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Fusion Protein:PRMT2-STX18

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PRMT2-STX18
	FusionPDB ID: 68925
	FusionGDB2.0 ID: 68925
		Hgene	Tgene
	Gene symbol	PRMT2	STX18
	Gene ID	3275	53407
	Gene name	protein arginine methyltransferase 2	syntaxin 18
	Synonyms	HRMT1L1	Ufe1
	Cytomap	21q22.3	4p16.3-p16.2
	Type of gene	protein-coding	protein-coding
	Description	protein arginine N-methyltransferase 2HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1HMT1 hnRNP methyltransferase-like 1PRMT2 alphaPRMT2 betaPRMT2 gammahistone-arginine N-methyltransferase PRMT2	syntaxin-18cell growth-inhibiting gene 9 protein
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000491389, ENST00000291705, ENST00000334494, ENST00000355680, ENST00000397628, ENST00000397637, ENST00000397638, ENST00000440086, ENST00000451211, ENST00000458387,	ENST00000306200, ENST00000505286,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 9 X 7=693	1 X 1 X 1=1
	# samples	12	1
	** MAII score	log2(12/693*10)=-2.5298209465287 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(1/1*10)=3.32192809488736
Fusion gene context	PubMed: PRMT2 [Title/Abstract] AND STX18 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PRMT2 [Title/Abstract] AND STX18 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PRMT2(48068531)-STX18(4473433), # samples:3
Anticipated loss of major functional domain due to fusion event.	PRMT2-STX18 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. PRMT2-STX18 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. PRMT2-STX18 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. PRMT2-STX18 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	PRMT2	GO:0016571	histone methylation	19405910
Hgene	PRMT2	GO:0032088	negative regulation of NF-kappaB transcription factor activity	16648481
Hgene	PRMT2	GO:0045892	negative regulation of transcription, DNA-templated	16648481
Hgene	PRMT2	GO:0045893	positive regulation of transcription, DNA-templated	12039952
Hgene	PRMT2	GO:0060765	regulation of androgen receptor signaling pathway	17587566

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr21:48068531/chr4:4473433)
- 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 PRMT2 (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 STX18 (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)
ENST00000355680	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	2417	1251	762	2009	415
ENST00000355680	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	3157	1251	762	2090	442
ENST00000397638	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	1860	694	205	1452	415
ENST00000397638	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	2600	694	205	1533	442
ENST00000291705	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	1830	664	175	1422	415
ENST00000291705	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	2570	664	175	1503	442
ENST00000458387	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	1830	664	175	1422	415
ENST00000458387	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	2570	664	175	1503	442
ENST00000451211	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	1830	664	175	1422	415
ENST00000451211	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	2570	664	175	1503	442
ENST00000397637	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	2609	1443	954	2201	415
ENST00000397637	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	3349	1443	954	2282	442
ENST00000334494	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	1822	656	167	1414	415
ENST00000334494	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	2562	656	167	1495	442
ENST00000397628	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	1801	635	146	1393	415
ENST00000397628	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	2541	635	146	1474	442
ENST00000440086	PRMT2	chr21	48068531	+	ENST00000505286	STX18	chr4	4473433	-	1794	628	139	1386	415
ENST00000440086	PRMT2	chr21	48068531	+	ENST00000306200	STX18	chr4	4473433	-	2534	628	139	1467	442

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
ENST00000355680	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.010468888	0.98953116
ENST00000355680	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.004617201	0.9953827
ENST00000397638	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.016059972	0.98394
ENST00000397638	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.004521224	0.9954788
ENST00000291705	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.018770732	0.9812292
ENST00000291705	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.00466451	0.9953355
ENST00000458387	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.018770732	0.9812292
ENST00000458387	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.00466451	0.9953355
ENST00000451211	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.018770732	0.9812292
ENST00000451211	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.00466451	0.9953355
ENST00000397637	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.00877074	0.9912293
ENST00000397637	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.00401551	0.99598455
ENST00000334494	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.019325105	0.9806749
ENST00000334494	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.004654889	0.99534506
ENST00000397628	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.020337125	0.97966284
ENST00000397628	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.004715184	0.99528486
ENST00000440086	ENST00000505286	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.020923303	0.97907674
ENST00000440086	ENST00000306200	PRMT2	chr21	48068531	+	STX18	chr4	4473433	-	0.004829967	0.99517006

