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Fusion Protein:VPS33A-ABCB9

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: VPS33A-ABCB9
	FusionPDB ID: 98375
	FusionGDB2.0 ID: 98375
		Hgene	Tgene
	Gene symbol	VPS33A	ABCB9
	Gene ID	65082	23457
	Gene name	VPS33A core subunit of CORVET and HOPS complexes	ATP binding cassette subfamily B member 9
	Synonyms	MPSPS	EST122234\|TAPL
	Cytomap	12q24.31	12q24.31
	Type of gene	protein-coding	protein-coding
	Description	vacuolar protein sorting-associated protein 33AVPS33A, CORVET/HOPS core subunitvacuolar protein sorting 33 homolog Avacuolar protein sorting 33A	ATP-binding cassette sub-family B member 9ABC transporter 9 proteinATP-binding cassette, sub-family B (MDR/TAP), member 9TAP-like protein
	Modification date	20200313	20200313
	UniProtAcc	.	Q9NP78 Main function of 5'-partner protein: FUNCTION: ATP-dependent low-affinity peptide transporter which translocates a broad spectrum of peptides from the cytosol to the lysosomal lumen. Displays a broad peptide length specificity from 6-mer up to at least 59-mer peptides with an optimum of 23-mers. Favors positively charged, aromatic or hydrophobic residues in the N- and C-terminal positions whereas negatively charged residues as well as asparagine and methionine are not favored. {ECO:0000269\|PubMed:15863492, ECO:0000269\|PubMed:17977821, ECO:0000269\|PubMed:18434309}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000267199, ENST00000451053, ENST00000542310,	ENST00000541983, ENST00000280560, ENST00000344275, ENST00000346530, ENST00000392439, ENST00000442028, ENST00000442833, ENST00000540285, ENST00000542678,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 8 X 5=240	3 X 3 X 3=27
	# samples	8	5
	** MAII score	log2(8/240*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/27*10)=0.888968687611256 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: VPS33A [Title/Abstract] AND ABCB9 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: VPS33A [Title/Abstract] AND ABCB9 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	VPS33A(122734417)-ABCB9(123435112), # samples:2
Anticipated loss of major functional domain due to fusion event.	VPS33A-ABCB9 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. VPS33A-ABCB9 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. VPS33A-ABCB9 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. VPS33A-ABCB9 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)

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
Hgene	VPS33A	GO:0016192	vesicle-mediated transport	15790593
Hgene	VPS33A	GO:0032400	melanosome localization	15790593
Hgene	VPS33A	GO:0032418	lysosome localization	15790593
Tgene	ABCB9	GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	17977821
Tgene	ABCB9	GO:0015833	peptide transport	17977821\|18434309\|22641697

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:122734417/chr12:123435112)
- 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 VPS33A (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 ABCB9 (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)
ENST00000267199	VPS33A	chr12	122734418	-	ENST00000344275	ABCB9	chr12	123435112	-	2420	888	41	2332	763
ENST00000267199	VPS33A	chr12	122734418	-	ENST00000442833	ABCB9	chr12	123435112	-	2613	888	41	2338	765
ENST00000267199	VPS33A	chr12	122734418	-	ENST00000280560	ABCB9	chr12	123435112	-	3505	888	41	2587	848
ENST00000267199	VPS33A	chr12	122734418	-	ENST00000540285	ABCB9	chr12	123435112	-	3316	888	41	2398	785
ENST00000267199	VPS33A	chr12	122734418	-	ENST00000346530	ABCB9	chr12	123435112	-	3376	888	41	2458	805
ENST00000267199	VPS33A	chr12	122734418	-	ENST00000392439	ABCB9	chr12	123435112	-	3500	888	41	2587	848
ENST00000267199	VPS33A	chr12	122734418	-	ENST00000442028	ABCB9	chr12	123435112	-	3508	888	41	2596	851
ENST00000267199	VPS33A	chr12	122734418	-	ENST00000542678	ABCB9	chr12	123435112	-	3499	888	41	2587	848
ENST00000267199	VPS33A	chr12	122734417	-	ENST00000344275	ABCB9	chr12	123435112	-	2420	888	41	2332	763
ENST00000267199	VPS33A	chr12	122734417	-	ENST00000442833	ABCB9	chr12	123435112	-	2613	888	41	2338	765
ENST00000267199	VPS33A	chr12	122734417	-	ENST00000280560	ABCB9	chr12	123435112	-	3505	888	41	2587	848
ENST00000267199	VPS33A	chr12	122734417	-	ENST00000540285	ABCB9	chr12	123435112	-	3316	888	41	2398	785
ENST00000267199	VPS33A	chr12	122734417	-	ENST00000346530	ABCB9	chr12	123435112	-	3376	888	41	2458	805
ENST00000267199	VPS33A	chr12	122734417	-	ENST00000392439	ABCB9	chr12	123435112	-	3500	888	41	2587	848
ENST00000267199	VPS33A	chr12	122734417	-	ENST00000442028	ABCB9	chr12	123435112	-	3508	888	41	2596	851
ENST00000267199	VPS33A	chr12	122734417	-	ENST00000542678	ABCB9	chr12	123435112	-	3499	888	41	2587	848

