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Fusion Protein:VMP1-BRCA1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: VMP1-BRCA1
	FusionPDB ID: 98195
	FusionGDB2.0 ID: 98195
		Hgene	Tgene
	Gene symbol	VMP1	BRCA1
	Gene ID	81671	672
	Gene name	vacuole membrane protein 1	BRCA1 DNA repair associated
	Synonyms	EPG3\|TANGO5\|TMEM49	BRCAI\|BRCC1\|BROVCA1\|FANCS\|IRIS\|PNCA4\|PPP1R53\|PSCP\|RNF53
	Cytomap	17q23.1	17q21.31
	Type of gene	protein-coding	protein-coding
	Description	vacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homolog	breast cancer type 1 susceptibility proteinBRCA1/BRCA2-containing complex, subunit 1Fanconi anemia, complementation group SRING finger protein 53breast and ovarian cancer susceptibility protein 1breast cancer 1, early onsetearly onset breast cancer
	Modification date	20200327	20200329
	UniProtAcc	.	UIMC1 Main function of 5'-partner protein: 719
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000262291, ENST00000536180, ENST00000537567, ENST00000539763, ENST00000545362, ENST00000588617,	ENST00000471181, ENST00000491747, ENST00000493795, ENST00000586385, ENST00000591534, ENST00000591849, ENST00000309486, ENST00000346315, ENST00000351666, ENST00000352993, ENST00000354071, ENST00000357654, ENST00000468300,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	34 X 17 X 12=6936	7 X 6 X 6=252
	# samples	38	7
	** MAII score	log2(38/6936*10)=-4.19003257489089 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/252*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: VMP1 [Title/Abstract] AND BRCA1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: VMP1 [Title/Abstract] AND BRCA1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	VMP1(57851246)-BRCA1(41234592), # samples:2
Anticipated loss of major functional domain due to fusion event.	VMP1-BRCA1 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. VMP1-BRCA1 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. VMP1-BRCA1 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. VMP1-BRCA1 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
Tgene	BRCA1	GO:0000724	double-strand break repair via homologous recombination	17349954
Tgene	BRCA1	GO:0006301	postreplication repair	17349954
Tgene	BRCA1	GO:0006302	double-strand break repair	22186889
Tgene	BRCA1	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	14654789
Tgene	BRCA1	GO:0016567	protein ubiquitination	17349954
Tgene	BRCA1	GO:0031398	positive regulation of protein ubiquitination	15965487
Tgene	BRCA1	GO:0035066	positive regulation of histone acetylation	20820192
Tgene	BRCA1	GO:0043627	response to estrogen	8895509
Tgene	BRCA1	GO:0045892	negative regulation of transcription, DNA-templated	16288014
Tgene	BRCA1	GO:0045893	positive regulation of transcription, DNA-templated	20160719
Tgene	BRCA1	GO:0045944	positive regulation of transcription by RNA polymerase II	16331276
Tgene	BRCA1	GO:0051571	positive regulation of histone H3-K4 methylation	20820192
Tgene	BRCA1	GO:0051573	negative regulation of histone H3-K9 methylation	20820192
Tgene	BRCA1	GO:0051865	protein autoubiquitination	12890688\|20351172
Tgene	BRCA1	GO:0070512	positive regulation of histone H4-K20 methylation	20820192
Tgene	BRCA1	GO:0071158	positive regulation of cell cycle arrest	21102443
Tgene	BRCA1	GO:0071681	cellular response to indole-3-methanol	10868478
Tgene	BRCA1	GO:0085020	protein K6-linked ubiquitination	12890688\|20351172
Tgene	BRCA1	GO:2000617	positive regulation of histone H3-K9 acetylation	20820192
Tgene	BRCA1	GO:2000620	positive regulation of histone H4-K16 acetylation	20820192

