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Fusion Protein:VPS53-NXN

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: VPS53-NXN
	FusionPDB ID: 98486
	FusionGDB2.0 ID: 98486
		Hgene	Tgene
	Gene symbol	VPS53	NXN
	Gene ID	55275	64359
	Gene name	VPS53 subunit of GARP complex	nucleoredoxin
	Synonyms	HCCS1\|PCH2E\|hVps53L\|pp13624	NRX\|RRS2\|TRG-4
	Cytomap	17p13.3	17p13.3
	Type of gene	protein-coding	protein-coding
	Description	vacuolar protein sorting-associated protein 53 homologVPS53, GARP complex subunit	nucleoredoxinnucleoredoxin 1
	Modification date	20200313	20200327
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000291074, ENST00000401468, ENST00000437048, ENST00000571805, ENST00000574029, ENST00000446250, ENST00000576149,	ENST00000537628, ENST00000575801, ENST00000577098, ENST00000538650, ENST00000336868,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	18 X 15 X 14=3780	17 X 15 X 5=1275
	# samples	24	20
	** MAII score	log2(24/3780*10)=-3.97727992349992 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(20/1275*10)=-2.6724253419715 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: VPS53 [Title/Abstract] AND NXN [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: VPS53 [Title/Abstract] AND NXN [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NXN(722678)-VPS53(465985), # samples:1 NXN(722679)-VPS53(465985), # samples:1 VPS53(613773)-NXN(729318), # samples:1
Anticipated loss of major functional domain due to fusion event.	NXN-VPS53 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. NXN-VPS53 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. VPS53-NXN 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. VPS53-NXN 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. NXN-VPS53 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. NXN-VPS53 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:722678/chr17:465985)
- 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.

Retention 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.

Fusion gene breakpoints across VPS53 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across NXN (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000437048	VPS53	chr17	613773	-	ENST00000336868	NXN	chr17	729318	-	2899	315	147	1262	371
ENST00000574029	VPS53	chr17	613773	-	ENST00000336868	NXN	chr17	729318	-	2873	289	121	1236	371
ENST00000291074	VPS53	chr17	613773	-	ENST00000336868	NXN	chr17	729318	-	2886	302	134	1249	371
ENST00000571805	VPS53	chr17	613773	-	ENST00000336868	NXN	chr17	729318	-	2889	305	137	1252	371
ENST00000401468	VPS53	chr17	613773	-	ENST00000336868	NXN	chr17	729318	-	2752	168	0	1115	371

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000437048	ENST00000336868	VPS53	chr17	613773	-	NXN	chr17	729318	-	0.003926317	0.9960737
ENST00000574029	ENST00000336868	VPS53	chr17	613773	-	NXN	chr17	729318	-	0.003762538	0.9962374
ENST00000291074	ENST00000336868	VPS53	chr17	613773	-	NXN	chr17	729318	-	0.003943762	0.9960562
ENST00000571805	ENST00000336868	VPS53	chr17	613773	-	NXN	chr17	729318	-	0.003911946	0.996088
ENST00000401468	ENST00000336868	VPS53	chr17	613773	-	NXN	chr17	729318	-	0.003741521	0.9962585

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 VPS53-NXN

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
VPS53	chr17	613773	NXN	chr17	729318	168	55	NAVEYINTLFPTEQLKLWNKYRISNI
VPS53	chr17	613773	NXN	chr17	729318	289	55	NAVEYINTLFPTEQLKLWNKYRISNI
VPS53	chr17	613773	NXN	chr17	729318	302	55	NAVEYINTLFPTEQLKLWNKYRISNI
VPS53	chr17	613773	NXN	chr17	729318	305	55	NAVEYINTLFPTEQLKLWNKYRISNI
VPS53	chr17	613773	NXN	chr17	729318	315	55	NAVEYINTLFPTEQLKLWNKYRISNI

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Potential FusionNeoAntigen Information of VPS53-NXN in HLA I

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.

