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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:APPBP2-SEPT9

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: APPBP2-SEPT9
FusionPDB ID: 5661
FusionGDB2.0 ID: 5661
HgeneTgene
Gene symbol

APPBP2

SEPT9

Gene ID

10513

10801

Gene nameamyloid beta precursor protein binding protein 2septin 9
SynonymsAPP-BP2|HS.84084|PAT1AF17q25|MSF|MSF1|NAPB|PNUTL4|SEPT9|SINT1|SeptD1
Cytomap

17q23.2

17q25.3

Type of geneprotein-codingprotein-coding
Descriptionamyloid protein-binding protein 2amyloid beta precursor protein (cytoplasmic tail) binding protein 2protein interacting with APP tail 1septin-9MLL septin-like fusion protein MSF-AOv/Br septinovarian/breast septinseptin D1
Modification date2020031320200328
UniProtAcc

Q92624

Main function of 5'-partner protein: FUNCTION: May play a role in intracellular protein transport. May be involved in the translocation of APP along microtubules toward the cell surface. {ECO:0000269|PubMed:9843960}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000083182, ENST00000592995, 
ENST00000591088, ENST00000592481, 
ENST00000592951, ENST00000427180, 
ENST00000541152, ENST00000585930, 
ENST00000590917, ENST00000592420, 
ENST00000329047, ENST00000423034, 
ENST00000427177, ENST00000427674, 
ENST00000431235, ENST00000449803, 
ENST00000588690, ENST00000590294, 
ENST00000591198, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 9 X 8=93628 X 12 X 9=3024
# samples 1527
** MAII scorelog2(15/936*10)=-2.64154602908752
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(27/3024*10)=-3.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: APPBP2 [Title/Abstract] AND SEPT9 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: APPBP2 [Title/Abstract] AND SEPT9 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)APPBP2(58577760)-SEPT9(75486824), # samples:1
Anticipated loss of major functional domain due to fusion event.APPBP2-SEPT9 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.
APPBP2-SEPT9 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.
APPBP2-SEPT9 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.
APPBP2-SEPT9 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
HgeneAPPBP2

GO:0046907

intracellular transport

9843960



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/chr17:58577760/chr17:75486824)
- 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 APPBP2 (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 SEPT9 (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)
ENST00000083182APPBP2chr1758577760-ENST00000427177SEPT9chr1775486824+2948515601013317
ENST00000083182APPBP2chr1758577760-ENST00000591198SEPT9chr1775486824+1385515601013317
ENST00000083182APPBP2chr1758577760-ENST00000449803SEPT9chr1775486824+2948515601013317
ENST00000083182APPBP2chr1758577760-ENST00000431235SEPT9chr1775486824+2952515601013317
ENST00000083182APPBP2chr1758577760-ENST00000329047SEPT9chr1775486824+2948515601013317
ENST00000083182APPBP2chr1758577760-ENST00000590294SEPT9chr1775486824+1311515601013317
ENST00000083182APPBP2chr1758577760-ENST00000588690SEPT9chr1775486824+2187515601013317
ENST00000083182APPBP2chr1758577760-ENST00000423034SEPT9chr1775486824+2950515601013317
ENST00000083182APPBP2chr1758577760-ENST00000427674SEPT9chr1775486824+2950515601013317

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
ENST00000083182ENST00000427177APPBP2chr1758577760-SEPT9chr1775486824+0.0020515140.99794847
ENST00000083182ENST00000591198APPBP2chr1758577760-SEPT9chr1775486824+0.0020188240.99798125
ENST00000083182ENST00000449803APPBP2chr1758577760-SEPT9chr1775486824+0.0020515140.99794847
ENST00000083182ENST00000431235APPBP2chr1758577760-SEPT9chr1775486824+0.0020428360.9979571
ENST00000083182ENST00000329047APPBP2chr1758577760-SEPT9chr1775486824+0.0020515140.99794847
ENST00000083182ENST00000590294APPBP2chr1758577760-SEPT9chr1775486824+0.0015304240.99846953
ENST00000083182ENST00000588690APPBP2chr1758577760-SEPT9chr1775486824+0.0024448240.9975552
ENST00000083182ENST00000423034APPBP2chr1758577760-SEPT9chr1775486824+0.0020365070.99796355
ENST00000083182ENST00000427674APPBP2chr1758577760-SEPT9chr1775486824+0.0020365070.99796355

