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Fusion Protein:PTDSS2-BACE2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTDSS2-BACE2
	FusionPDB ID: 69893
	FusionGDB2.0 ID: 69893
		Hgene	Tgene
	Gene symbol	PTDSS2	BACE2
	Gene ID	81490	25825
	Gene name	phosphatidylserine synthase 2	beta-secretase 2
	Synonyms	PSS2	AEPLC\|ALP56\|ASP1\|ASP21\|BAE2\|CDA13\|CEAP1\|DRAP
	Cytomap	11p15.5	21q22.2-q22.3
	Type of gene	protein-coding	protein-coding
	Description	phosphatidylserine synthase 2PSS-2ptdSer synthase 2serine-exchange enzyme II	beta-secretase 256 kDa aspartic-like proteaseDown syndrome region aspartic proteaseSLCO3A1/BACE2 fusionaspartyl protease 1beta-site APP-cleaving enzyme 2beta-site amyloid beta A4 precursor protein-cleaving enzyme 2memapsin-1membrane-associated asp
	Modification date	20200313	20200313
	UniProtAcc	.	Q9Y5Z0 Main function of 5'-partner protein: FUNCTION: Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves APP, between residues 690 and 691, leading to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase. It has also been shown that it can cleave APP between residues 671 and 672. Responsible also for the proteolytic processing of CLTRN in pancreatic beta cells (PubMed:21907142). {ECO:0000269\|PubMed:10591213, ECO:0000269\|PubMed:11083922, ECO:0000269\|PubMed:11423558, ECO:0000269\|PubMed:15857888, ECO:0000269\|PubMed:16816112, ECO:0000269\|PubMed:21907142}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000530087, ENST00000308020,	ENST00000328735, ENST00000330333, ENST00000347667, ENST00000466122,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 3 X 6=162	14 X 9 X 8=1008
	# samples	9	14
	** MAII score	log2(9/162*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/1008*10)=-2.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PTDSS2 [Title/Abstract] AND BACE2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PTDSS2 [Title/Abstract] AND BACE2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTDSS2(479152)-BACE2(42647298), # samples:1
Anticipated loss of major functional domain due to fusion event.	PTDSS2-BACE2 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. PTDSS2-BACE2 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. PTDSS2-BACE2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. PTDSS2-BACE2 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
Tgene	BACE2	GO:0006509	membrane protein ectodomain proteolysis	10591213

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:479152/chr21:42647298)
- 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 PTDSS2 (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 BACE2 (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)

ENST00000308020

PTDSS2

chr11

479152

ENST00000328735

BACE2

chr21

42647298

1838

611

176

667

163

ENST00000308020

PTDSS2

chr11

479152

ENST00000347667

BACE2

chr21

42647298

7759

611

176

667

163

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
ENST00000308020	ENST00000328735	PTDSS2	chr11	479152	+	BACE2	chr21	42647298	+	0.37278315	0.6272169
ENST00000308020	ENST00000347667	PTDSS2	chr11	479152	+	BACE2	chr21	42647298	+	0.16246055	0.8375395

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 PTDSS2-BACE2

+/-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
PTDSS2	chr11	479152	BACE2	chr21	42647298	611	144	SVVYELFLIFILFQKLQVLQCLKFPG

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Potential FusionNeoAntigen Information of PTDSS2-BACE2 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.