VPS53-NXN_613773_729318.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:03	FPTEQLKL	0.9765	0.7844	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:02	FPTEQLKL	0.8721	0.7381	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:04	FPTEQLKL	0.8721	0.7381	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:01	FPTEQLKLW	0.9956	0.7713	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:05	FPTEQLKLW	0.9944	0.5303	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:08	FPTEQLKLW	0.9882	0.7469	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B58:02	FPTEQLKLW	0.9538	0.8572	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:01	EQLKLWNKY	0.9495	0.5657	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:02	EQLKLWNKY	0.9381	0.7115	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A30:08	TLFPTEQLK	0.8376	0.6835	7	16
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B44:03	TEQLKLWNKY	0.9997	0.8152	11	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:22	TLFPTEQLKL	0.9882	0.6587	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:01	TEQLKLWNKY	0.9812	0.6918	11	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:27	TLFPTEQLKL	0.9788	0.6902	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:11	TLFPTEQLKL	0.9674	0.6756	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:60	TLFPTEQLKL	0.9665	0.6221	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:67	TLFPTEQLKL	0.966	0.6371	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:30	TLFPTEQLKL	0.966	0.6371	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:24	TLFPTEQLKL	0.966	0.6371	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:04	TLFPTEQLKL	0.9584	0.6958	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:38	TLFPTEQLKL	0.9541	0.7001	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:16	TLFPTEQLKL	0.9501	0.502	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B53:01	LFPTEQLKLW	0.9168	0.5273	8	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:35	TLFPTEQLKL	0.8778	0.6739	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:19	TLFPTEQLKL	0.8312	0.5497	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:29	TLFPTEQLKL	0.7977	0.6418	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:20	TLFPTEQLKL	0.7945	0.6407	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B57:01	TLFPTEQLKLW	0.9999	0.9818	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B58:02	TLFPTEQLKLW	0.9996	0.963	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B58:01	TLFPTEQLKLW	0.9988	0.963	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B57:03	TLFPTEQLKLW	0.9985	0.9808	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A32:13	TLFPTEQLKLW	0.9983	0.9751	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B53:01	TLFPTEQLKLW	0.9848	0.5608	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:12	FPTEQLKL	0.8721	0.7381	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B42:01	FPTEQLKL	0.8148	0.5266	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B39:10	FPTEQLKL	0.622	0.8351	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:21	EQLKLWNKY	0.9323	0.6507	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:05	EQLKLWNKY	0.8961	0.5168	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:31	EQLKLWNKY	0.8628	0.5321	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C07:29	LFPTEQLKL	0.5359	0.9626	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C07:13	LFPTEQLKL	0.5093	0.94	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C04:14	LFPTEQLKL	0.463	0.8408	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C04:10	LFPTEQLKL	0.4112	0.8599	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C04:07	LFPTEQLKL	0.3823	0.8791	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C01:30	LFPTEQLKL	0.155	0.96	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C01:17	LFPTEQLKL	0.0897	0.9465	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:01	TLFPTEQLKL	0.966	0.6371	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:13	FPTEQLKL	0.9825	0.7888	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:17	FPTEQLKL	0.9791	0.6162	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:30	FPTEQLKL	0.9791	0.6162	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:24	FPTEQLKL	0.8764	0.7792	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:09	FPTEQLKL	0.8721	0.7381	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B67:01	FPTEQLKL	0.7007	0.6432	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B08:12	FPTEQLKL	0.6528	0.6496	9	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:77	FPTEQLKLW	0.9956	0.7713	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:23	FPTEQLKLW	0.995	0.732	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:17	FPTEQLKLW	0.9949	0.6278	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:30	FPTEQLKLW	0.9949	0.6278	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:13	FPTEQLKLW	0.991	0.6162	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:24	FPTEQLKLW	0.9851	0.7889	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:27	EQLKLWNKY	0.9836	0.5923	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:135	EQLKLWNKY	0.9827	0.5745	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:50	EQLKLWNKY	0.9656	0.6352	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C03:06	NTLFPTEQL	0.9591	0.992	6	15
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:04	EQLKLWNKY	0.9576	0.5982	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:07	EQLKLWNKY	0.9557	0.5384	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:05	EQLKLWNKY	0.9495	0.5657	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:11	EQLKLWNKY	0.9405	0.5377	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:06	EQLKLWNKY	0.9388	0.5572	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:03	EQLKLWNKY	0.9275	0.5506	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A68:02	NTLFPTEQL	0.9138	0.8155	6	15
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:12	EQLKLWNKY	0.9117	0.5527	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:20	EQLKLWNKY	0.8983	0.6406	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:28	EQLKLWNKY	0.8713	0.6436	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:24	EQLKLWNKY	0.8652	0.5713	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B35:20	EQLKLWNKY	0.8384	0.6713	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A69:01	NTLFPTEQL	0.8372	0.8622	6	15
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B48:02	EQLKLWNKY	0.5467	0.5936	12	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C04:04	LFPTEQLKL	0.4995	0.8653	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:07	FPTEQLKLW	0.4299	0.7993	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C18:01	LFPTEQLKL	0.3954	0.8816	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C04:01	LFPTEQLKL	0.3823	0.8791	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A25:01	FPTEQLKLW	0.2791	0.9225	9	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C14:02	LFPTEQLKL	0.1934	0.9574	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C14:03	LFPTEQLKL	0.1934	0.9574	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C01:03	LFPTEQLKL	0.0751	0.9105	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-C01:02	LFPTEQLKL	0.0736	0.9423	8	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B44:26	TEQLKLWNKY	0.9997	0.8152	11	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B44:07	TEQLKLWNKY	0.9997	0.8152	11	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B44:13	TEQLKLWNKY	0.9997	0.8152	11	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:03	TLFPTEQLKL	0.9887	0.8001	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:05	TEQLKLWNKY	0.9812	0.6918	11	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A02:14	TLFPTEQLKL	0.9615	0.6882	7	17
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B18:11	TEQLKLWNKY	0.9594	0.6252	11	21
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B53:02	LFPTEQLKLW	0.9282	0.566	8	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B57:10	TLFPTEQLKLW	0.9999	0.9818	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B57:04	TLFPTEQLKLW	0.9998	0.7823	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:24	TLFPTEQLKLW	0.9997	0.9631	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-A32:01	TLFPTEQLKLW	0.9989	0.9901	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B15:13	TLFPTEQLKLW	0.9984	0.8837	7	18
VPS53-NXN	chr17	613773	chr17	729318	302	HLA-B53:02	TLFPTEQLKLW	0.9729	0.6528	7	18