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 APPBP2-SEPT9

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
APPBP2chr1758577760SEPT9chr1775486824515151LEVFAKVLRALDKSLRPLDIEFMKRL

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Potential FusionNeoAntigen Information of APPBP2-SEPT9 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.
APPBP2-SEPT9_58577760_75486824.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)
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:60ALDKSLRPL0.96750.5592918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:11ALDKSLRPL0.96660.6316918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:13ALDKSLRPL0.95680.7479918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:27ALDKSLRPL0.95640.6756918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:16ALDKSLRPL0.9560.5215918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:04ALDKSLRPL0.94790.5844918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:38ALDKSLRPL0.93850.7734918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:35ALDKSLRPL0.78140.5923918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B57:01KSLRPLDIEF0.99980.97051222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B58:02KSLRPLDIEF0.99930.92851222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B58:01KSLRPLDIEF0.99860.89151222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B57:03KSLRPLDIEF0.99820.98091222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:16KSLRPLDIEF0.99820.73881222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:17KSLRPLDIEF0.99720.91121222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:01KSLRPLDIEF0.99170.93221222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:25KSLRPLDIEF0.9910.93161222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A32:13KSLRPLDIEF0.90870.89051222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A74:11KVLRALDKSLR0.98650.5316516
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A74:09KVLRALDKSLR0.98650.5316516
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A74:03KVLRALDKSLR0.98650.5316516
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C05:09ALDKSLRPL0.99990.9064918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C08:15ALDKSLRPL0.99990.9691918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A02:07ALDKSLRPL0.96960.5808918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B14:03DKSLRPLDI0.19220.52821120
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C15:06RALDKSLRPL0.99960.9216818
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:07KSLRPLDIEF0.99360.63721222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C01:03ALDKSLRPL0.99990.8655918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C08:02ALDKSLRPL0.99990.9691918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C04:03ALDKSLRPL0.99990.8079918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C05:01ALDKSLRPL0.99990.9064918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B07:13ALDKSLRPL0.55360.8155918
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B57:10KSLRPLDIEF0.99980.97051222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C15:05RALDKSLRPL0.99960.8689818
APPBP2-SEPT9chr1758577760chr1775486824515HLA-C15:02RALDKSLRPL0.99940.8479818
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B58:06KSLRPLDIEF0.99930.7611222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B57:04KSLRPLDIEF0.99920.71511222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B57:02KSLRPLDIEF0.99380.93421222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:35KSLRPLDIEF0.99280.89551222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:39KSLRPLDIEF0.99220.88061222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:125KSLRPLDIEF0.99170.93221222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:33KSLRPLDIEF0.99170.93221222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:34KSLRPLDIEF0.99170.93221222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:27KSLRPLDIEF0.99140.93641222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:135KSLRPLDIEF0.99080.94461222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:24KSLRPLDIEF0.98990.92441222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-B15:50KSLRPLDIEF0.98980.84741222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A32:01KSLRPLDIEF0.97930.83321222
APPBP2-SEPT9chr1758577760chr1775486824515HLA-A74:01KVLRALDKSLR0.98650.5316516

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Potential FusionNeoAntigen Information of APPBP2-SEPT9 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.
APPBP2-SEPT9_58577760_75486824.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)
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0801LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0803LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0805LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0814LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0816LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0818LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0823LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0826LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0827LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0829LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0833LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0835LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0836LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0837LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0838LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0839LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-0840LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1102AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1113AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1116AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1121AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1134AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1134FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1136AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1157AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1165AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1192AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1204AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1204FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1204VFAKVLRALDKSLRP217
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1209AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1209FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1209VFAKVLRALDKSLRP217
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1301AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1303LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1312LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1312EVFAKVLRALDKSLR116
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1313LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1313EVFAKVLRALDKSLR116
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1315AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1317AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1319AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1320AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1321LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1321EVFAKVLRALDKSLR116
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1322AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1327AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1330LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1330EVFAKVLRALDKSLR116
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1335AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1344AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1344FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1349LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1351AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1352AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1353AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1355LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1357AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1359AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1361AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1364AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1366LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1368AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1369AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1371AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1371FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1378AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1379AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1380AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1383AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1386AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1387AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1390LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1391AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1392AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1395LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1398AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1406AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1406FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1412AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1417AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1417FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1420AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1420FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1421AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1429AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1429FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1429VFAKVLRALDKSLRP217
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1430AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1433AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1452AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1452FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1452VFAKVLRALDKSLRP217
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1453LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1463LEVFAKVLRALDKSL015
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1480AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1481AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1483AKVLRALDKSLRPLD419
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1483FAKVLRALDKSLRPL318
APPBP2-SEPT9chr1758577760chr1775486824515DRB1-1485LEVFAKVLRALDKSL015