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 PRMT2-STX18

+/-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
PRMT2	chr21	48068531	STX18	chr4	4473433	1251	163	ISLFCAHYARPRAISHIGKLRDFLLE
PRMT2	chr21	48068531	STX18	chr4	4473433	1443	163	ISLFCAHYARPRAISHIGKLRDFLLE
PRMT2	chr21	48068531	STX18	chr4	4473433	628	163	ISLFCAHYARPRAISHIGKLRDFLLE
PRMT2	chr21	48068531	STX18	chr4	4473433	635	163	ISLFCAHYARPRAISHIGKLRDFLLE
PRMT2	chr21	48068531	STX18	chr4	4473433	656	163	ISLFCAHYARPRAISHIGKLRDFLLE
PRMT2	chr21	48068531	STX18	chr4	4473433	664	163	ISLFCAHYARPRAISHIGKLRDFLLE
PRMT2	chr21	48068531	STX18	chr4	4473433	694	163	ISLFCAHYARPRAISHIGKLRDFLLE

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Potential FusionNeoAntigen Information of PRMT2-STX18 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.

PRMT2-STX18_48068531_4473433.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)
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:17	RAISHIGKL	0.9975	0.8562	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:16	RAISHIGKL	0.9968	0.6385	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B39:06	AHYARPRAI	0.9952	0.8171	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B39:01	AHYARPRAI	0.9933	0.864	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B38:02	AHYARPRAI	0.9866	0.9439	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B38:01	AHYARPRAI	0.986	0.9303	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B14:02	AHYARPRAI	0.9772	0.7089	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B14:01	AHYARPRAI	0.9772	0.7089	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-A30:08	RAISHIGKL	0.9734	0.6689	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:37	AHYARPRAI	0.5026	0.5523	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:18	AHYARPRAI	0.4664	0.7085	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B52:01	RAISHIGKL	0.3427	0.5787	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B13:01	RAISHIGKL	0.2972	0.6979	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B52:01	AHYARPRAI	0.0045	0.9118	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B07:12	RPRAISHI	0.9984	0.5377	9	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C15:04	RAISHIGKL	0.9998	0.9054	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C15:06	RAISHIGKL	0.9997	0.9035	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:19	RAISHIGKL	0.9994	0.9712	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:07	RAISHIGKL	0.9994	0.9814	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:08	RAISHIGKL	0.9992	0.846	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C04:06	RAISHIGKL	0.9984	0.7967	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B39:09	AHYARPRAI	0.9939	0.5955	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B39:12	AHYARPRAI	0.9933	0.8675	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:03	RAISHIGKL	0.9891	0.988	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:12	RAISHIGKL	0.989	0.9098	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:04	RAISHIGKL	0.9879	0.9916	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C02:06	RAISHIGKL	0.986	0.9638	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B39:05	AHYARPRAI	0.9851	0.8661	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:29	RAISHIGKL	0.985	0.9121	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:14	RAISHIGKL	0.9834	0.9687	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:16	RAISHIGKL	0.9832	0.9516	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C08:04	RAISHIGKL	0.9635	0.9596	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C08:13	RAISHIGKL	0.9635	0.9596	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:29	ARPRAISHI	0.9075	0.9311	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:16	YARPRAISH	0.901	0.9575	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:19	ARPRAISHI	0.8956	0.7694	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C08:03	RAISHIGKL	0.8881	0.9807	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:12	YARPRAISH	0.8101	0.9309	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:13	ARPRAISHI	0.7938	0.9149	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:05	AHYARPRAI	0.7841	0.9577	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:95	AHYARPRAI	0.7778	0.7396	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:27	AHYARPRAI	0.7344	0.9447	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:13	AHYARPRAI	0.722	0.8862	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:29	AHYARPRAI	0.7089	0.9335	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:19	AHYARPRAI	0.678	0.7192	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:04	YARPRAISH	0.6586	0.923	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:46	AHYARPRAI	0.6304	0.8513	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:10	AHYARPRAI	0.6174	0.9504	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:04	YARPRAISH	0.6006	0.9929	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C01:17	RAISHIGKL	0.599	0.9084	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:03	YARPRAISH	0.5925	0.9918	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C15:04	YARPRAISH	0.5917	0.9096	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B14:03	AHYARPRAI	0.2008	0.664	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:14	YARPRAISH	0.1432	0.9733	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:16	AHYARPRAI	0.0107	0.9645	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B27:14	RPRAISHIGK	0.7845	0.6876	9	19
