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Fusion Protein:THUMPD2-VSNL1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: THUMPD2-VSNL1
	FusionPDB ID: 90807
	FusionGDB2.0 ID: 90807
		Hgene	Tgene
	Gene symbol	THUMPD2	VSNL1
	Gene ID	80745	7447
	Gene name	THUMP domain containing 2	visinin like 1
	Synonyms	C2orf8	HLP3\|HPCAL3\|HUVISL1\|VILIP\|VILIP-1
	Cytomap	2p22.1\|2p22-p21	2p24.2
	Type of gene	protein-coding	protein-coding
	Description	THUMP domain-containing protein 2SAM-dependent methyltransferaseepididymis secretory sperm binding protein	visinin-like protein 1VLP-1hippocalcin-like protein 3
	Modification date	20200313	20200329
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000260619, ENST00000454352, ENST00000505747, ENST00000403537,	ENST00000483921, ENST00000295156, ENST00000404666, ENST00000406397,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 4 X 4=80	7 X 8 X 6=336
	# samples	6	9
	** MAII score	log2(6/80*10)=-0.415037499278844 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/336*10)=-1.90046432644909 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: THUMPD2 [Title/Abstract] AND VSNL1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: THUMPD2 [Title/Abstract] AND VSNL1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	THUMPD2(40006254)-VSNL1(17830677), # samples:3
Anticipated loss of major functional domain due to fusion event.	THUMPD2-VSNL1 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. THUMPD2-VSNL1 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. THUMPD2-VSNL1 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. THUMPD2-VSNL1 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:40006254/chr2:17830677)
- 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 THUMPD2 (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 VSNL1 (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)
ENST00000505747	THUMPD2	chr2	40006254	-	ENST00000404666	VSNL1	chr2	17830677	+	1252	154	28	567	179
ENST00000505747	THUMPD2	chr2	40006254	-	ENST00000295156	VSNL1	chr2	17830677	+	1613	154	28	567	179
ENST00000505747	THUMPD2	chr2	40006254	-	ENST00000406397	VSNL1	chr2	17830677	+	2192	154	28	567	179
ENST00000260619	THUMPD2	chr2	40006254	-	ENST00000404666	VSNL1	chr2	17830677	+	1134	36	0	449	149
ENST00000260619	THUMPD2	chr2	40006254	-	ENST00000295156	VSNL1	chr2	17830677	+	1495	36	0	449	149
ENST00000260619	THUMPD2	chr2	40006254	-	ENST00000406397	VSNL1	chr2	17830677	+	2074	36	0	449	149
ENST00000454352	THUMPD2	chr2	40006254	-	ENST00000404666	VSNL1	chr2	17830677	+	1137	39	3	452	149
ENST00000454352	THUMPD2	chr2	40006254	-	ENST00000295156	VSNL1	chr2	17830677	+	1498	39	3	452	149
ENST00000454352	THUMPD2	chr2	40006254	-	ENST00000406397	VSNL1	chr2	17830677	+	2077	39	3	452	149
ENST00000505747	THUMPD2	chr2	40006253	-	ENST00000404666	VSNL1	chr2	17830676	+	1252	154	28	567	179
ENST00000505747	THUMPD2	chr2	40006253	-	ENST00000295156	VSNL1	chr2	17830676	+	1613	154	28	567	179
ENST00000505747	THUMPD2	chr2	40006253	-	ENST00000406397	VSNL1	chr2	17830676	+	2192	154	28	567	179
ENST00000260619	THUMPD2	chr2	40006253	-	ENST00000404666	VSNL1	chr2	17830676	+	1134	36	0	449	149
ENST00000260619	THUMPD2	chr2	40006253	-	ENST00000295156	VSNL1	chr2	17830676	+	1495	36	0	449	149
ENST00000260619	THUMPD2	chr2	40006253	-	ENST00000406397	VSNL1	chr2	17830676	+	2074	36	0	449	149
ENST00000454352	THUMPD2	chr2	40006253	-	ENST00000404666	VSNL1	chr2	17830676	+	1137	39	3	452	149
ENST00000454352	THUMPD2	chr2	40006253	-	ENST00000295156	VSNL1	chr2	17830676	+	1498	39	3	452	149
ENST00000454352	THUMPD2	chr2	40006253	-	ENST00000406397	VSNL1	chr2	17830676	+	2077	39	3	452	149