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Potential FusionNeoAntigen Information of VPS53-NXN in HLA II

VPS53-NXN_613773_729318.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1102	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1102	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1102	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1103	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1103	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1114	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1114	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1116	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1116	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1116	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1120	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1120	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1121	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1121	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1121	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1136	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1136	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1148	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1148	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1155	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1155	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1159	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1159	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1163	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1163	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1165	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1165	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1165	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1168	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1168	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1170	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1170	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1170	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1176	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1176	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1185	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1185	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1186	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1186	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1301	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1301	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1301	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1302	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1302	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1304	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1304	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1304	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1308	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1308	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1309	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1309	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1315	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1315	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1315	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1316	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1316	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1317	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1317	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1317	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1319	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1319	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1319	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1320	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1320	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1322	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1322	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1322	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1323	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1323	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1324	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1324	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1327	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1327	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1329	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1329	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1331	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1331	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1332	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1332	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1334	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1334	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1335	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1335	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1335	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1336	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1336	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1339	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1339	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1343	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1343	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1343	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1348	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1348	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1351	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1351	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1351	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1352	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1352	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1352	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1353	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1353	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1353	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1354	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1354	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1354	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1357	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1357	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1357	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1359	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1359	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1359	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1361	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1361	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1364	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1364	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1364	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1368	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1368	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1368	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1369	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1369	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1369	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1370	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1370	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1371	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1371	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1372	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1372	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1373	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1373	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1374	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1374	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1375	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1375	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1376	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1376	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1378	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1378	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1379	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1379	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1379	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1380	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1380	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1380	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1383	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1383	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1383	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1384	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1384	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1387	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1387	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1387	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1391	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1391	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1391	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1392	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1392	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1392	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1393	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1393	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1393	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1397	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1397	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1398	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1398	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1398	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1399	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1399	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1416	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1416	TEQLKLWNKYRISNI	11	26
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1416	FPTEQLKLWNKYRIS	9	24
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1437	PTEQLKLWNKYRISN	10	25
VPS53-NXN	chr17	613773	chr17	729318	302	DRB1-1437	TEQLKLWNKYRISNI	11	26

