase MGST3glutathione peroxidase MGST3microsomal GST-3microsomal GST-IIImicrosomal glutathione S-transferase IIIspeckle-type POZ proteinHIB homolog 1roadkill homolog 1
Modification date2020031320200329
UniProtAcc

O14880

Main function of 5'-partner protein: FUNCTION: Catalyzes oxydation of hydroxy-fatty acids (PubMed:9278457). Also catalyzes the conjugation of a reduced glutathione to leukotriene A4 in vitro (PubMed:9278457). May participate in the lipid metabolism (PubMed:9278457). {ECO:0000269|PubMed:9278457, ECO:0000303|PubMed:9278457}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000367883, ENST00000367884, 
ENST00000367885, ENST00000367886, 
ENST00000367888, ENST00000367889, 
ENST00000461759, 		ENST00000513080, 
ENST00000347630, ENST00000393328, 
ENST00000393331, ENST00000503676, 
ENST00000504102, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 5 X 4=12018 X 13 X 6=1404
# samples 618
** MAII scorelog2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(18/1404*10)=-2.96347412397489
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: MGST3 [Title/Abstract] AND SPOP [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: MGST3 [Title/Abstract] AND SPOP [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)MGST3(165621237)-SPOP(47679312), # samples:1
Anticipated loss of major functional domain due to fusion event.MGST3-SPOP 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.
MGST3-SPOP 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
HgeneMGST3

GO:0006629

lipid metabolic process

9278457

HgeneMGST3

GO:0019370

leukotriene biosynthetic process

9278457



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/chr1:165621237/chr17:47679312)
- 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 MGST3 (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 SPOP (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)
ENST00000367889MGST3chr1165621237+ENST00000393328SPOPchr1747679312-2391666440799119
ENST00000367889MGST3chr1165621237+ENST00000393331SPOPchr1747679312-2389666440799119
ENST00000367889MGST3chr1165621237+ENST00000347630SPOPchr1747679312-2389666440799119
ENST00000367889MGST3chr1165621237+ENST00000504102SPOPchr1747679312-12696661198836120
ENST00000367889MGST3chr1165621237+ENST00000503676SPOPchr1747679312-1072666440799119
ENST00000367888MGST3chr1165621237+ENST00000393328SPOPchr1747679312-203931488447119
ENST00000367888MGST3chr1165621237+ENST00000393331SPOPchr1747679312-203731488447119
ENST00000367888MGST3chr1165621237+ENST00000347630SPOPchr1747679312-203731488447119
ENST00000367888MGST3chr1165621237+ENST00000504102SPOPchr1747679312-917314846484120
ENST00000367888MGST3chr1165621237+ENST00000503676SPOPchr1747679312-72031488447119
ENST00000367885MGST3chr1165621237+ENST00000393328SPOPchr1747679312-205633121464147
ENST00000367885MGST3chr1165621237+ENST00000393331SPOPchr1747679312-205433121464147
ENST00000367885MGST3chr1165621237+ENST00000347630SPOPchr1747679312-205433121464147
ENST00000367885MGST3chr1165621237+ENST00000504102SPOPchr1747679312-93433121464147
ENST00000367885MGST3chr1165621237+ENST00000503676SPOPchr1747679312-73733121464147
ENST00000367884MGST3chr1165621237+ENST00000393328SPOPchr1747679312-2092367141500119
ENST00000367884MGST3chr1165621237+ENST00000393331SPOPchr1747679312-2090367141500119
ENST00000367884MGST3chr1165621237+ENST00000347630SPOPchr1747679312-2090367141500119
ENST00000367884MGST3chr1165621237+ENST00000504102SPOPchr1747679312-970367899537120
ENST00000367884MGST3chr1165621237+ENST00000503676SPOPchr1747679312-773367141500119
ENST00000367883MGST3chr1165621237+ENST00000393328SPOPchr1747679312-208235789490133
ENST00000367883MGST3chr1165621237+ENST00000393331SPOPchr1747679312-208035789490133
ENST00000367883MGST3chr1165621237+ENST00000347630SPOPchr1747679312-208035789490133
ENST00000367883MGST3chr1165621237+ENST00000504102SPOPchr1747679312-96035789490133
ENST00000367883MGST3chr1165621237+ENST00000503676SPOPchr1747679312-76335789490133
ENST00000367886MGST3chr1165621237+ENST00000393328SPOPchr1747679312-19932680401133
ENST00000367886MGST3chr1165621237+ENST00000393331SPOPchr1747679312-19912680401133
ENST00000367886MGST3chr1165621237+ENST00000347630SPOPchr1747679312-19912680401133
ENST00000367886MGST3chr1165621237+ENST00000504102SPOPchr1747679312-8712680401133
ENST00000367886MGST3chr1165621237+ENST00000503676SPOPchr1747679312-6742680401133

