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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:GMDS-VAPB

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: GMDS-VAPB
FusionPDB ID: 33475
FusionGDB2.0 ID: 33475
HgeneTgene
Gene symbol

GMDS

VAPB

Gene ID

2762

9217

Gene nameGDP-mannose 4,6-dehydrataseVAMP associated protein B and C
SynonymsGMD|SDR3E1ALS8|VAMP-B|VAP-B
Cytomap

6p25.3

20q13.32

Type of geneprotein-codingprotein-coding
DescriptionGDP-mannose 4,6 dehydrataseGDP-D-mannose dehydrataseshort chain dehydrogenase/reductase family 3E, member 1vesicle-associated membrane protein-associated protein B/CVAMP (vesicle-associated membrane protein)-associated protein B and CVAMP-associated 33 kDa protein
Modification date2020031320200313
UniProtAcc

O60547

Main function of 5'-partner protein: FUNCTION: Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose. {ECO:0000269|PubMed:9525924}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000380815, ENST00000530927, 
ENST00000467288, 		ENST00000265619, 
ENST00000395802, ENST00000475243, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score28 X 19 X 15=798011 X 11 X 6=726
# samples 3212
** MAII scorelog2(32/7980*10)=-4.64024493622235
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/726*10)=-2.59693514238723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: GMDS [Title/Abstract] AND VAPB [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: GMDS [Title/Abstract] AND VAPB [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GMDS(1930337)-VAPB(57019133), # samples:3
Anticipated loss of major functional domain due to fusion event.GMDS-VAPB 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.
GMDS-VAPB 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.
GMDS-VAPB seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
GMDS-VAPB seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
GMDS-VAPB seems lost the major protein functional domain in Tgene partner, which is a cell metabolism 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
HgeneGMDS

GO:0019673

GDP-mannose metabolic process

9525924

HgeneGMDS

GO:0042351

'de novo' GDP-L-fucose biosynthetic process

9525924

TgeneVAPB

GO:0019048

modulation by virus of host morphology or physiology

16227268

TgeneVAPB

GO:0036498

IRE1-mediated unfolded protein response

20940299



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/chr6:1930337/chr20:57019133)
- 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 GMDS (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 VAPB (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)
ENST00000530927GMDSchr61960101-ENST00000475243VAPBchr2057019133+762660148689213
ENST00000380815GMDSchr61960101-ENST00000475243VAPBchr2057019133+7938913421001319

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
ENST00000530927ENST00000475243GMDSchr61960101-VAPBchr2057019133+0.0008677770.9991322
ENST00000380815ENST00000475243GMDSchr61960101-VAPBchr2057019133+0.0006482070.9993518

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 GMDS-VAPB

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
GMDSchr61960101VAPBchr2057019133601184VNGILFNHESPRRGRRWTADEEDSAE
GMDSchr61960101VAPBchr2057019133913290VNGILFNHESPRRGRRWTADEEDSAE

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Potential FusionNeoAntigen Information of GMDS-VAPB 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.
GMDS-VAPB_1960101_57019133.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)
GMDS-VAPBchr61960101chr2057019133913HLA-B58:02ESPRRGRRW0.68510.5476817
GMDS-VAPBchr61960101chr2057019133913HLA-B07:02SPRRGRRWTA0.99390.5175919
GMDS-VAPBchr61960101chr2057019133913HLA-B44:03HESPRRGRRW0.98010.7261717
GMDS-VAPBchr61960101chr2057019133913HLA-B07:04SPRRGRRWTA0.90180.5086919
GMDS-VAPBchr61960101chr2057019133913HLA-B58:06ESPRRGRRW0.62580.5837817
GMDS-VAPBchr61960101chr2057019133913HLA-B07:22SPRRGRRWTA0.99390.5175919
GMDS-VAPBchr61960101chr2057019133913HLA-B44:07HESPRRGRRW0.98010.7261717
GMDS-VAPBchr61960101chr2057019133913HLA-B44:26HESPRRGRRW0.98010.7261717
GMDS-VAPBchr61960101chr2057019133913HLA-B44:13HESPRRGRRW0.98010.7261717