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:57851246/chr17:41234592)
- 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 VMP1 (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 BRCA1 (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)
ENST00000262291	VMP1	chr17	57851246	+	ENST00000357654	BRCA1	chr17	41234592	-	3814	1024	253	2430	725
ENST00000262291	VMP1	chr17	57851246	+	ENST00000351666	BRCA1	chr17	41234592	-	3813	1024	253	2430	725
ENST00000262291	VMP1	chr17	57851246	+	ENST00000309486	BRCA1	chr17	41234592	-	3813	1024	253	2430	725
ENST00000262291	VMP1	chr17	57851246	+	ENST00000346315	BRCA1	chr17	41234592	-	3096	1024	253	1713	486
ENST00000262291	VMP1	chr17	57851246	+	ENST00000354071	BRCA1	chr17	41234592	-	3018	1024	253	1635	460
ENST00000262291	VMP1	chr17	57851246	+	ENST00000352993	BRCA1	chr17	41234592	-	3813	1024	253	2430	725
ENST00000262291	VMP1	chr17	57851246	+	ENST00000468300	BRCA1	chr17	41234592	-	3227	1024	253	2247	664
ENST00000537567	VMP1	chr17	57851246	+	ENST00000357654	BRCA1	chr17	41234592	-	3429	639	327	2045	572
ENST00000537567	VMP1	chr17	57851246	+	ENST00000351666	BRCA1	chr17	41234592	-	3428	639	327	2045	572
ENST00000537567	VMP1	chr17	57851246	+	ENST00000309486	BRCA1	chr17	41234592	-	3428	639	327	2045	572
ENST00000537567	VMP1	chr17	57851246	+	ENST00000346315	BRCA1	chr17	41234592	-	2711	639	327	1328	333
ENST00000537567	VMP1	chr17	57851246	+	ENST00000354071	BRCA1	chr17	41234592	-	2633	639	327	1250	307
ENST00000537567	VMP1	chr17	57851246	+	ENST00000352993	BRCA1	chr17	41234592	-	3428	639	327	2045	572
ENST00000537567	VMP1	chr17	57851246	+	ENST00000468300	BRCA1	chr17	41234592	-	2842	639	327	1862	511
ENST00000539763	VMP1	chr17	57851246	+	ENST00000357654	BRCA1	chr17	41234592	-	3493	703	238	2109	623
ENST00000539763	VMP1	chr17	57851246	+	ENST00000351666	BRCA1	chr17	41234592	-	3492	703	238	2109	623
ENST00000539763	VMP1	chr17	57851246	+	ENST00000309486	BRCA1	chr17	41234592	-	3492	703	238	2109	623
ENST00000539763	VMP1	chr17	57851246	+	ENST00000346315	BRCA1	chr17	41234592	-	2775	703	238	1392	384
ENST00000539763	VMP1	chr17	57851246	+	ENST00000354071	BRCA1	chr17	41234592	-	2697	703	238	1314	358
ENST00000539763	VMP1	chr17	57851246	+	ENST00000352993	BRCA1	chr17	41234592	-	3492	703	238	2109	623
ENST00000539763	VMP1	chr17	57851246	+	ENST00000468300	BRCA1	chr17	41234592	-	2906	703	238	1926	562
ENST00000536180	VMP1	chr17	57851246	+	ENST00000357654	BRCA1	chr17	41234592	-	3523	733	310	2139	609
ENST00000536180	VMP1	chr17	57851246	+	ENST00000351666	BRCA1	chr17	41234592	-	3522	733	310	2139	609
ENST00000536180	VMP1	chr17	57851246	+	ENST00000309486	BRCA1	chr17	41234592	-	3522	733	310	2139	609
ENST00000536180	VMP1	chr17	57851246	+	ENST00000346315	BRCA1	chr17	41234592	-	2805	733	310	1422	370
ENST00000536180	VMP1	chr17	57851246	+	ENST00000354071	BRCA1	chr17	41234592	-	2727	733	310	1344	344
ENST00000536180	VMP1	chr17	57851246	+	ENST00000352993	BRCA1	chr17	41234592	-	3522	733	310	2139	609
ENST00000536180	VMP1	chr17	57851246	+	ENST00000468300	BRCA1	chr17	41234592	-	2936	733	310	1956	548
ENST00000545362	VMP1	chr17	57851246	+	ENST00000357654	BRCA1	chr17	41234592	-	3389	599	41	2005	654
ENST00000545362	VMP1	chr17	57851246	+	ENST00000351666	BRCA1	chr17	41234592	-	3388	599	41	2005	654
ENST00000545362	VMP1	chr17	57851246	+	ENST00000309486	BRCA1	chr17	41234592	-	3388	599	41	2005	654
ENST00000545362	VMP1	chr17	57851246	+	ENST00000346315	BRCA1	chr17	41234592	-	2671	599	41	1288	415
ENST00000545362	VMP1	chr17	57851246	+	ENST00000354071	BRCA1	chr17	41234592	-	2593	599	41	1210	389
ENST00000545362	VMP1	chr17	57851246	+	ENST00000352993	BRCA1	chr17	41234592	-	3388	599	41	2005	654
ENST00000545362	VMP1	chr17	57851246	+	ENST00000468300	BRCA1	chr17	41234592	-	2802	599	41	1822	593