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Fusion breakpoint peptide structures of APPBP2-SEPT9

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
10098VLRALDKSLRPLDIAPPBP2SEPT9chr1758577760chr1775486824515

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of APPBP2-SEPT9

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-B14:023BVN10098VLRALDKSLRPLDI-7.38756-7.50096
HLA-B14:023BVN10098VLRALDKSLRPLDI-6.17376-7.20906
HLA-B52:013W3910098VLRALDKSLRPLDI-6.82178-6.93518
HLA-B52:013W3910098VLRALDKSLRPLDI-5.12185-6.15715
HLA-A11:014UQ210098VLRALDKSLRPLDI-9.73713-9.85053
HLA-A24:025HGA10098VLRALDKSLRPLDI-6.9463-7.0597
HLA-A24:025HGA10098VLRALDKSLRPLDI-5.98739-7.02269
HLA-B44:053DX810098VLRALDKSLRPLDI-5.60116-6.63646
HLA-B44:053DX810098VLRALDKSLRPLDI-4.76903-4.88243
HLA-B35:011A1N10098VLRALDKSLRPLDI-5.57109-5.68449
HLA-B35:011A1N10098VLRALDKSLRPLDI-3.51702-4.55232

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Vaccine Design for the FusionNeoAntigens of APPBP2-SEPT9

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
APPBP2-SEPT9chr1758577760chr17754868241120DKSLRPLDITAAAAGCCTCAGGCCCCTGGACATCGA
APPBP2-SEPT9chr1758577760chr17754868241222KSLRPLDIEFAAGCCTCAGGCCCCTGGACATCGAGTTTAT
APPBP2-SEPT9chr1758577760chr1775486824516KVLRALDKSLRAGTACTGAGAGCTTTGGATAAAAGCCTCAGGCC
APPBP2-SEPT9chr1758577760chr1775486824818RALDKSLRPLAGCTTTGGATAAAAGCCTCAGGCCCCTGGA
APPBP2-SEPT9chr1758577760chr1775486824918ALDKSLRPLTTTGGATAAAAGCCTCAGGCCCCTGGA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
APPBP2-SEPT9chr1758577760chr1775486824015LEVFAKVLRALDKSLGGAAGTTTTTGCTAAAGTACTGAGAGCTTTGGATAAAAGCCTCAG
APPBP2-SEPT9chr1758577760chr1775486824116EVFAKVLRALDKSLRAGTTTTTGCTAAAGTACTGAGAGCTTTGGATAAAAGCCTCAGGCC
APPBP2-SEPT9chr1758577760chr1775486824217VFAKVLRALDKSLRPTTTTGCTAAAGTACTGAGAGCTTTGGATAAAAGCCTCAGGCCCCT
APPBP2-SEPT9chr1758577760chr1775486824318FAKVLRALDKSLRPLTGCTAAAGTACTGAGAGCTTTGGATAAAAGCCTCAGGCCCCTGGA
APPBP2-SEPT9chr1758577760chr1775486824419AKVLRALDKSLRPLDTAAAGTACTGAGAGCTTTGGATAAAAGCCTCAGGCCCCTGGACAT

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Information of the samples that have these potential fusion neoantigens of APPBP2-SEPT9

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
BRCAAPPBP2-SEPT9chr1758577760ENST00000083182chr1775486824ENST00000329047TCGA-EW-A2FS-01A

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Potential target of CAR-T therapy development for APPBP2-SEPT9

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 APPBP2-SEPT9

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 APPBP2-SEPT9

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