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
ENST00000505747	ENST00000404666	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.001805438	0.9981945
ENST00000505747	ENST00000295156	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.001292481	0.99870753
ENST00000505747	ENST00000406397	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.000911073	0.9990889
ENST00000260619	ENST00000404666	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.001843087	0.99815696
ENST00000260619	ENST00000295156	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.001407542	0.99859244
ENST00000260619	ENST00000406397	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.001444849	0.9985551
ENST00000454352	ENST00000404666	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.001931314	0.99806875
ENST00000454352	ENST00000295156	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.001475116	0.99852496
ENST00000454352	ENST00000406397	THUMPD2	chr2	40006254	-	VSNL1	chr2	17830677	+	0.001813555	0.9981864
ENST00000505747	ENST00000404666	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.001805438	0.9981945
ENST00000505747	ENST00000295156	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.001292481	0.99870753
ENST00000505747	ENST00000406397	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.000911073	0.9990889
ENST00000260619	ENST00000404666	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.001843087	0.99815696
ENST00000260619	ENST00000295156	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.001407542	0.99859244
ENST00000260619	ENST00000406397	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.001444849	0.9985551
ENST00000454352	ENST00000404666	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.001931314	0.99806875
ENST00000454352	ENST00000295156	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.001475116	0.99852496
ENST00000454352	ENST00000406397	THUMPD2	chr2	40006253	-	VSNL1	chr2	17830676	+	0.001813555	0.9981864

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 THUMPD2-VSNL1

+/-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
THUMPD2	chr2	40006253	VSNL1	chr2	17830676	154	41	FVMREVRARLAATQFFPYGDASKFAQ
THUMPD2	chr2	40006254	VSNL1	chr2	17830677	154	41	FVMREVRARLAATQFFPYGDASKFAQ

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Potential FusionNeoAntigen Information of THUMPD2-VSNL1 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.

