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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:ATP6V0A1-MSI2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ATP6V0A1-MSI2
FusionPDB ID: 8085
FusionGDB2.0 ID: 8085
HgeneTgene
Gene symbol

ATP6V0A1

MSI2

Gene ID

535

124540

Gene nameATPase H+ transporting V0 subunit a1musashi RNA binding protein 2
SynonymsATP6N1|ATP6N1A|Stv1|VPP1|Vph1|a1MSI2H
Cytomap

17q21.2

17q22

Type of geneprotein-codingprotein-coding
DescriptionV-type proton ATPase 116 kDa subunit a isoform 1V-type proton ATPase 116 kDa subunit aATPase, H+ transporting, lysosomal V0 subunit a1ATPase, H+ transporting, lysosomal non-catalytic accessory protein 1 (110/116kD)H(+)-transporting two-sector ATPase, RNA-binding protein Musashi homolog 2musashi homolog 2musashi-2
Modification date2020032420200313
UniProtAcc

Q93050

Main function of 5'-partner protein: FUNCTION: Required for assembly and activity of the vacuolar ATPase. Potential role in differential targeting and regulation of the enzyme for a specific organelle (By similarity). {ECO:0000250}.

Q96DH6

Main function of 5'-partner protein: FUNCTION: RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system (By similarity). {ECO:0000250}.
Ensembl transtripts involved in fusion geneENST idsENST00000264649, ENST00000343619, 
ENST00000393829, ENST00000537728, 
ENST00000546249, ENST00000585525, 
ENST00000544137, ENST00000587797, 
ENST00000579505, ENST00000284073, 
ENST00000322684, ENST00000416426, 
ENST00000442934, ENST00000579180, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score20 X 17 X 9=306026 X 18 X 10=4680
# samples 2230
** MAII scorelog2(22/3060*10)=-3.79795622405535
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(30/4680*10)=-3.96347412397489
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ATP6V0A1 [Title/Abstract] AND MSI2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ATP6V0A1 [Title/Abstract] AND MSI2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ATP6V0A1(40635149)-MSI2(55607037), # samples:2
Anticipated loss of major functional domain due to fusion event.ATP6V0A1-MSI2 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.
ATP6V0A1-MSI2 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.
ATP6V0A1-MSI2 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.
ATP6V0A1-MSI2 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 button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:40635149/chr17:55607037)
- 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 ATP6V0A1 (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 MSI2 (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)
ENST00000393829ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607037+2217977741612512
ENST00000393829ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607037+6727977741558494
ENST00000393829ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607037+2409977741339421
ENST00000393829ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607037+2339977741558494
ENST00000393829ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607037+2414977741339421
ENST00000546249ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607037+2217977741612512
ENST00000546249ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607037+6727977741558494
ENST00000546249ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607037+2409977741339421
ENST00000546249ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607037+2339977741558494
ENST00000546249ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607037+2414977741339421
ENST00000537728ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607037+2054814401449469
ENST00000537728ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607037+6564814401395451
ENST00000537728ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607037+2246814401176378
ENST00000537728ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607037+2176814401395451
ENST00000537728ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607037+2251814401176378
ENST00000264649ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607037+2202962381597519
ENST00000264649ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607037+6712962381543501
ENST00000264649ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607037+2394962381324428
ENST00000264649ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607037+2324962381543501
ENST00000264649ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607037+2399962381324428
ENST00000585525ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607037+2044804301439469
ENST00000585525ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607037+6554804301385451
ENST00000585525ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607037+2236804301166378
ENST00000585525ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607037+2166804301385451
ENST00000585525ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607037+2241804301166378
ENST00000343619ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607037+2173933301568512
ENST00000343619ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607037+6683933301514494
ENST00000343619ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607037+2365933301295421
ENST00000343619ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607037+2295933301514494
ENST00000343619ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607037+2370933301295421
ENST00000393829ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607036+2217977741612512
ENST00000393829ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607036+6727977741558494
ENST00000393829ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607036+2409977741339421
ENST00000393829ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607036+2339977741558494
ENST00000393829ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607036+2414977741339421
ENST00000546249ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607036+2217977741612512
ENST00000546249ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607036+6727977741558494
ENST00000546249ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607036+2409977741339421
ENST00000546249ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607036+2339977741558494
ENST00000546249ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607036+2414977741339421
ENST00000537728ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607036+2054814401449469
ENST00000537728ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607036+6564814401395451
ENST00000537728ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607036+2246814401176378
ENST00000537728ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607036+2176814401395451
ENST00000537728ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607036+2251814401176378
ENST00000264649ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607036+2202962381597519
ENST00000264649ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607036+6712962381543501
ENST00000264649ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607036+2394962381324428
ENST00000264649ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607036+2324962381543501
ENST00000264649ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607036+2399962381324428
ENST00000585525ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607036+2044804301439469
ENST00000585525ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607036+6554804301385451
ENST00000585525ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607036+2236804301166378
ENST00000585525ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607036+2166804301385451
ENST00000585525ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607036+2241804301166378
ENST00000343619ATP6V0A1chr1740635149+ENST00000416426MSI2chr1755607036+2173933301568512
ENST00000343619ATP6V0A1chr1740635149+ENST00000284073MSI2chr1755607036+6683933301514494
ENST00000343619ATP6V0A1chr1740635149+ENST00000322684MSI2chr1755607036+2365933301295421
ENST00000343619ATP6V0A1chr1740635149+ENST00000442934MSI2chr1755607036+2295933301514494
ENST00000343619ATP6V0A1chr1740635149+ENST00000579180MSI2chr1755607036+2370933301295421