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
ENST00000367889ENST00000393328MGST3chr1165621237+SPOPchr1747679312-0.886490050.11350995
ENST00000367889ENST00000393331MGST3chr1165621237+SPOPchr1747679312-0.87883090.12116913
ENST00000367889ENST00000347630MGST3chr1165621237+SPOPchr1747679312-0.87883090.12116913
ENST00000367889ENST00000504102MGST3chr1165621237+SPOPchr1747679312-0.75286520.2471348
ENST00000367889ENST00000503676MGST3chr1165621237+SPOPchr1747679312-0.726640460.27335948
ENST00000367888ENST00000393328MGST3chr1165621237+SPOPchr1747679312-0.914814230.08518577
ENST00000367888ENST00000393331MGST3chr1165621237+SPOPchr1747679312-0.909902160.09009782
ENST00000367888ENST00000347630MGST3chr1165621237+SPOPchr1747679312-0.909902160.09009782
ENST00000367888ENST00000504102MGST3chr1165621237+SPOPchr1747679312-0.748823340.25117663
ENST00000367888ENST00000503676MGST3chr1165621237+SPOPchr1747679312-0.545610670.45438936
ENST00000367885ENST00000393328MGST3chr1165621237+SPOPchr1747679312-0.67225590.32774407
ENST00000367885ENST00000393331MGST3chr1165621237+SPOPchr1747679312-0.66556220.33443776
ENST00000367885ENST00000347630MGST3chr1165621237+SPOPchr1747679312-0.66556220.33443776
ENST00000367885ENST00000504102MGST3chr1165621237+SPOPchr1747679312-0.598000650.4019994
ENST00000367885ENST00000503676MGST3chr1165621237+SPOPchr1747679312-0.433864650.5661353
ENST00000367884ENST00000393328MGST3chr1165621237+SPOPchr1747679312-0.7766630.22333704
ENST00000367884ENST00000393331MGST3chr1165621237+SPOPchr1747679312-0.77029380.22970618
ENST00000367884ENST00000347630MGST3chr1165621237+SPOPchr1747679312-0.77029380.22970618
ENST00000367884ENST00000504102MGST3chr1165621237+SPOPchr1747679312-0.419593160.5804069
ENST00000367884ENST00000503676MGST3chr1165621237+SPOPchr1747679312-0.202373330.7976267
ENST00000367883ENST00000393328MGST3chr1165621237+SPOPchr1747679312-0.72858060.2714194
ENST00000367883ENST00000393331MGST3chr1165621237+SPOPchr1747679312-0.725645070.2743549
ENST00000367883ENST00000347630MGST3chr1165621237+SPOPchr1747679312-0.725645070.2743549
ENST00000367883ENST00000504102MGST3chr1165621237+SPOPchr1747679312-0.627279040.37272093
ENST00000367883ENST00000503676MGST3chr1165621237+SPOPchr1747679312-0.449742560.55025744
ENST00000367886ENST00000393328MGST3chr1165621237+SPOPchr1747679312-0.75709950.24290048
ENST00000367886ENST00000393331MGST3chr1165621237+SPOPchr1747679312-0.756623270.24337678
ENST00000367886ENST00000347630MGST3chr1165621237+SPOPchr1747679312-0.756623270.24337678
ENST00000367886ENST00000504102MGST3chr1165621237+SPOPchr1747679312-0.46584790.5341521
ENST00000367886ENST00000503676MGST3chr1165621237+SPOPchr1747679312-0.306672570.6933274

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 MGST3-SPOP

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

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Potential FusionNeoAntigen Information of MGST3-SPOP 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.

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)

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Potential FusionNeoAntigen Information of MGST3-SPOP 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 MGST3-SPOP

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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MGST3-SPOP

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

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Vaccine Design for the FusionNeoAntigens of MGST3-SPOP

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

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 MGST3-SPOP

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

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Potential target of CAR-T therapy development for MGST3-SPOP

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 MGST3-SPOP

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 MGST3-SPOP

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