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Fusion Protein:SLC9B1-LRRK1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SLC9B1-LRRK1
	FusionPDB ID: 83576
	FusionGDB2.0 ID: 83576
		Hgene	Tgene
	Gene symbol	SLC9B1	LRRK1
	Gene ID	150159	79705
	Gene name	solute carrier family 9 member B1	leucine rich repeat kinase 1
	Synonyms	NHA1\|NHEDC1	RIPK6\|Roco1
	Cytomap	4q24	15q26.3
	Type of gene	protein-coding	protein-coding
	Description	sodium/hydrogen exchanger 9B1NHE domain-containing protein 1Na(+)/H(+) exchanger-like domain-containing protein 1sodium/hydrogen exchanger-like domain-containing protein 1solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member	leucine-rich repeat serine/threonine-protein kinase 1
	Modification date	20200313	20200313
	UniProtAcc	.	Q38SD2 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000296422, ENST00000394789, ENST00000512651,	ENST00000532029, ENST00000532145, ENST00000284395, ENST00000388948,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 2=18	4 X 4 X 4=64
	# samples	3	4
	** MAII score	log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(4/64*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SLC9B1 [Title/Abstract] AND LRRK1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SLC9B1 [Title/Abstract] AND LRRK1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SLC9B1(103912800)-LRRK1(101586186), # samples:1
Anticipated loss of major functional domain due to fusion event.	SLC9B1-LRRK1 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. SLC9B1-LRRK1 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. SLC9B1-LRRK1 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. SLC9B1-LRRK1 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/chr4:103912800/chr15:101586186)
- 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 SLC9B1 (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 LRRK1 (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)
ENST00000394789	SLC9B1	chr4	103912800	-	ENST00000388948	LRRK1	chr15	101586186	+	4540	191	39	3275	1078
ENST00000394789	SLC9B1	chr4	103912800	-	ENST00000284395	LRRK1	chr15	101586186	+	4538	191	39	3275	1078
ENST00000296422	SLC9B1	chr4	103912800	-	ENST00000388948	LRRK1	chr15	101586186	+	4560	211	14	3295	1093
ENST00000296422	SLC9B1	chr4	103912800	-	ENST00000284395	LRRK1	chr15	101586186	+	4558	211	14	3295	1093

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
ENST00000394789	ENST00000388948	SLC9B1	chr4	103912800	-	LRRK1	chr15	101586186	+	0.000702135	0.99929786
ENST00000394789	ENST00000284395	SLC9B1	chr4	103912800	-	LRRK1	chr15	101586186	+	0.000701497	0.99929845
ENST00000296422	ENST00000388948	SLC9B1	chr4	103912800	-	LRRK1	chr15	101586186	+	0.000725691	0.9992743
ENST00000296422	ENST00000284395	SLC9B1	chr4	103912800	-	LRRK1	chr15	101586186	+	0.000725037	0.999275

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 SLC9B1-LRRK1

+/-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
SLC9B1	chr4	103912800	LRRK1	chr15	101586186	191	50	IWRMKTSKHLQLLSYLLPHLLPSKPG
SLC9B1	chr4	103912800	LRRK1	chr15	101586186	211	65	IWRMKTSKHLQLLSYLLPHLLPSKPG

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Potential FusionNeoAntigen Information of SLC9B1-LRRK1 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.

