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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:VMP1-BCAS3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: VMP1-BCAS3
FusionPDB ID: 98194
FusionGDB2.0 ID: 98194
HgeneTgene
Gene symbol

VMP1

BCAS3

Gene ID

81671

54828

Gene namevacuole membrane protein 1BCAS3 microtubule associated cell migration factor
SynonymsEPG3|TANGO5|TMEM49GAOB1|MAAB
Cytomap

17q23.1

17q23.2

Type of geneprotein-codingprotein-coding
Descriptionvacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homologbreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1
Modification date2020032720200313
UniProtAcc.

Q9H6U6

Main function of 5'-partner protein: FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.
Ensembl transtripts involved in fusion geneENST idsENST00000262291, ENST00000536180, 
ENST00000537567, ENST00000539763, 
ENST00000545362, ENST00000588617, 
ENST00000585812, ENST00000390652, 
ENST00000407086, ENST00000408905, 
ENST00000585744, ENST00000588462, 
ENST00000588874, ENST00000589222, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score34 X 17 X 12=693645 X 32 X 19=27360
# samples 3853
** MAII scorelog2(38/6936*10)=-4.19003257489089
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(53/27360*10)=-5.6899320603227
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: VMP1 [Title/Abstract] AND BCAS3 [Title/Abstract] AND fusion [Title/Abstract]

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing (pmid: 26040699)
Fusion neoantigen context

PubMed: VMP1 [Title/Abstract] AND BCAS3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BCAS3(58988063)-VMP1(57895073), # samples:5
VMP1(57842499)-BCAS3(59001768), # samples:3
Anticipated loss of major functional domain due to fusion event.BCAS3-VMP1 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.
BCAS3-VMP1 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.
VMP1-BCAS3 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.
VMP1-BCAS3 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.
BCAS3-VMP1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
BCAS3-VMP1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneBCAS3

GO:0043085

positive regulation of catalytic activity

17505058

TgeneBCAS3

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

TgeneBCAS3

GO:0071391

cellular response to estrogen stimulus

17505058



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/chr17:58988063/chr17:57895073)
- 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 VMP1 (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 BCAS3 (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)
ENST00000262291VMP1chr1757842499+ENST00000589222BCAS3chr1759001768+35048922532685810
ENST00000262291VMP1chr1757842499+ENST00000407086BCAS3chr1759001768+33478922532640795
ENST00000262291VMP1chr1757842499+ENST00000390652BCAS3chr1759001768+33998922532685810
ENST00000262291VMP1chr1757842499+ENST00000408905BCAS3chr1759001768+34138922532706817
ENST00000262291VMP1chr1757842499+ENST00000588462BCAS3chr1759001768+34588922532751832
ENST00000262291VMP1chr1757842499+ENST00000585744BCAS3chr1759001768+26868922532685811
ENST00000262291VMP1chr1757842499+ENST00000588874BCAS3chr1759001768+33468922532640795
ENST00000537567VMP1chr1757842499+ENST00000589222BCAS3chr1759001768+31195073272300657
ENST00000537567VMP1chr1757842499+ENST00000407086BCAS3chr1759001768+29625073272255642
ENST00000537567VMP1chr1757842499+ENST00000390652BCAS3chr1759001768+30145073272300657
ENST00000537567VMP1chr1757842499+ENST00000408905BCAS3chr1759001768+30285073272321664
ENST00000537567VMP1chr1757842499+ENST00000588462BCAS3chr1759001768+30735073272366679
ENST00000537567VMP1chr1757842499+ENST00000585744BCAS3chr1759001768+23015073272300657
ENST00000537567VMP1chr1757842499+ENST00000588874BCAS3chr1759001768+29615073272255642
ENST00000539763VMP1chr1757842499+ENST00000589222BCAS3chr1759001768+31835712382364708
ENST00000539763VMP1chr1757842499+ENST00000407086BCAS3chr1759001768+30265712382319693
ENST00000539763VMP1chr1757842499+ENST00000390652BCAS3chr1759001768+30785712382364708
ENST00000539763VMP1chr1757842499+ENST00000408905BCAS3chr1759001768+30925712382385715
ENST00000539763VMP1chr1757842499+ENST00000588462BCAS3chr1759001768+31375712382430730
ENST00000539763VMP1chr1757842499+ENST00000585744BCAS3chr1759001768+23655712382364709
ENST00000539763VMP1chr1757842499+ENST00000588874BCAS3chr1759001768+30255712382319693
ENST00000536180VMP1chr1757842499+ENST00000589222BCAS3chr1759001768+32136013102394694
ENST00000536180VMP1chr1757842499+ENST00000407086BCAS3chr1759001768+30566013102349679
ENST00000536180VMP1chr1757842499+ENST00000390652BCAS3chr1759001768+31086013102394694
ENST00000536180VMP1chr1757842499+ENST00000408905BCAS3chr1759001768+31226013102415701
ENST00000536180VMP1chr1757842499+ENST00000588462BCAS3chr1759001768+31676013102460716
ENST00000536180VMP1chr1757842499+ENST00000585744BCAS3chr1759001768+23956013102394695
ENST00000536180VMP1chr1757842499+ENST00000588874BCAS3chr1759001768+30556013102349679