THUMPD2-VSNL1_40006253_17830676.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)
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:05	ARLAATQFF	0.9997	0.6084	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:04	ARLAATQFF	0.9997	0.6463	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B57:01	RARLAATQF	0.9943	0.9641	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:01	RARLAATQF	0.9942	0.789	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:08	LAATQFFPY	0.9935	0.89	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:01	LAATQFFPY	0.9935	0.9184	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:25	RARLAATQF	0.9915	0.8794	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:17	RARLAATQF	0.9883	0.8075	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B58:02	RARLAATQF	0.9877	0.9291	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:16	RARLAATQF	0.9829	0.6846	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:03	RARLAATQF	0.9096	0.6885	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:05	LAATQFFPY	0.8849	0.6852	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B57:03	RARLAATQF	0.8772	0.9622	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-A30:08	RARLAATQF	0.8044	0.8281	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:03	ARLAATQFF	0.5086	0.7685	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:18	ARLAATQFF	0.4457	0.7351	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:04	VRARLAATQF	0.9996	0.5193	5	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:04	RARLAATQFF	0.9986	0.5642	6	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B57:03	RARLAATQFF	0.9878	0.9659	6	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:05	ARLAATQFFPY	1	0.601	7	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:04	ARLAATQFFPY	1	0.7067	7	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:14	ARLAATQFF	0.9996	0.6219	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:95	ARLAATQFF	0.997	0.7463	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:05	ARLAATQFF	0.9965	0.9714	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:31	LAATQFFPY	0.9933	0.9255	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:03	ARLAATQFF	0.9932	0.6414	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:07	RARLAATQF	0.9906	0.6063	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:27	ARLAATQFF	0.9894	0.9625	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:29	ARLAATQFF	0.972	0.9158	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:46	ARLAATQFF	0.9197	0.8717	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:19	ARLAATQFF	0.9143	0.7681	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:04	RARLAATQF	0.9057	0.8212	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:13	ARLAATQFF	0.8909	0.9376	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B07:04	RARLAATQF	0.8777	0.5072	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:10	ARLAATQFF	0.8729	0.9645	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:67	ARLAATQFF	0.8673	0.9493	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:80	ARLAATQFF	0.8673	0.9493	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:05	RARLAATQF	0.7849	0.8166	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C12:12	RARLAATQF	0.7662	0.9538	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C15:04	RARLAATQF	0.7634	0.89	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C03:14	RARLAATQF	0.7138	0.9696	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C03:14	LAATQFFPY	0.5237	0.9458	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C12:16	ARLAATQFF	0.0578	0.9655	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:03	RARLAATQFF	0.9452	0.5095	6	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:03	ARLAATQFFPY	0.9997	0.6178	7	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:08	ARLAATQFF	0.9997	0.5063	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:10	ARLAATQFF	0.9997	0.7836	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:06	ARLAATQFF	0.9995	0.6884	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:01	ARLAATQFF	0.998	0.7166	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:11	LAATQFFPY	0.9968	0.918	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:09	ARLAATQFF	0.9961	0.5957	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:135	RARLAATQF	0.9948	0.7877	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B57:10	RARLAATQF	0.9943	0.9641	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:27	RARLAATQF	0.9943	0.8405	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:34	RARLAATQF	0.9942	0.789	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:33	RARLAATQF	0.9942	0.789	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:125	RARLAATQF	0.9942	0.789	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:11	RARLAATQF	0.9938	0.734	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:77	LAATQFFPY	0.9935	0.9184	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:20	LAATQFFPY	0.9932	0.9672	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:23	LAATQFFPY	0.9931	0.9251	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:11	LAATQFFPY	0.9923	0.854	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B58:06	RARLAATQF	0.992	0.8847	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:39	RARLAATQF	0.9918	0.7552	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:24	RARLAATQF	0.9917	0.7847	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:43	RARLAATQF	0.9917	0.7422	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:35	RARLAATQF	0.9916	0.7921	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:08	LAATQFFPY	0.991	0.8529	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B57:04	RARLAATQF	0.9882	0.7199	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:43	LAATQFFPY	0.9877	0.8603	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B07:13	RARLAATQF	0.9854	0.8537	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:24	LAATQFFPY	0.9801	0.887	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:50	RARLAATQF	0.9769	0.883	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-A32:01	RARLAATQF	0.9671	0.9428	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:17	ARLAATQFF	0.967	0.9679	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:30	LAATQFFPY	0.9617	0.8377	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:17	LAATQFFPY	0.9617	0.8377	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:54	RARLAATQF	0.9524	0.7423	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:12	RARLAATQF	0.941	0.7204	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:68	RARLAATQF	0.9332	0.5315	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C03:02	LAATQFFPY	0.9042	0.9614	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:02	ARLAATQFF	0.8673	0.9493	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-A30:01	RARLAATQF	0.8162	0.9172	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C02:10	RARLAATQF	0.8117	0.9446	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C02:02	RARLAATQF	0.8117	0.9446	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C06:08	ARLAATQFF	0.8097	0.9773	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C07:22	ARLAATQFF	0.8035	0.7853	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C03:02	RARLAATQF	0.8032	0.9554	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B57:02	RARLAATQF	0.7913	0.9271	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C16:04	RARLAATQF	0.7679	0.9779	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C15:09	RARLAATQF	0.7634	0.89	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C12:02	LAATQFFPY	0.7621	0.9661	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B35:28	RARLAATQF	0.756	0.8913	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C12:03	RARLAATQF	0.7387	0.9781	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C12:02	RARLAATQF	0.7327	0.9635	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C03:05	RARLAATQF	0.5673	0.8619	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C03:17	RARLAATQF	0.5305	0.9601	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C16:01	RARLAATQF	0.5033	0.9813	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C16:01	LAATQFFPY	0.4261	0.9642	9	18
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C16:02	RARLAATQF	0.3235	0.9914	6	15
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C06:06	ARLAATQFF	0.1755	0.9907	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B15:68	ARLAATQFF	0.0635	0.6021	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C06:02	ARLAATQFF	0.0263	0.9885	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-C06:17	ARLAATQFF	0.0263	0.9885	7	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:10	RARLAATQFF	0.9988	0.7148	6	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B58:06	RARLAATQFF	0.9979	0.8521	6	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:06	RARLAATQFF	0.9935	0.5588	6	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B57:02	RARLAATQFF	0.9643	0.9404	6	16
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	HLA-B27:10	ARLAATQFFPY	1	0.8231	7	18