SLC9B1-LRRK1_103912800_101586186.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)
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B52:01	LSYLLPHL	0.998	0.9216	12	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:18	KHLQLLSY	0.8636	0.5576	7	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B39:01	KHLQLLSYL	0.9966	0.8039	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:22	LLSYLLPHL	0.9956	0.6828	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B38:01	KHLQLLSYL	0.9942	0.928	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B38:02	KHLQLLSYL	0.994	0.9159	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:17	LSYLLPHLL	0.9936	0.9447	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B58:01	LSYLLPHLL	0.9933	0.9156	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B57:01	LSYLLPHLL	0.9932	0.9734	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B58:02	LSYLLPHLL	0.9927	0.9177	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:11	LLSYLLPHL	0.9916	0.6804	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:16	LSYLLPHLL	0.9916	0.8022	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B57:03	LSYLLPHLL	0.9913	0.9881	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:27	LLSYLLPHL	0.9907	0.7333	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:24	LLSYLLPHL	0.9905	0.6663	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:67	LLSYLLPHL	0.9905	0.6663	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:30	LLSYLLPHL	0.9905	0.6663	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:13	LLSYLLPHL	0.9904	0.787	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:60	LLSYLLPHL	0.9902	0.6538	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:21	LLSYLLPHL	0.9874	0.7694	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:04	LLSYLLPHL	0.9817	0.7168	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:38	LLSYLLPHL	0.9743	0.8044	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:35	LLSYLLPHL	0.9603	0.6931	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B52:01	LSYLLPHLL	0.9321	0.9333	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:29	LLSYLLPHL	0.9315	0.6707	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:20	LLSYLLPHL	0.9	0.6676	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A32:13	LSYLLPHLL	0.791	0.9848	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:03	SKHLQLLSY	0.3689	0.556	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:37	KHLQLLSYL	0.2476	0.5053	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B38:01	KHLQLLSYLL	0.9843	0.9406	7	17
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B38:01	SKHLQLLSYL	0.9716	0.9142	6	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:04	QLLSYLLPHL	0.9645	0.6419	10	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B57:01	KTSKHLQLLSY	0.9994	0.9218	4	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:17	KTSKHLQLLSY	0.9981	0.8595	4	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B58:02	KTSKHLQLLSY	0.9974	0.8611	4	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C15:04	LSYLLPHLL	0.9992	0.8963	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C15:06	LSYLLPHLL	0.9991	0.9375	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:07	LSYLLPHLL	0.999	0.9816	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:08	LSYLLPHLL	0.9988	0.9533	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:19	LSYLLPHLL	0.9988	0.9941	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:95	SKHLQLLSY	0.9974	0.5697	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:02	LLSYLLPHL	0.9957	0.5411	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C04:06	LSYLLPHLL	0.9947	0.9512	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:05	LLSYLLPHL	0.9935	0.6895	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B39:05	KHLQLLSYL	0.9916	0.7752	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:07	LLSYLLPHL	0.9909	0.6783	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:01	LLSYLLPHL	0.9905	0.6663	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C06:03	LSYLLPHLL	0.9811	0.9964	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C12:04	LSYLLPHLL	0.9792	0.9965	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C12:12	LSYLLPHLL	0.9783	0.9654	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:14	LSYLLPHLL	0.9774	0.9838	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C08:04	LSYLLPHLL	0.9704	0.9706	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C08:13	LSYLLPHLL	0.9704	0.9706	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:13	KHLQLLSYL	0.9335	0.8698	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B51:07	LSYLLPHLL	0.9228	0.9365	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:19	SKHLQLLSY	0.8692	0.6053	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:80	SKHLQLLSY	0.8308	0.8693	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:67	SKHLQLLSY	0.8308	0.8693	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:10	SKHLQLLSY	0.8254	0.8981	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:46	SKHLQLLSY	0.8128	0.7703	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C02:06	LSYLLPHLL	0.7238	0.98	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:21	SKHLQLLSY	0.713	0.7726	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:04	SKHLQLLSY	0.4093	0.8432	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C12:16	SKHLQLLSY	0.1314	0.9152	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C15:09	LSYLLPHLL	0.9992	0.8963	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C15:02	LSYLLPHLL	0.9989	0.8897	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C15:05	LSYLLPHLL	0.9988	0.9011	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:05	LSYLLPHLL	0.9986	0.9698	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:04	LSYLLPHLL	0.9981	0.9943	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:03	LSYLLPHLL	0.9981	0.9943	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:17	LSYLLPHLL	0.9981	0.9851	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:01	SKHLQLLSY	0.9974	0.5352	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:02	LSYLLPHLL	0.9963	0.9815	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B39:31	KHLQLLSYL	0.9961	0.8039	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:03	LLSYLLPHL	0.9959	0.8003	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B38:05	KHLQLLSYL	0.9942	0.928	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B57:10	LSYLLPHLL	0.9932	0.9734	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B58:06	LSYLLPHLL	0.9912	0.8123	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:14	LLSYLLPHL	0.9875	0.7236	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-A02:06	LLSYLLPHL	0.9874	0.7694	11	20
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C16:04	LSYLLPHLL	0.986	0.9901	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C03:06	LSYLLPHLL	0.9825	0.9941	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C12:03	LSYLLPHLL	0.9806	0.9888	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C06:02	LSYLLPHLL	0.9771	0.9962	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C06:17	LSYLLPHLL	0.9771	0.9962	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C16:02	LSYLLPHLL	0.9743	0.9924	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B57:02	LSYLLPHLL	0.9528	0.976	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C16:01	LSYLLPHLL	0.9338	0.987	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C12:02	LSYLLPHLL	0.9152	0.9846	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:17	SKHLQLLSY	0.8799	0.9151	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B35:13	LSYLLPHLL	0.8519	0.9249	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:02	SKHLQLLSY	0.8308	0.8693	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B51:06	LSYLLPHLL	0.8165	0.5923	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B51:09	LSYLLPHLL	0.8075	0.5539	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C07:22	SKHLQLLSY	0.791	0.5151	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:50	SKHLQLLSY	0.781	0.8117	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C06:08	LSYLLPHLL	0.7797	0.9911	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C17:01	LSYLLPHLL	0.7356	0.9214	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:09	KHLQLLSYL	0.7119	0.5226	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C02:02	LSYLLPHLL	0.6765	0.9795	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-C02:10	LSYLLPHLL	0.6765	0.9795	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B35:28	SKHLQLLSY	0.6737	0.7759	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:35	SKHLQLLSY	0.6194	0.8053	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B39:11	KHLQLLSYL	0.4915	0.7359	7	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B18:04	SKHLQLLSY	0.3947	0.8694	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B48:02	SKHLQLLSY	0.3742	0.7552	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:53	SKHLQLLSY	0.2767	0.8136	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B18:06	SKHLQLLSY	0.2381	0.8392	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B15:54	SKHLQLLSY	0.1713	0.7774	6	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B07:13	LSYLLPHLL	0.0887	0.8294	12	21
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B38:05	KHLQLLSYLL	0.9843	0.9406	7	17
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B38:05	SKHLQLLSYL	0.9716	0.9142	6	16
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B57:04	KTSKHLQLLSY	0.9995	0.7704	4	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B57:10	KTSKHLQLLSY	0.9994	0.9218	4	15
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	211	HLA-B58:06	KTSKHLQLLSY	0.9984	0.776	4	15