PTDSS2-BACE2_479152_42647298.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)
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B08:01	LFQKLQVL	0.9967	0.6274	11	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:04	ILFQKLQV	0.9908	0.8291	10	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B08:09	ILFQKLQV	0.9907	0.7767	10	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:13	ILFQKLQV	0.9816	0.6694	10	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B08:01	ILFQKLQVL	0.9975	0.8004	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B08:09	ILFQKLQVL	0.9933	0.7931	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:60	FILFQKLQV	0.9913	0.6532	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:30	FILFQKLQV	0.9908	0.619	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:24	FILFQKLQV	0.9908	0.619	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:67	FILFQKLQV	0.9908	0.619	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:11	FILFQKLQV	0.9905	0.6582	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:21	FILFQKLQV	0.9895	0.7379	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:22	ILFQKLQVL	0.9869	0.7846	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:35	FILFQKLQV	0.9827	0.6626	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:04	FILFQKLQV	0.9812	0.8882	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:29	FILFQKLQV	0.981	0.6284	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:67	ILFQKLQVL	0.9791	0.7235	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:24	ILFQKLQVL	0.9791	0.7235	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:30	ILFQKLQVL	0.9791	0.7235	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:60	ILFQKLQVL	0.9777	0.7254	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:11	ILFQKLQVL	0.976	0.7634	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:20	FILFQKLQV	0.9755	0.6294	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:27	FILFQKLQV	0.972	0.7231	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:04	ILFQKLQVL	0.9713	0.8624	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:17	FILFQKLQV	0.971	0.6038	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:27	ILFQKLQVL	0.9702	0.7425	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:13	FILFQKLQV	0.9696	0.7783	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:17	ILFQKLQVL	0.9682	0.5412	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:21	ILFQKLQVL	0.9674	0.8179	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:13	ILFQKLQVL	0.9633	0.7956	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:16	FILFQKLQV	0.963	0.5086	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:38	ILFQKLQVL	0.9536	0.7345	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:16	ILFQKLQVL	0.9488	0.6398	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:38	FILFQKLQV	0.9475	0.6782	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:19	FILFQKLQV	0.9303	0.5784	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B14:02	ILFQKLQVL	0.9108	0.8087	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B14:01	ILFQKLQVL	0.9108	0.8087	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:35	ILFQKLQVL	0.8938	0.7512	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:29	ILFQKLQVL	0.871	0.7275	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:19	ILFQKLQVL	0.866	0.5791	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:20	ILFQKLQVL	0.8363	0.731	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:25	ILFQKLQVL	0.7802	0.9565	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A32:13	ILFQKLQVL	0.7404	0.9756	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B08:09	FQKLQVLQC	0.5667	0.8112	12	21
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B46:01	ILFQKLQVL	0.3166	0.5116	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B52:01	ILFQKLQVL	0.2799	0.9691	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B13:02	ILFQKLQVL	0.1186	0.5935	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B13:01	ILFQKLQVL	0.0583	0.9575	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:04	FILFQKLQVL	0.9436	0.8662	9	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:17	FILFQKLQVL	0.9333	0.6345	9	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B42:02	ILFQKLQVL	0.9974	0.7819	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:01	FILFQKLQV	0.9908	0.619	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:02	ILFQKLQVL	0.9878	0.7263	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C12:12	ILFQKLQVL	0.9872	0.9626	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:05	ILFQKLQVL	0.9818	0.8447	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:07	ILFQKLQVL	0.9813	0.7347	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C06:03	ILFQKLQVL	0.981	0.9965	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C12:04	ILFQKLQVL	0.9809	0.9967	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:01	ILFQKLQVL	0.9791	0.7235	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:08	ILFQKLQVL	0.9725	0.9556	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:19	ILFQKLQVL	0.9709	0.992	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:07	ILFQKLQVL	0.9495	0.9793	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:04	ILFQKLQVL	0.903	0.9224	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C12:16	ILFQKLQVL	0.8823	0.9769	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:07	ILFQKLQVL	0.872	0.8246	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C04:06	ILFQKLQVL	0.8496	0.9715	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:04	FQKLQVLQC	0.8389	0.8839	12	21
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B14:03	ILFQKLQVL	0.7433	0.898	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:67	ILFQKLQVL	0.6412	0.9124	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:80	ILFQKLQVL	0.6412	0.9124	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:29	ILFQKLQVL	0.6205	0.9679	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:10	ILFQKLQVL	0.6173	0.9539	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:05	ILFQKLQVL	0.6097	0.9841	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:13	ILFQKLQVL	0.5923	0.8904	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:46	ILFQKLQVL	0.5834	0.8187	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:19	ILFQKLQVL	0.5824	0.7435	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C01:17	ILFQKLQVL	0.5753	0.9598	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C02:06	ILFQKLQVL	0.5683	0.975	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:14	ILFQKLQVL	0.4892	0.9874	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:27	ILFQKLQVL	0.4364	0.9552	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C01:30	ILFQKLQVL	0.3778	0.9755	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:02	FILFQKLQVL	0.9623	0.8253	9	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B08:18	LFQKLQVL	0.9967	0.6274	11	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C14:02	LFQKLQVL	0.9426	0.9785	11	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C14:03	LFQKLQVL	0.9426	0.9785	11	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C14:02	IFILFQKL	0.8487	0.9672	8	16
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C14:03	IFILFQKL	0.8487	0.9672	8	16
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B08:18	ILFQKLQVL	0.9975	0.8004	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:06	FILFQKLQV	0.9895	0.7379	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:14	FILFQKLQV	0.9895	0.7291	9	18
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:03	ILFQKLQVL	0.9859	0.8376	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C06:02	ILFQKLQVL	0.982	0.996	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C06:17	ILFQKLQVL	0.982	0.996	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:04	ILFQKLQVL	0.9801	0.9932	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:03	ILFQKLQVL	0.9801	0.9932	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:17	ILFQKLQVL	0.9727	0.9792	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:14	ILFQKLQVL	0.9678	0.8018	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:06	ILFQKLQVL	0.9674	0.8179	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:05	ILFQKLQVL	0.9616	0.9456	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C03:67	ILFQKLQVL	0.9536	0.9898	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:24	ILFQKLQVL	0.9368	0.9205	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:27	ILFQKLQVL	0.9351	0.9268	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A32:01	ILFQKLQVL	0.9089	0.9836	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:35	ILFQKLQVL	0.9053	0.9264	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:73	ILFQKLQVL	0.9037	0.9729	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C12:02	ILFQKLQVL	0.9001	0.981	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C06:06	ILFQKLQVL	0.8914	0.9902	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C04:04	ILFQKLQVL	0.8392	0.9631	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:04	ILFQKLQVL	0.8108	0.963	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:30	ILFQKLQVL	0.7807	0.9535	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B15:39	ILFQKLQVL	0.7708	0.8829	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B08:12	ILFQKLQVL	0.7686	0.9467	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C06:08	ILFQKLQVL	0.68	0.9933	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:02	ILFQKLQVL	0.6412	0.9124	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C07:17	ILFQKLQVL	0.6126	0.9759	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C01:03	ILFQKLQVL	0.6041	0.9614	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C01:02	ILFQKLQVL	0.5963	0.9565	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-C17:01	ILFQKLQVL	0.4142	0.9223	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B07:13	ILFQKLQVL	0.248	0.8775	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-B39:02	ILFQKLQVL	0.2224	0.9725	10	19
PTDSS2-BACE2	chr11	479152	chr21	42647298	611	HLA-A02:03	FILFQKLQVL	0.9329	0.8908	9	19