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Potential FusionNeoAntigen Information of GMDS-VAPB 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.
GMDS-VAPB_1960101_57019133.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)
GMDS-VAPBchr61960101chr2057019133913DRB1-0303VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-0303NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-0307VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-0324VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-0324NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-0340VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1102VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1107VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1114VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1114NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1116VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1120VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1120NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1121VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1134VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1136VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1148VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1165VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1168VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1168NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1179VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1182VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1186VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1186NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1301VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1302VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1302NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1308VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1309VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1316VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1316NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1317VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1319VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1319NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1320VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1322VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1323VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1323NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1327VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1327NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1329VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1329NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1334VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1334NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1335VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1336VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1339VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1339NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1341VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1341NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1344VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1351VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1352VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1353VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1353NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1359VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1361VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1361NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1364VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1368VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1369VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1370VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1371VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1371NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1372VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1373VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1373NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1374VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1374NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1378VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1379VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1380VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1383VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1384VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1386VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1387VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1391VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1392VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1396VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1396NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1397VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1397NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1398VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1399VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1399NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1402VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1406VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1417VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1419VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1419NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1420VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1421VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1424VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1424NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1429VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1437VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1441VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1446VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1447VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1447NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1452VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1452NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1481VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1483VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1489VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1489NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB1-1494VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1498VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1525VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB1-1525NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB3-0204VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB5-0106VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB5-0106NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB5-0106GILFNHESPRRGRRW217
GMDS-VAPBchr61960101chr2057019133913DRB5-0111VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB5-0111NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB5-0202NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB5-0202VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB5-0203NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB5-0203VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB5-0204VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB5-0204NGILFNHESPRRGRR116
GMDS-VAPBchr61960101chr2057019133913DRB5-0205VNGILFNHESPRRGR015
GMDS-VAPBchr61960101chr2057019133913DRB5-0205NGILFNHESPRRGRR116

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Fusion breakpoint peptide structures of GMDS-VAPB

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
6176NHESPRRGRRWTADGMDSVAPBchr61960101chr2057019133913

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of GMDS-VAPB

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-B14:023BVN6176NHESPRRGRRWTAD-7.9962-8.1096
HLA-B14:023BVN6176NHESPRRGRRWTAD-5.70842-6.74372
HLA-B52:013W396176NHESPRRGRRWTAD-6.83737-6.95077
HLA-B52:013W396176NHESPRRGRRWTAD-4.4836-5.5189
HLA-A11:014UQ26176NHESPRRGRRWTAD-10.0067-10.1201
HLA-A11:014UQ26176NHESPRRGRRWTAD-9.03915-10.0745
HLA-A24:025HGA6176NHESPRRGRRWTAD-6.56204-6.67544
HLA-A24:025HGA6176NHESPRRGRRWTAD-5.42271-6.45801
HLA-B44:053DX86176NHESPRRGRRWTAD-7.85648-8.89178
HLA-B44:053DX86176NHESPRRGRRWTAD-5.3978-5.5112
HLA-A02:016TDR6176NHESPRRGRRWTAD-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of GMDS-VAPB

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
GMDS-VAPBchr61960101chr2057019133717HESPRRGRRWATGAGAGTCCCAGAAGAGGAAGAAGATGGA
GMDS-VAPBchr61960101chr2057019133817ESPRRGRRWAGAGTCCCAGAAGAGGAAGAAGATGGA
GMDS-VAPBchr61960101chr2057019133919SPRRGRRWTAGTCCCAGAAGAGGAAGAAGATGGACTGCGG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
GMDS-VAPBchr61960101chr2057019133015VNGILFNHESPRRGRTGAACGGCATTCTCTTCAATCATGAGAGTCCCAGAAGAGGAAGAA
GMDS-VAPBchr61960101chr2057019133116NGILFNHESPRRGRRACGGCATTCTCTTCAATCATGAGAGTCCCAGAAGAGGAAGAAGAT
GMDS-VAPBchr61960101chr2057019133217GILFNHESPRRGRRWGCATTCTCTTCAATCATGAGAGTCCCAGAAGAGGAAGAAGATGGA

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Information of the samples that have these potential fusion neoantigens of GMDS-VAPB

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
PAADGMDS-VAPBchr61960101ENST00000380815chr2057019133ENST00000475243TCGA-IB-7647

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Potential target of CAR-T therapy development for GMDS-VAPB

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
TgeneVAPBchr6:1960101chr20:57019133ENST0000039580213223_2430100.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneVAPBchr6:1960101chr20:57019133ENST0000047524346223_2430244.0TransmembraneHelical%3B Anchor for type IV membrane protein

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 GMDS-VAPB

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 GMDS-VAPB

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