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
ENST00000267199	ENST00000344275	VPS33A	chr12	122734418	-	ABCB9	chr12	123435112	-	0.008030662	0.9919694
ENST00000267199	ENST00000442833	VPS33A	chr12	122734418	-	ABCB9	chr12	123435112	-	0.005210703	0.99478936
ENST00000267199	ENST00000280560	VPS33A	chr12	122734418	-	ABCB9	chr12	123435112	-	0.004542613	0.9954574
ENST00000267199	ENST00000540285	VPS33A	chr12	122734418	-	ABCB9	chr12	123435112	-	0.006596552	0.9934035
ENST00000267199	ENST00000346530	VPS33A	chr12	122734418	-	ABCB9	chr12	123435112	-	0.005659508	0.9943404
ENST00000267199	ENST00000392439	VPS33A	chr12	122734418	-	ABCB9	chr12	123435112	-	0.004595412	0.9954046
ENST00000267199	ENST00000442028	VPS33A	chr12	122734418	-	ABCB9	chr12	123435112	-	0.004635215	0.9953648
ENST00000267199	ENST00000542678	VPS33A	chr12	122734418	-	ABCB9	chr12	123435112	-	0.004660438	0.9953395
ENST00000267199	ENST00000344275	VPS33A	chr12	122734417	-	ABCB9	chr12	123435112	-	0.008030662	0.9919694
ENST00000267199	ENST00000442833	VPS33A	chr12	122734417	-	ABCB9	chr12	123435112	-	0.005210703	0.99478936
ENST00000267199	ENST00000280560	VPS33A	chr12	122734417	-	ABCB9	chr12	123435112	-	0.004542613	0.9954574
ENST00000267199	ENST00000540285	VPS33A	chr12	122734417	-	ABCB9	chr12	123435112	-	0.006596552	0.9934035
ENST00000267199	ENST00000346530	VPS33A	chr12	122734417	-	ABCB9	chr12	123435112	-	0.005659508	0.9943404
ENST00000267199	ENST00000392439	VPS33A	chr12	122734417	-	ABCB9	chr12	123435112	-	0.004595412	0.9954046
ENST00000267199	ENST00000442028	VPS33A	chr12	122734417	-	ABCB9	chr12	123435112	-	0.004635215	0.9953648
ENST00000267199	ENST00000542678	VPS33A	chr12	122734417	-	ABCB9	chr12	123435112	-	0.004660438	0.9953395

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 VPS33A-ABCB9

+/-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
VPS33A	chr12	122734417	ABCB9	chr12	123435112	888	283	EGLIDEIYGIQNRETFLPYYTGRAID
VPS33A	chr12	122734418	ABCB9	chr12	123435112	888	283	EGLIDEIYGIQNRETFLPYYTGRAID

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Potential FusionNeoAntigen Information of VPS33A-ABCB9 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.