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Potential FusionNeoAntigen Information of PTDSS2-BACE2 in HLA II

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)

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Fusion breakpoint peptide structures of PTDSS2-BACE2

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
2443	FLIFILFQKLQVLQ	PTDSS2	BACE2	chr11	479152	chr21	42647298	611

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTDSS2-BACE2

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	2443	FLIFILFQKLQVLQ	-5.97758	-6.09098
HLA-B14:02	3BVN	2443	FLIFILFQKLQVLQ	-5.15013	-6.18543
HLA-B52:01	3W39	2443	FLIFILFQKLQVLQ	-6.29935	-6.41275
HLA-B52:01	3W39	2443	FLIFILFQKLQVLQ	-6.07479	-7.11009
HLA-A24:02	5HGA	2443	FLIFILFQKLQVLQ	-7.25246	-8.28776
HLA-A24:02	5HGA	2443	FLIFILFQKLQVLQ	-6.23064	-6.34404
HLA-B44:05	3DX8	2443	FLIFILFQKLQVLQ	-4.66421	-5.69951
HLA-B44:05	3DX8	2443	FLIFILFQKLQVLQ	-4.52141	-4.63481
HLA-A02:01	6TDR	2443	FLIFILFQKLQVLQ	-7.72945	-7.84285

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Vaccine Design for the FusionNeoAntigens of PTDSS2-BACE2

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
PTDSS2-BACE2	chr11	479152	chr21	42647298	10	18	ILFQKLQV	CTCTTCCAGAAATTGCAGGTGCTG
PTDSS2-BACE2	chr11	479152	chr21	42647298	10	19	ILFQKLQVL	CTCTTCCAGAAATTGCAGGTGCTGCAG
PTDSS2-BACE2	chr11	479152	chr21	42647298	11	19	LFQKLQVL	TTCCAGAAATTGCAGGTGCTGCAG
PTDSS2-BACE2	chr11	479152	chr21	42647298	12	21	FQKLQVLQC	CAGAAATTGCAGGTGCTGCAGTGTCTG
PTDSS2-BACE2	chr11	479152	chr21	42647298	8	16	IFILFQKL	TTTATACTCTTCCAGAAATTGCAG
PTDSS2-BACE2	chr11	479152	chr21	42647298	9	18	FILFQKLQV	ATACTCTTCCAGAAATTGCAGGTGCTG
PTDSS2-BACE2	chr11	479152	chr21	42647298	9	19	FILFQKLQVL	ATACTCTTCCAGAAATTGCAGGTGCTGCAG

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

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Information of the samples that have these potential fusion neoantigens of PTDSS2-BACE2

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
STAD	PTDSS2-BACE2	chr11	479152	ENST00000308020	chr21	42647298	ENST00000328735	TCGA-EQ-A4SO-01A

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Potential target of CAR-T therapy development for PTDSS2-BACE2

Predicted 3D structure. We used RoseTTAFold.

360_PTDSS2-BACE2_b3fee_pred.pdb

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

Hgene

PTDSS2

chr11:479152

chr21:42647298

ENST00000308020

127_147

145

488.0

Transmembrane

Helical

Hgene

PTDSS2

chr11:479152

chr21:42647298

ENST00000308020

63_83

145

488.0

Transmembrane

Helical

Hgene

PTDSS2

chr11:479152

chr21:42647298

ENST00000308020

97_117

145

488.0

Transmembrane

Helical

Tgene

BACE2

chr11:479152

chr21:42647298

ENST00000328735

474_494

397.0

Transmembrane

Helical

Tgene

BACE2

chr11:479152

chr21:42647298

ENST00000330333

474_494

519.0

Transmembrane

Helical

Tgene

BACE2

chr11:479152

chr21:42647298

ENST00000347667

474_494

469.0

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
PTDSS2	chr11	479152	ENST00000308020	BACE2	chr21	42647298	ENST00000328735

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Related Drugs to PTDSS2-BACE2

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 PTDSS2-BACE2

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)