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Fusion breakpoint peptide structures of VPS53-NXN

3D 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 name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
6420	NTLFPTEQLKLWNK	VPS53	NXN	chr17	613773	chr17	729318	302

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of VPS53-NXN

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	6420	NTLFPTEQLKLWNK	-7.9962	-8.1096
HLA-B14:02	3BVN	6420	NTLFPTEQLKLWNK	-5.70842	-6.74372
HLA-B52:01	3W39	6420	NTLFPTEQLKLWNK	-6.83737	-6.95077
HLA-B52:01	3W39	6420	NTLFPTEQLKLWNK	-4.4836	-5.5189
HLA-A11:01	4UQ2	6420	NTLFPTEQLKLWNK	-10.0067	-10.1201
HLA-A11:01	4UQ2	6420	NTLFPTEQLKLWNK	-9.03915	-10.0745
HLA-A24:02	5HGA	6420	NTLFPTEQLKLWNK	-6.56204	-6.67544
HLA-A24:02	5HGA	6420	NTLFPTEQLKLWNK	-5.42271	-6.45801
HLA-B44:05	3DX8	6420	NTLFPTEQLKLWNK	-7.85648	-8.89178
HLA-B44:05	3DX8	6420	NTLFPTEQLKLWNK	-5.3978	-5.5112
HLA-A02:01	6TDR	6420	NTLFPTEQLKLWNK	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of VPS53-NXN

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
VPS53-NXN	chr17	613773	chr17	729318	11	21	TEQLKLWNKY	GAGCAACTCAAACTTTGGAACAAATACCGA
VPS53-NXN	chr17	613773	chr17	729318	12	21	EQLKLWNKY	CAACTCAAACTTTGGAACAAATACCGA
VPS53-NXN	chr17	613773	chr17	729318	6	15	NTLFPTEQL	ACCCTGTTCCCAACCGAGCAACTCAAA
VPS53-NXN	chr17	613773	chr17	729318	7	16	TLFPTEQLK	CTGTTCCCAACCGAGCAACTCAAACTT
VPS53-NXN	chr17	613773	chr17	729318	7	17	TLFPTEQLKL	CTGTTCCCAACCGAGCAACTCAAACTTTGG
VPS53-NXN	chr17	613773	chr17	729318	7	18	TLFPTEQLKLW	CTGTTCCCAACCGAGCAACTCAAACTTTGGAAC
VPS53-NXN	chr17	613773	chr17	729318	8	17	LFPTEQLKL	TTCCCAACCGAGCAACTCAAACTTTGG
VPS53-NXN	chr17	613773	chr17	729318	8	18	LFPTEQLKLW	TTCCCAACCGAGCAACTCAAACTTTGGAAC
VPS53-NXN	chr17	613773	chr17	729318	9	17	FPTEQLKL	CCAACCGAGCAACTCAAACTTTGG
VPS53-NXN	chr17	613773	chr17	729318	9	18	FPTEQLKLW	CCAACCGAGCAACTCAAACTTTGGAAC

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
VPS53-NXN	chr17	613773	chr17	729318	10	25	PTEQLKLWNKYRISN	ACCGAGCAACTCAAACTTTGGAACAAATACCGAATTTCCAACATT
VPS53-NXN	chr17	613773	chr17	729318	11	26	TEQLKLWNKYRISNI	GAGCAACTCAAACTTTGGAACAAATACCGAATTTCCAACATTCCA
VPS53-NXN	chr17	613773	chr17	729318	9	24	FPTEQLKLWNKYRIS	CCAACCGAGCAACTCAAACTTTGGAACAAATACCGAATTTCCAAC

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Information of the samples that have these potential fusion neoantigens of VPS53-NXN

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 type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
LUAD	VPS53-NXN	chr17	613773	ENST00000291074	chr17	729318	ENST00000336868	TCGA-50-5066-02A

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Potential target of CAR-T therapy development for VPS53-NXN

Predicted 3D structure. We used RoseTTAFold.

Retention 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'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to VPS53-NXN

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to VPS53-NXN

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)