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
ENST00000262291ENST00000589222VMP1chr1757842499+BCAS3chr1759001768+0.0037852110.9962148
ENST00000262291ENST00000407086VMP1chr1757842499+BCAS3chr1759001768+0.0049857170.99501425
ENST00000262291ENST00000390652VMP1chr1757842499+BCAS3chr1759001768+0.0035932060.99640673
ENST00000262291ENST00000408905VMP1chr1757842499+BCAS3chr1759001768+0.0040427580.9959572
ENST00000262291ENST00000588462VMP1chr1757842499+BCAS3chr1759001768+0.0029645180.9970355
ENST00000262291ENST00000585744VMP1chr1757842499+BCAS3chr1759001768+0.0052393210.9947607
ENST00000262291ENST00000588874VMP1chr1757842499+BCAS3chr1759001768+0.0049632350.9950368
ENST00000537567ENST00000589222VMP1chr1757842499+BCAS3chr1759001768+0.0058256790.9941743
ENST00000537567ENST00000407086VMP1chr1757842499+BCAS3chr1759001768+0.0087905840.9912094
ENST00000537567ENST00000390652VMP1chr1757842499+BCAS3chr1759001768+0.0097215650.9902784
ENST00000537567ENST00000408905VMP1chr1757842499+BCAS3chr1759001768+0.007098330.9929016
ENST00000537567ENST00000588462VMP1chr1757842499+BCAS3chr1759001768+0.0081631410.99183685
ENST00000537567ENST00000585744VMP1chr1757842499+BCAS3chr1759001768+0.0134466960.9865534
ENST00000537567ENST00000588874VMP1chr1757842499+BCAS3chr1759001768+0.008751310.9912487
ENST00000539763ENST00000589222VMP1chr1757842499+BCAS3chr1759001768+0.0130485310.9869515
ENST00000539763ENST00000407086VMP1chr1757842499+BCAS3chr1759001768+0.0177294720.98227054
ENST00000539763ENST00000390652VMP1chr1757842499+BCAS3chr1759001768+0.0130438270.9869561
ENST00000539763ENST00000408905VMP1chr1757842499+BCAS3chr1759001768+0.0149628980.985037
ENST00000539763ENST00000588462VMP1chr1757842499+BCAS3chr1759001768+0.0119398150.9880602
ENST00000539763ENST00000585744VMP1chr1757842499+BCAS3chr1759001768+0.0153858940.98461413
ENST00000539763ENST00000588874VMP1chr1757842499+BCAS3chr1759001768+0.0177024880.98229754
ENST00000536180ENST00000589222VMP1chr1757842499+BCAS3chr1759001768+0.0081608020.99183923
ENST00000536180ENST00000407086VMP1chr1757842499+BCAS3chr1759001768+0.0119056950.9880943
ENST00000536180ENST00000390652VMP1chr1757842499+BCAS3chr1759001768+0.0108961940.9891038
ENST00000536180ENST00000408905VMP1chr1757842499+BCAS3chr1759001768+0.009756750.99024326
ENST00000536180ENST00000588462VMP1chr1757842499+BCAS3chr1759001768+0.0088976050.99110234
ENST00000536180ENST00000585744VMP1chr1757842499+BCAS3chr1759001768+0.014513670.98548627
ENST00000536180ENST00000588874VMP1chr1757842499+BCAS3chr1759001768+0.0118958720.98810416