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Potential FusionNeoAntigen Information of THUMPD2-VSNL1 in HLA II

THUMPD2-VSNL1_40006253_17830676.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)
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	154	DRB5-0203	ATQFFPYGDASKFAQ	11	26

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Fusion breakpoint peptide structures of THUMPD2-VSNL1

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
7705	RARLAATQFFPYGD	THUMPD2	VSNL1	chr2	40006253	chr2	17830676	154

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of THUMPD2-VSNL1

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	7705	RARLAATQFFPYGD	-7.9962	-8.1096
HLA-B14:02	3BVN	7705	RARLAATQFFPYGD	-5.70842	-6.74372
HLA-B52:01	3W39	7705	RARLAATQFFPYGD	-6.83737	-6.95077
HLA-B52:01	3W39	7705	RARLAATQFFPYGD	-4.4836	-5.5189
HLA-A11:01	4UQ2	7705	RARLAATQFFPYGD	-10.0067	-10.1201
HLA-A11:01	4UQ2	7705	RARLAATQFFPYGD	-9.03915	-10.0745
HLA-A24:02	5HGA	7705	RARLAATQFFPYGD	-6.56204	-6.67544
HLA-A24:02	5HGA	7705	RARLAATQFFPYGD	-5.42271	-6.45801
HLA-B44:05	3DX8	7705	RARLAATQFFPYGD	-7.85648	-8.89178
HLA-B44:05	3DX8	7705	RARLAATQFFPYGD	-5.3978	-5.5112
HLA-A02:01	6TDR	7705	RARLAATQFFPYGD	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of THUMPD2-VSNL1

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
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	5	15	VRARLAATQF	CGGGCGCGGCTGGCGGCCACGCAGTTCTTT
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	6	15	RARLAATQF	GCGCGGCTGGCGGCCACGCAGTTCTTT
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	6	16	RARLAATQFF	GCGCGGCTGGCGGCCACGCAGTTCTTTCCT
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	7	16	ARLAATQFF	CGGCTGGCGGCCACGCAGTTCTTTCCT
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	7	18	ARLAATQFFPY	CGGCTGGCGGCCACGCAGTTCTTTCCTTATGGA
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	9	18	LAATQFFPY	GCGGCCACGCAGTTCTTTCCTTATGGA

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
THUMPD2-VSNL1	chr2	40006253	chr2	17830676	11	26	ATQFFPYGDASKFAQ	ACGCAGTTCTTTCCTTATGGAGACGCCTCCAAGTTTGCCCAGCAT

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Information of the samples that have these potential fusion neoantigens of THUMPD2-VSNL1

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	THUMPD2-VSNL1	chr2	40006253	ENST00000505747	chr2	17830676	ENST00000295156	TCGA-55-A4DG

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Potential target of CAR-T therapy development for THUMPD2-VSNL1

Predicted 3D structure. We used RoseTTAFold.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to THUMPD2-VSNL1

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 THUMPD2-VSNL1

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)