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B07:12	RPRAISHIGKL	0.9993	0.563	9	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:06	HYARPRAI	0.913	0.9833	6	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C14:02	HYARPRAI	0.7471	0.8893	6	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C14:03	HYARPRAI	0.7471	0.8893	6	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C15:09	RAISHIGKL	0.9998	0.9054	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C15:05	RAISHIGKL	0.9996	0.9271	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C15:02	RAISHIGKL	0.9996	0.9023	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:17	RAISHIGKL	0.9989	0.9597	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B27:06	ARPRAISHI	0.9988	0.801	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:04	RAISHIGKL	0.9987	0.9806	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:03	RAISHIGKL	0.9987	0.9806	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:05	RAISHIGKL	0.9987	0.9184	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:67	RAISHIGKL	0.9986	0.8869	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:02	RAISHIGKL	0.9977	0.9577	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C16:04	RAISHIGKL	0.9968	0.9671	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:22	RAISHIGKL	0.9941	0.6772	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C16:02	RAISHIGKL	0.9941	0.9932	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B39:02	AHYARPRAI	0.9939	0.9049	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B39:31	AHYARPRAI	0.9938	0.8644	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:06	RAISHIGKL	0.9919	0.9321	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:17	RAISHIGKL	0.991	0.9909	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:02	RAISHIGKL	0.991	0.9909	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C16:01	RAISHIGKL	0.9885	0.9794	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:03	RAISHIGKL	0.9884	0.97	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C02:02	RAISHIGKL	0.9863	0.9726	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C02:10	RAISHIGKL	0.9863	0.9726	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B38:05	AHYARPRAI	0.986	0.9303	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:08	RAISHIGKL	0.984	0.9856	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:02	RAISHIGKL	0.9687	0.9581	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:11	YARPRAISH	0.9493	0.859	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:08	YARPRAISH	0.9381	0.8412	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B07:13	RAISHIGKL	0.9268	0.7236	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B35:43	YARPRAISH	0.9267	0.844	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:30	RAISHIGKL	0.9211	0.721	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C17:01	RAISHIGKL	0.9037	0.686	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B35:11	YARPRAISH	0.8962	0.8391	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:08	ARPRAISHI	0.8899	0.9868	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C08:01	RAISHIGKL	0.8881	0.9807	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:06	RAISHIGKL	0.8474	0.9908	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B35:13	RAISHIGKL	0.8443	0.8277	11	20
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B15:09	AHYARPRAI	0.8324	0.6429	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:02	YARPRAISH	0.8323	0.9701	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:02	YARPRAISH	0.8056	0.964	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:01	AHYARPRAI	0.7704	0.6893	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:22	ARPRAISHI	0.7502	0.7415	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C15:09	YARPRAISH	0.5917	0.9096	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:22	AHYARPRAI	0.5836	0.6658	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:04	ARPRAISHI	0.5366	0.957	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B39:11	AHYARPRAI	0.5254	0.5684	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C12:03	YARPRAISH	0.5171	0.9794	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C02:02	YARPRAISH	0.4006	0.9856	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C02:10	YARPRAISH	0.4006	0.9856	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C16:04	YARPRAISH	0.3184	0.9715	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:04	AHYARPRAI	0.2902	0.9028	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C03:67	AHYARPRAI	0.29	0.9724	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C07:17	YARPRAISH	0.2611	0.9605	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:06	ARPRAISHI	0.2308	0.9888	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C16:02	YARPRAISH	0.1539	0.9893	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:17	ARPRAISHI	0.1492	0.9892	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:02	ARPRAISHI	0.1492	0.9892	8	17
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:06	AHYARPRAI	0.1313	0.9904	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:08	AHYARPRAI	0.0419	0.9935	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C16:01	YARPRAISH	0.0197	0.9754	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B18:07	YARPRAISH	0.0175	0.7662	7	16
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:17	AHYARPRAI	0.0089	0.9938	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-C06:02	AHYARPRAI	0.0089	0.9938	5	14
PRMT2-STX18	chr21	48068531	chr4	4473433	664	HLA-B27:10	RPRAISHIGK	0.7792	0.7204	9	19

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Potential FusionNeoAntigen Information of PRMT2-STX18 in HLA II