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Potential FusionNeoAntigen Information of SLC9B1-LRRK1 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 SLC9B1-LRRK1

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
8688	SKHLQLLSYLLPHL	SLC9B1	LRRK1	chr4	103912800	chr15	101586186	211

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SLC9B1-LRRK1

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-B57:03	2BVO	8688	SKHLQLLSYLLPHL	-3.01019	-4.04549
HLA-A03:01	2XPG	8688	SKHLQLLSYLLPHL	-6.28383	-7.31913
HLA-A03:01	2XPG	8688	SKHLQLLSYLLPHL	-5.59305	-5.70645
HLA-B14:02	3BVN	8688	SKHLQLLSYLLPHL	-4.73996	-4.85336
HLA-B14:02	3BVN	8688	SKHLQLLSYLLPHL	-3.09097	-4.12627
HLA-B52:01	3W39	8688	SKHLQLLSYLLPHL	-5.54594	-5.65934
HLA-B52:01	3W39	8688	SKHLQLLSYLLPHL	-3.57843	-4.61373
HLA-B18:01	4JQV	8688	SKHLQLLSYLLPHL	-5.65575	-5.76915
HLA-B18:01	4JQV	8688	SKHLQLLSYLLPHL	-3.07606	-4.11136
HLA-A11:01	4UQ2	8688	SKHLQLLSYLLPHL	-9.68638	-9.79978
HLA-A11:01	4UQ2	8688	SKHLQLLSYLLPHL	-6.73518	-7.77048
HLA-A24:02	5HGA	8688	SKHLQLLSYLLPHL	-6.73076	-6.84416
HLA-A24:02	5HGA	8688	SKHLQLLSYLLPHL	-4.20633	-5.24163
HLA-B27:05	6PYJ	8688	SKHLQLLSYLLPHL	-4.80839	-4.92179
HLA-B27:05	6PYJ	8688	SKHLQLLSYLLPHL	-4.77877	-5.81407
HLA-B27:03	6PZ5	8688	SKHLQLLSYLLPHL	-3.90263	-4.93793
HLA-B44:05	3DX8	8688	SKHLQLLSYLLPHL	-5.97396	-6.08736
HLA-B44:05	3DX8	8688	SKHLQLLSYLLPHL	-5.02247	-6.05777
HLA-A02:01	6TDR	8688	SKHLQLLSYLLPHL	-4.7023	-5.7376

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Vaccine Design for the FusionNeoAntigens of SLC9B1-LRRK1

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
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	10	20	QLLSYLLPHL	ACTCCTCAGCTACCTCCTGCCCCATCTCCT
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	11	20	LLSYLLPHL	CCTCAGCTACCTCCTGCCCCATCTCCT
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	12	20	LSYLLPHL	CAGCTACCTCCTGCCCCATCTCCT
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	12	21	LSYLLPHLL	CAGCTACCTCCTGCCCCATCTCCTTCC
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	4	15	KTSKHLQLLSY	AACTTCCAAACATCTACAACTCCTCAGCTACCT
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	6	15	SKHLQLLSY	CAAACATCTACAACTCCTCAGCTACCT
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	6	16	SKHLQLLSYL	CAAACATCTACAACTCCTCAGCTACCTCCT
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	7	15	KHLQLLSY	ACATCTACAACTCCTCAGCTACCT
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	7	16	KHLQLLSYL	ACATCTACAACTCCTCAGCTACCTCCT
SLC9B1-LRRK1	chr4	103912800	chr15	101586186	7	17	KHLQLLSYLL	ACATCTACAACTCCTCAGCTACCTCCTGCC

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 SLC9B1-LRRK1

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
LGG	SLC9B1-LRRK1	chr4	103912800	ENST00000296422	chr15	101586186	ENST00000284395	TCGA-E1-5304-01A

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Potential target of CAR-T therapy development for SLC9B1-LRRK1

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 SLC9B1-LRRK1

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 SLC9B1-LRRK1

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)