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
ENST00000262291	ENST00000357654	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000997482	0.9990025
ENST00000262291	ENST00000351666	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.00099385	0.9990062
ENST00000262291	ENST00000309486	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.00099385	0.9990062
ENST00000262291	ENST00000346315	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001053168	0.99894685
ENST00000262291	ENST00000354071	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000910196	0.99908984
ENST00000262291	ENST00000352993	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.00099385	0.9990062
ENST00000262291	ENST00000468300	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001806842	0.9981932
ENST00000537567	ENST00000357654	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000676894	0.9993231
ENST00000537567	ENST00000351666	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.00067458	0.9993254
ENST00000537567	ENST00000309486	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.00067458	0.9993254
ENST00000537567	ENST00000346315	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001575971	0.99842405
ENST00000537567	ENST00000354071	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001444761	0.99855524
ENST00000537567	ENST00000352993	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.00067458	0.9993254
ENST00000537567	ENST00000468300	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001207338	0.99879265
ENST00000539763	ENST00000357654	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000566277	0.9994337
ENST00000539763	ENST00000351666	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000565464	0.99943453
ENST00000539763	ENST00000309486	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000565464	0.99943453
ENST00000539763	ENST00000346315	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001041425	0.9989586
ENST00000539763	ENST00000354071	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.002556994	0.99744296
ENST00000539763	ENST00000352993	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000565464	0.99943453
ENST00000539763	ENST00000468300	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001576579	0.99842346
ENST00000536180	ENST00000357654	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.00090823	0.99909174
ENST00000536180	ENST00000351666	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000905252	0.9990947
ENST00000536180	ENST00000309486	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000905252	0.9990947
ENST00000536180	ENST00000346315	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001070908	0.9989291
ENST00000536180	ENST00000354071	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001163163	0.9988368
ENST00000536180	ENST00000352993	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000905252	0.9990947
ENST00000536180	ENST00000468300	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001490974	0.998509
ENST00000545362	ENST00000357654	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000594136	0.99940586
ENST00000545362	ENST00000351666	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000591741	0.99940825
ENST00000545362	ENST00000309486	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000591741	0.99940825
ENST00000545362	ENST00000346315	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001012047	0.998988
ENST00000545362	ENST00000354071	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001035183	0.9989648
ENST00000545362	ENST00000352993	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.000591741	0.99940825
ENST00000545362	ENST00000468300	VMP1	chr17	57851246	+	BRCA1	chr17	41234592	-	0.001548533	0.9984515

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 VMP1-BRCA1

+/-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
VMP1	chr17	57851246	BRCA1	chr17	41234592	1024	257	EFEEMLEHAESAQQRDTMQHNLIKLQ
VMP1	chr17	57851246	BRCA1	chr17	41234592	599	186	EFEEMLEHAESAQQRDTMQHNLIKLQ
VMP1	chr17	57851246	BRCA1	chr17	41234592	639	104	EFEEMLEHAESAQQRDTMQHNLIKLQ
VMP1	chr17	57851246	BRCA1	chr17	41234592	703	155	EFEEMLEHAESAQQRDTMQHNLIKLQ
VMP1	chr17	57851246	BRCA1	chr17	41234592	733	141	EFEEMLEHAESAQQRDTMQHNLIKLQ

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Potential FusionNeoAntigen Information of VMP1-BRCA1 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.

VMP1-BRCA1_57851246_41234592.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)
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B44:03	AESAQQRDTM	0.9979	0.7219	8	18
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B48:01	QQRDTMQHNL	0.9735	0.737	12	22
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B15:04	QQRDTMQHNL	0.9917	0.9004	12	22
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-C16:01	SAQQRDTM	0.9308	0.958	10	18
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B15:50	AQQRDTMQH	0.9896	0.8885	11	20
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B44:07	AESAQQRDTM	0.9979	0.7219	8	18
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B44:13	AESAQQRDTM	0.9979	0.7219	8	18
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B44:26	AESAQQRDTM	0.9979	0.7219	8	18
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B40:04	AESAQQRDTM	0.9938	0.6552	8	18
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B15:73	QQRDTMQHNL	0.9811	0.9692	12	22
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B15:30	QQRDTMQHNL	0.9753	0.9682	12	22
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B41:03	AESAQQRDTM	0.7537	0.6546	8	18
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	HLA-B40:21	QQRDTMQHNL	0.4902	0.6784	12	22