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
ENST00000393829ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607037+0.0005120910.9994879
ENST00000393829ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001431610.9998568
ENST00000393829ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607037+0.0006781790.9993218
ENST00000393829ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607037+0.0004145880.99958545
ENST00000393829ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607037+0.0006729740.99932706
ENST00000546249ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607037+0.0005120910.9994879
ENST00000546249ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001431610.9998568
ENST00000546249ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607037+0.0006781790.9993218
ENST00000546249ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607037+0.0004145880.99958545
ENST00000546249ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607037+0.0006729740.99932706
ENST00000537728ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001947620.9998053
ENST00000537728ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607037+3.93E-050.99996066
ENST00000537728ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001323140.9998677
ENST00000537728ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001300490.99986994
ENST00000537728ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001294860.99987054
ENST00000264649ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607037+0.0003976440.9996024
ENST00000264649ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607037+9.12E-050.9999088
ENST00000264649ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607037+0.0004626340.99953735
ENST00000264649ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607037+0.000322930.99967706
ENST00000264649ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607037+0.0004592560.9995408
ENST00000585525ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001946680.9998054
ENST00000585525ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607037+3.91E-050.9999609
ENST00000585525ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001338410.9998661
ENST00000585525ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001287060.99987125
ENST00000585525ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001308070.9998692
ENST00000343619ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607037+0.0005135030.99948645
ENST00000343619ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607037+0.0001403510.9998596
ENST00000343619ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607037+0.0006693460.99933064
ENST00000343619ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607037+0.0004096690.99959034
ENST00000343619ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607037+0.000663830.9993362
ENST00000393829ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607036+0.0005120910.9994879
ENST00000393829ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001431610.9998568
ENST00000393829ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607036+0.0006781790.9993218
ENST00000393829ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607036+0.0004145880.99958545
ENST00000393829ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607036+0.0006729740.99932706
ENST00000546249ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607036+0.0005120910.9994879
ENST00000546249ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001431610.9998568
ENST00000546249ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607036+0.0006781790.9993218
ENST00000546249ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607036+0.0004145880.99958545
ENST00000546249ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607036+0.0006729740.99932706
ENST00000537728ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001947620.9998053
ENST00000537728ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607036+3.93E-050.99996066
ENST00000537728ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001323140.9998677
ENST00000537728ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001300490.99986994
ENST00000537728ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001294860.99987054
ENST00000264649ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607036+0.0003976440.9996024
ENST00000264649ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607036+9.12E-050.9999088
ENST00000264649ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607036+0.0004626340.99953735
ENST00000264649ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607036+0.000322930.99967706
ENST00000264649ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607036+0.0004592560.9995408
ENST00000585525ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001946680.9998054
ENST00000585525ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607036+3.91E-050.9999609
ENST00000585525ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001338410.9998661
ENST00000585525ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001287060.99987125
ENST00000585525ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001308070.9998692
ENST00000343619ENST00000416426ATP6V0A1chr1740635149+MSI2chr1755607036+0.0005135030.99948645
ENST00000343619ENST00000284073ATP6V0A1chr1740635149+MSI2chr1755607036+0.0001403510.9998596
ENST00000343619ENST00000322684ATP6V0A1chr1740635149+MSI2chr1755607036+0.0006693460.99933064
ENST00000343619ENST00000442934ATP6V0A1chr1740635149+MSI2chr1755607036+0.0004096690.99959034
ENST00000343619ENST00000579180ATP6V0A1chr1740635149+MSI2chr1755607036+0.000663830.9993362