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 VMP1-BCAS3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
VMP1chr1757842499BCAS3chr175900176850760SIISKVRIEACMWVLVSEDSDSDGIV
VMP1chr1757842499BCAS3chr1759001768571111SIISKVRIEACMWVLVSEDSDSDGIV
VMP1chr1757842499BCAS3chr175900176860197SIISKVRIEACMWVLVSEDSDSDGIV
VMP1chr1757842499BCAS3chr1759001768892213SIISKVRIEACMWVLVSEDSDSDGIV

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Potential FusionNeoAntigen Information of VMP1-BCAS3 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.
VMP1-BCAS3_57842499_59001768.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)
VMP1-BCAS3chr1757842499chr1759001768892HLA-B27:07VRIEACMWVL0.99930.7391515
VMP1-BCAS3chr1757842499chr1759001768892HLA-B27:06VRIEACMWVL0.99960.9234515
VMP1-BCAS3chr1757842499chr1759001768892HLA-B27:08VRIEACMWVL0.99960.8518515
VMP1-BCAS3chr1757842499chr1759001768892HLA-B27:09VRIEACMWVL0.99930.8715515

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Potential FusionNeoAntigen Information of VMP1-BCAS3 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 VMP1-BCAS3

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
7929RIEACMWVLVSEDSVMP1BCAS3chr1757842499chr1759001768892

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of VMP1-BCAS3

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-B14:023BVN7929RIEACMWVLVSEDS-7.9962-8.1096
HLA-B14:023BVN7929RIEACMWVLVSEDS-5.70842-6.74372
HLA-B52:013W397929RIEACMWVLVSEDS-6.83737-6.95077
HLA-B52:013W397929RIEACMWVLVSEDS-4.4836-5.5189
HLA-A11:014UQ27929RIEACMWVLVSEDS-10.0067-10.1201
HLA-A11:014UQ27929RIEACMWVLVSEDS-9.03915-10.0745
HLA-A24:025HGA7929RIEACMWVLVSEDS-6.56204-6.67544
HLA-A24:025HGA7929RIEACMWVLVSEDS-5.42271-6.45801
HLA-B44:053DX87929RIEACMWVLVSEDS-7.85648-8.89178
HLA-B44:053DX87929RIEACMWVLVSEDS-5.3978-5.5112
HLA-A02:016TDR7929RIEACMWVLVSEDS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of VMP1-BCAS3

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
VMP1-BCAS3chr1757842499chr1759001768515VRIEACMWVLGTTAGGATTGAAGCCTGCATGTGGGTGCTT

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 VMP1-BCAS3

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
UCECVMP1-BCAS3chr1757842499ENST00000262291chr1759001768ENST00000390652TCGA-EY-A4KR-01A

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Potential target of CAR-T therapy development for VMP1-BCAS3

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
HgeneVMP1chr17:57842499chr17:59001768ENST00000262291+612110_130194407.0TransmembraneHelical
HgeneVMP1chr17:57842499chr17:59001768ENST00000262291+61244_64194407.0TransmembraneHelical
HgeneVMP1chr17:57842499chr17:59001768ENST00000262291+61278_98194407.0TransmembraneHelical

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 VMP1-BCAS3

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 VMP1-BCAS3

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