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Potential FusionNeoAntigen Information of VMP1-BRCA1 in HLA II

VMP1-BRCA1_57851246_41234592.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)
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0403	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0403	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0413	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0413	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0427	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0427	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0439	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0439	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0440	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0441	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0441	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0444	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0446	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0446	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0449	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0449	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0450	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0450	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0451	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0452	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0452	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0455	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0460	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0460	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0468	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0471	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0471	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0478	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0478	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0479	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0485	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0485	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0488	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0906	EEMLEHAESAQQRDT	2	17
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-0906	FEEMLEHAESAQQRD	1	16
VMP1-BRCA1	chr17	57851246	chr17	41234592	1024	DRB1-1410	EEMLEHAESAQQRDT	2	17

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Fusion breakpoint peptide structures of VMP1-BRCA1

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
1769	EHAESAQQRDTMQH	VMP1	BRCA1	chr17	57851246	chr17	41234592	1024

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of VMP1-BRCA1

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	1769	EHAESAQQRDTMQH	-7.71897	-8.75427
HLA-B14:02	3BVN	1769	EHAESAQQRDTMQH	-5.42937	-5.54277
HLA-B52:01	3W39	1769	EHAESAQQRDTMQH	-7.35534	-7.46874
HLA-B52:01	3W39	1769	EHAESAQQRDTMQH	-5.87088	-6.90618
HLA-A11:01	4UQ2	1769	EHAESAQQRDTMQH	-6.49186	-7.52716
HLA-A11:01	4UQ2	1769	EHAESAQQRDTMQH	10000.1	10000
HLA-A24:02	5HGA	1769	EHAESAQQRDTMQH	-7.92254	-8.03594
HLA-A24:02	5HGA	1769	EHAESAQQRDTMQH	-7.01673	-8.05203
HLA-B27:05	6PYJ	1769	EHAESAQQRDTMQH	-4.67474	-5.71004
HLA-B44:05	3DX8	1769	EHAESAQQRDTMQH	-7.23401	-7.34741
HLA-B44:05	3DX8	1769	EHAESAQQRDTMQH	-3.39794	-4.43324

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Vaccine Design for the FusionNeoAntigens of VMP1-BRCA1

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
VMP1-BRCA1	chr17	57851246	chr17	41234592	10	18	SAQQRDTM	TCTGCACAACAGAGGGATACCATG
VMP1-BRCA1	chr17	57851246	chr17	41234592	11	20	AQQRDTMQH	GCACAACAGAGGGATACCATGCAACAT
VMP1-BRCA1	chr17	57851246	chr17	41234592	12	22	QQRDTMQHNL	CAACAGAGGGATACCATGCAACATAACCTG
VMP1-BRCA1	chr17	57851246	chr17	41234592	8	18	AESAQQRDTM	GCAGAGTCTGCACAACAGAGGGATACCATG

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
VMP1-BRCA1	chr17	57851246	chr17	41234592	1	16	FEEMLEHAESAQQRD	TTTGAAGAGATGCTGGAACATGCAGAGTCTGCACAACAGAGGGAT
VMP1-BRCA1	chr17	57851246	chr17	41234592	2	17	EEMLEHAESAQQRDT	GAAGAGATGCTGGAACATGCAGAGTCTGCACAACAGAGGGATACC

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Information of the samples that have these potential fusion neoantigens of VMP1-BRCA1

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
SARC	VMP1-BRCA1	chr17	57851246	ENST00000262291	chr17	41234592	ENST00000309486	TCGA-KF-A41W-01A

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Potential target of CAR-T therapy development for VMP1-BRCA1

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

Hgene

VMP1

chr17:57851246

chr17:41234592

ENST00000262291

110_130

238

407.0

Transmembrane

Helical

Hgene

VMP1

chr17:57851246

chr17:41234592

ENST00000262291

44_64

238

407.0

Transmembrane

Helical

Hgene

VMP1

chr17:57851246

chr17:41234592

ENST00000262291

78_98

238

407.0

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 VMP1-BRCA1

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 VMP1-BRCA1

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)