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 ATP6V0A1-MSI2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ATP6V0A1chr1740635149MSI2chr1755607036804258ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607036814258ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607036933301ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607036962308ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607036977301ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607037804258ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607037814258ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607037933301ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607037962308ASGVNTRIDDLQMVEDAMLMFDKTTN
ATP6V0A1chr1740635149MSI2chr1755607037977301ASGVNTRIDDLQMVEDAMLMFDKTTN

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Potential FusionNeoAntigen Information of ATP6V0A1-MSI2 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.
ATP6V0A1-MSI2_40635149_55607036.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)
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B27:07TRIDDLQMV0.99940.6943514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B27:04TRIDDLQMV0.99930.7115514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B39:06TRIDDLQMV0.99890.8396514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B39:24TRIDDLQMV0.99850.6203514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B39:01TRIDDLQMV0.99780.907514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B38:02TRIDDLQMV0.99690.964514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B35:08MVEDAMLMF0.96810.871221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B35:01MVEDAMLMF0.9530.90361221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B48:01LQMVEDAML0.95190.58921019
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B13:01LQMVEDAML0.58890.98951019
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C05:09RIDDLQMV10.9751614
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B27:14TRIDDLQMV0.99930.7456514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C05:09MVEDAMLMF0.99740.96111221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B39:12TRIDDLQMV0.99730.9103514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B73:01TRIDDLQMV0.99490.8001514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:05TRIDDLQMV0.99310.9757514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:95TRIDDLQMV0.98190.8375514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:27TRIDDLQMV0.98170.9727514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:13TRIDDLQMV0.97770.9457514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:29TRIDDLQMV0.96380.954514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B15:31MVEDAMLMF0.95940.87591221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B15:21MVEDAMLMF0.95940.95341221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B15:21QMVEDAMLM0.87980.97191120
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:19TRIDDLQMV0.87430.8806514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:80TRIDDLQMV0.84890.9717514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:67TRIDDLQMV0.84890.9717514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:10TRIDDLQMV0.83750.98514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C03:14MVEDAMLMF0.7830.98011221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C12:16TRIDDLQMV0.02390.9703514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C05:01RIDDLQMV10.9751614
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C04:03RIDDLQMV10.8873614
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B27:09TRIDDLQMV0.99940.7917514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B27:06TRIDDLQMV0.99930.778514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B27:08TRIDDLQMV0.99930.6823514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B39:31TRIDDLQMV0.99780.9073514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C05:01MVEDAMLMF0.99740.96111221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C04:03MVEDAMLMF0.99730.76441221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:01TRIDDLQMV0.98220.8287514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C06:08TRIDDLQMV0.97630.9895514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C03:02MVEDAMLMF0.96050.97461221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B35:77MVEDAMLMF0.9530.90361221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B35:23MVEDAMLMF0.95160.90031221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B15:13MVEDAMLMF0.8880.77091221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-A25:01MVEDAMLMF0.87580.82891221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C06:06TRIDDLQMV0.85670.9909514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:02TRIDDLQMV0.84890.9717514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B15:73LQMVEDAML0.80990.78821019
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:04TRIDDLQMV0.80320.9537514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B15:30LQMVEDAML0.70930.80371019
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B57:02MVEDAMLMF0.67650.82141221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B15:08MVEDAMLMF0.6670.88061221
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C07:22TRIDDLQMV0.66540.7946514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B40:21LQMVEDAML0.64180.53671019
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C06:17TRIDDLQMV0.09950.9952514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-C06:02TRIDDLQMV0.09950.9952514
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-B40:21QMVEDAMLM0.05140.63581120
ATP6V0A1-MSI2chr1740635149chr1755607036962HLA-A69:01NTRIDDLQMV0.90730.6101414