PRMT2-STX18_48068531_4473433.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)
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0801	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0801	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0805	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0806	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0806	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0806	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0810	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0810	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0810	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0812	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0812	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0812	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0816	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0816	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0818	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0822	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0822	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0822	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0826	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0826	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0829	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0829	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0829	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0839	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0839	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-0840	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1154	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1154	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1154	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1303	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1303	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1303	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1304	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1304	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1304	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-13101	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-13101	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-13101	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1310	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1310	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1310	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1312	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1312	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1312	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1313	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1313	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1313	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1321	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1321	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1321	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1330	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1330	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1330	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1332	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1332	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1332	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1338	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1348	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1348	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1348	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1349	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1349	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1355	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1355	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1355	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1358	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1358	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1358	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1365	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1366	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1366	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1375	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1375	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1375	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1381	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1381	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1381	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1388	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1388	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1389	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1389	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1389	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1390	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1390	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1390	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1393	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1393	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1393	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1394	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1394	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1394	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1395	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1395	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1395	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1473	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1473	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1473	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1474	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1474	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1474	PRAISHIGKLRDFLL	10	25
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1478	RPRAISHIGKLRDFL	9	24
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1478	ARPRAISHIGKLRDF	8	23
PRMT2-STX18	chr21	48068531	chr4	4473433	664	DRB1-1478	PRAISHIGKLRDFLL	10	25

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Fusion breakpoint peptide structures of PRMT2-STX18

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
3554	HYARPRAISHIGKL	PRMT2	STX18	chr21	48068531	chr4	4473433	664

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PRMT2-STX18

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	3554	HYARPRAISHIGKL	-7.15543	-7.26883
HLA-B14:02	3BVN	3554	HYARPRAISHIGKL	-4.77435	-5.80965
HLA-B52:01	3W39	3554	HYARPRAISHIGKL	-6.80875	-6.92215
HLA-B52:01	3W39	3554	HYARPRAISHIGKL	-4.20386	-5.23916
HLA-A11:01	4UQ2	3554	HYARPRAISHIGKL	-7.5194	-8.5547
HLA-A11:01	4UQ2	3554	HYARPRAISHIGKL	-6.9601	-7.0735
HLA-A24:02	5HGA	3554	HYARPRAISHIGKL	-7.52403	-7.63743
HLA-A24:02	5HGA	3554	HYARPRAISHIGKL	-5.82433	-6.85963
HLA-B27:05	6PYJ	3554	HYARPRAISHIGKL	-3.28285	-4.31815
HLA-B44:05	3DX8	3554	HYARPRAISHIGKL	-5.91172	-6.94702
HLA-B44:05	3DX8	3554	HYARPRAISHIGKL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of PRMT2-STX18

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
PRMT2-STX18	chr21	48068531	chr4	4473433	11	20	RAISHIGKL	AGAGCGATTTCTCACATTGGCAAACTG
PRMT2-STX18	chr21	48068531	chr4	4473433	5	14	AHYARPRAI	GCACACTATGCGCGGCCTAGAGCGATT
PRMT2-STX18	chr21	48068531	chr4	4473433	6	14	HYARPRAI	CACTATGCGCGGCCTAGAGCGATT
PRMT2-STX18	chr21	48068531	chr4	4473433	7	16	YARPRAISH	TATGCGCGGCCTAGAGCGATTTCTCAC
PRMT2-STX18	chr21	48068531	chr4	4473433	8	17	ARPRAISHI	GCGCGGCCTAGAGCGATTTCTCACATT
PRMT2-STX18	chr21	48068531	chr4	4473433	9	17	RPRAISHI	CGGCCTAGAGCGATTTCTCACATT
PRMT2-STX18	chr21	48068531	chr4	4473433	9	19	RPRAISHIGK	CGGCCTAGAGCGATTTCTCACATTGGCAAA
PRMT2-STX18	chr21	48068531	chr4	4473433	9	20	RPRAISHIGKL	CGGCCTAGAGCGATTTCTCACATTGGCAAACTG

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
PRMT2-STX18	chr21	48068531	chr4	4473433	10	25	PRAISHIGKLRDFLL	CCTAGAGCGATTTCTCACATTGGCAAACTGAGAGATTTTCTTCTG
PRMT2-STX18	chr21	48068531	chr4	4473433	8	23	ARPRAISHIGKLRDF	GCGCGGCCTAGAGCGATTTCTCACATTGGCAAACTGAGAGATTTT
PRMT2-STX18	chr21	48068531	chr4	4473433	9	24	RPRAISHIGKLRDFL	CGGCCTAGAGCGATTTCTCACATTGGCAAACTGAGAGATTTTCTT

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Information of the samples that have these potential fusion neoantigens of PRMT2-STX18

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	PRMT2-STX18	chr21	48068531	ENST00000291705	chr4	4473433	ENST00000306200	TCGA-93-A4JP-01A

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Potential target of CAR-T therapy development for PRMT2-STX18

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

STX18

chr21:48068531

chr4:4473433

ENST00000306200

310_330

336.0

Transmembrane

Helical%3B Anchor for type IV membrane protein

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 PRMT2-STX18

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 PRMT2-STX18

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)