VPS33A-ABCB9_122734417_123435112.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)
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B47:01	RETFLPYY	0.9989	0.5983	12	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B18:01	RETFLPYY	0.9909	0.917	12	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B46:01	YGIQNRETF	0.9735	0.5937	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B35:05	YGIQNRETF	0.9655	0.8454	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:18	NRETFLPYY	0.2173	0.7287	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:01	IQNRETFLPY	0.9998	0.8454	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A24:25	IYGIQNRETF	0.9987	0.596	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A24:20	IYGIQNRETF	0.9983	0.5935	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A24:15	IYGIQNRETF	0.998	0.6079	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A24:31	IYGIQNRETF	0.9977	0.5716	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A24:17	IYGIQNRETF	0.9917	0.6308	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:25	IQNRETFLPY	0.9891	0.836	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A24:14	IYGIQNRETF	0.9684	0.6395	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:03	IQNRETFLPY	0.7583	0.6628	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A26:02	EIYGIQNRETF	0.9997	0.629	5	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A26:15	EIYGIQNRETF	0.9991	0.6576	5	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A26:14	EIYGIQNRETF	0.9991	0.6576	5	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A31:02	RETFLPYYTGR	0.9949	0.7012	12	23
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:19	YGIQNRETF	0.9964	0.9898	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B40:06	RETFLPYYT	0.9926	0.6707	12	21
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C12:12	YGIQNRETF	0.9567	0.9327	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:95	NRETFLPYY	0.9482	0.5805	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:27	NRETFLPYY	0.9225	0.9412	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:14	YGIQNRETF	0.9163	0.9851	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:05	NRETFLPYY	0.8409	0.9483	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:19	NRETFLPYY	0.7851	0.5473	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:67	NRETFLPYY	0.7479	0.9024	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:80	NRETFLPYY	0.7479	0.9024	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:10	NRETFLPYY	0.7257	0.9317	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:46	NRETFLPYY	0.705	0.771	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C12:16	NRETFLPYY	0.0216	0.9542	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A24:02	IYGIQNRETF	0.9983	0.5935	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:07	IQNRETFLPY	0.9982	0.614	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:04	IQNRETFLPY	0.9907	0.8628	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:05	IQNRETFLPY	0.9356	0.8278	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A26:01	EIYGIQNRETF	0.9991	0.6576	5	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A31:01	RETFLPYYTGR	0.9938	0.69	12	23
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B18:11	RETFLPYY	0.9938	0.9216	12	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B18:08	RETFLPYY	0.9911	0.762	12	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B18:05	RETFLPYY	0.9909	0.917	12	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B18:06	RETFLPYY	0.9902	0.9165	12	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:04	YGIQNRETF	0.999	0.9908	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:03	YGIQNRETF	0.999	0.9908	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:02	YGIQNRETF	0.9986	0.9838	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:67	YGIQNRETF	0.998	0.9852	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:17	YGIQNRETF	0.9916	0.9809	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:05	YGIQNRETF	0.9911	0.957	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C12:02	YGIQNRETF	0.9828	0.9783	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:08	YGIQNRETF	0.9781	0.9481	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C16:04	YGIQNRETF	0.975	0.9857	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B35:43	YGIQNRETF	0.9721	0.9504	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B35:17	YGIQNRETF	0.9708	0.9278	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B35:30	YGIQNRETF	0.9708	0.9278	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:01	NRETFLPYY	0.95	0.5472	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C16:01	YGIQNRETF	0.9124	0.9887	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B35:13	YGIQNRETF	0.9121	0.9645	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C03:06	YGIQNRETF	0.7783	0.9908	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B35:24	YGIQNRETF	0.7728	0.9711	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:17	NRETFLPYY	0.7642	0.9621	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:02	NRETFLPYY	0.7479	0.9024	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C07:22	NRETFLPYY	0.6644	0.6686	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C02:02	YGIQNRETF	0.5896	0.9881	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C02:10	YGIQNRETF	0.5896	0.9881	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B07:13	YGIQNRETF	0.2103	0.8567	7	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C06:06	NRETFLPYY	0.0103	0.9759	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C06:02	NRETFLPYY	0.0031	0.9933	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C06:17	NRETFLPYY	0.0031	0.9933	11	20
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:34	IQNRETFLPY	0.9998	0.8454	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:135	IQNRETFLPY	0.9998	0.8327	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:27	IQNRETFLPY	0.9998	0.8456	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:33	IQNRETFLPY	0.9998	0.8454	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:125	IQNRETFLPY	0.9998	0.8454	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:50	IQNRETFLPY	0.9997	0.8826	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:12	IQNRETFLPY	0.9988	0.8467	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:35	IQNRETFLPY	0.9982	0.8187	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:53	IQNRETFLPY	0.9961	0.8263	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:39	IQNRETFLPY	0.9895	0.7384	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:54	IQNRETFLPY	0.975	0.8054	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C14:03	IYGIQNRETF	0.9696	0.9723	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-C14:02	IYGIQNRETF	0.9696	0.9723	6	16
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:20	IQNRETFLPY	0.9436	0.8843	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B35:28	IQNRETFLPY	0.9294	0.8831	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-B15:68	IQNRETFLPY	0.8391	0.5383	9	19
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	HLA-A25:01	EIYGIQNRETF	0.9996	0.9262	5	16

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Potential FusionNeoAntigen Information of VPS33A-ABCB9 in HLA II

VPS33A-ABCB9_122734417_123435112.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)
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-0475	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1502	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1502	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1508	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1508	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1511	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1511	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1514	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1514	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1515	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1515	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1519	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1519	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1526	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1526	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1527	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1529	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1530	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1530	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1531	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1531	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1538	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1538	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1539	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1539	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1544	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1544	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1547	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1547	QNRETFLPYYTGRAI	10	25
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1604	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1605	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1607	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1609	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB1-1610	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB5-0103	NRETFLPYYTGRAID	11	26
VPS33A-ABCB9	chr12	122734417	chr12	123435112	888	DRB5-0203	NRETFLPYYTGRAID	11	26