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Potential FusionNeoAntigen Information of ATP6V0A1-MSI2 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 ATP6V0A1-MSI2

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
7927RIDDLQMVEDAMLMATP6V0A1MSI2chr1740635149chr1755607036962

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ATP6V0A1-MSI2

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-B14:023BVN7927RIDDLQMVEDAMLM-7.9962-8.1096
HLA-B14:023BVN7927RIDDLQMVEDAMLM-5.70842-6.74372
HLA-B52:013W397927RIDDLQMVEDAMLM-6.83737-6.95077
HLA-B52:013W397927RIDDLQMVEDAMLM-4.4836-5.5189
HLA-A11:014UQ27927RIDDLQMVEDAMLM-10.0067-10.1201
HLA-A11:014UQ27927RIDDLQMVEDAMLM-9.03915-10.0745
HLA-A24:025HGA7927RIDDLQMVEDAMLM-6.56204-6.67544
HLA-A24:025HGA7927RIDDLQMVEDAMLM-5.42271-6.45801
HLA-B44:053DX87927RIDDLQMVEDAMLM-7.85648-8.89178
HLA-B44:053DX87927RIDDLQMVEDAMLM-5.3978-5.5112
HLA-A02:016TDR7927RIDDLQMVEDAMLM-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ATP6V0A1-MSI2

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
ATP6V0A1-MSI2chr1740635149chr17556070361019LQMVEDAMLCTCCAAATGGTGGAAGATGCAATGCTG
ATP6V0A1-MSI2chr1740635149chr17556070361120QMVEDAMLMCAAATGGTGGAAGATGCAATGCTGATG
ATP6V0A1-MSI2chr1740635149chr17556070361221MVEDAMLMFATGGTGGAAGATGCAATGCTGATGTTT
ATP6V0A1-MSI2chr1740635149chr1755607036414NTRIDDLQMVAATACCAGGATTGATGATCTCCAAATGGTG
ATP6V0A1-MSI2chr1740635149chr1755607036514TRIDDLQMVACCAGGATTGATGATCTCCAAATGGTG
ATP6V0A1-MSI2chr1740635149chr1755607036614RIDDLQMVAGGATTGATGATCTCCAAATGGTG

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 ATP6V0A1-MSI2

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
BRCAATP6V0A1-MSI2chr1740635149ENST00000264649chr1755607036ENST00000284073TCGA-EW-A1J1

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Potential target of CAR-T therapy development for ATP6V0A1-MSI2

check button Predicted 3D structure. We used RoseTTAFold.
50_ATP6V0A1-MSI2_6affd_pred.pdb


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
ATP6V0A1chr1740635149ENST00000264649MSI2chr1755607036ENST00000284073
ATP6V0A1chr1740635149ENST00000264649MSI2chr1755607036ENST00000322684
ATP6V0A1chr1740635149ENST00000264649MSI2chr1755607036ENST00000416426
ATP6V0A1chr1740635149ENST00000343619MSI2chr1755607036ENST00000284073
ATP6V0A1chr1740635149ENST00000343619MSI2chr1755607036ENST00000322684
ATP6V0A1chr1740635149ENST00000343619MSI2chr1755607036ENST00000416426
ATP6V0A1chr1740635149ENST00000537728MSI2chr1755607036ENST00000284073
ATP6V0A1chr1740635149ENST00000537728MSI2chr1755607036ENST00000322684
ATP6V0A1chr1740635149ENST00000537728MSI2chr1755607036ENST00000416426

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Related Drugs to ATP6V0A1-MSI2

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 ATP6V0A1-MSI2

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