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Fusion breakpoint peptide structures of VPS33A-ABCB9

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
4077	IYGIQNRETFLPYY	VPS33A	ABCB9	chr12	122734417	chr12	123435112	888

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of VPS33A-ABCB9

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	4077	IYGIQNRETFLPYY	-6.01316	-6.12656
HLA-B14:02	3BVN	4077	IYGIQNRETFLPYY	-3.92858	-4.96388
HLA-B52:01	3W39	4077	IYGIQNRETFLPYY	-5.92102	-6.95632
HLA-B52:01	3W39	4077	IYGIQNRETFLPYY	-4.84472	-4.95812
HLA-A24:02	5HGA	4077	IYGIQNRETFLPYY	-8.26357	-9.29887
HLA-A24:02	5HGA	4077	IYGIQNRETFLPYY	-7.03366	-7.14706
HLA-B44:05	3DX8	4077	IYGIQNRETFLPYY	-6.13971	-6.25311
HLA-B44:05	3DX8	4077	IYGIQNRETFLPYY	-5.20728	-6.24258
HLA-A02:01	6TDR	4077	IYGIQNRETFLPYY	-5.28864	-5.40204

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Vaccine Design for the FusionNeoAntigens of VPS33A-ABCB9

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
VPS33A-ABCB9	chr12	122734417	chr12	123435112	11	20	NRETFLPYY	AGAACAGAGAGACCTTCCTGCCCTACT
VPS33A-ABCB9	chr12	122734417	chr12	123435112	12	20	RETFLPYY	ACAGAGAGACCTTCCTGCCCTACT
VPS33A-ABCB9	chr12	122734417	chr12	123435112	12	21	RETFLPYYT	ACAGAGAGACCTTCCTGCCCTACTACA
VPS33A-ABCB9	chr12	122734417	chr12	123435112	12	23	RETFLPYYTGR	ACAGAGAGACCTTCCTGCCCTACTACACGGGCC
VPS33A-ABCB9	chr12	122734417	chr12	123435112	5	16	EIYGIQNRETF	ATGAAATTTATGGCATTCAGAACAGAGAGACCT
VPS33A-ABCB9	chr12	122734417	chr12	123435112	6	16	IYGIQNRETF	AAATTTATGGCATTCAGAACAGAGAGACCT
VPS33A-ABCB9	chr12	122734417	chr12	123435112	7	16	YGIQNRETF	TTTATGGCATTCAGAACAGAGAGACCT
VPS33A-ABCB9	chr12	122734417	chr12	123435112	9	19	IQNRETFLPY	GCATTCAGAACAGAGAGACCTTCCTGCCCT

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
VPS33A-ABCB9	chr12	122734417	chr12	123435112	10	25	QNRETFLPYYTGRAI	TTCAGAACAGAGAGACCTTCCTGCCCTACTACACGGGCCGCGCCA
VPS33A-ABCB9	chr12	122734417	chr12	123435112	11	26	NRETFLPYYTGRAID	AGAACAGAGAGACCTTCCTGCCCTACTACACGGGCCGCGCCATTG

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Information of the samples that have these potential fusion neoantigens of VPS33A-ABCB9

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
ESCA	VPS33A-ABCB9	chr12	122734417	ENST00000267199	chr12	123435112	ENST00000280560	TCGA-L5-A4OQ

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Potential target of CAR-T therapy development for VPS33A-ABCB9

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

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000280560

225_245

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000280560

319_339

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000280560

416_436

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000344275

225_245

682.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000344275

319_339

682.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000344275

416_436

682.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000346530

225_245

724.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000346530

319_339

724.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000346530

416_436

724.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000392439

225_245

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000392439

319_339

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000392439

416_436

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000442833

225_245

684.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000442833

319_339

684.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000442833

416_436

684.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000540285

225_245

704.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000540285

319_339

704.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000540285

416_436

704.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000542678

225_245

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000542678

319_339

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734417

chr12:123435112

ENST00000542678

416_436

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000280560

225_245

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000280560

319_339

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000280560

416_436

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000344275

225_245

682.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000344275

319_339

682.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000344275

416_436

682.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000346530

225_245

724.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000346530

319_339

724.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000346530

416_436

724.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000392439

225_245

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000392439

319_339

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000392439

416_436

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000442833

225_245

684.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000442833

319_339

684.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000442833

416_436

684.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000540285

225_245

704.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000540285

319_339

704.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000540285

416_436

704.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000542678

225_245

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000542678

319_339

767.0

Transmembrane

Helical

Tgene

ABCB9

chr12:122734418

chr12:123435112

ENST00000542678

416_436

767.0

Transmembrane

Helical

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 VPS33A-ABCB9

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 VPS33A-ABCB9

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)