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Fusion Protein:SCYL1-ASNA1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SCYL1-ASNA1
	FusionPDB ID: 79767
	FusionGDB2.0 ID: 79767
		Hgene	Tgene
	Gene symbol	SCYL1	ASNA1
	Gene ID	57410	439
	Gene name	SCY1 like pseudokinase 1	guided entry of tail-anchored proteins factor 3, ATPase
	Synonyms	GKLP\|HT019\|NKTL\|NTKL\|P105\|SCAR21\|TAPK\|TEIF\|TRAP	ARSA-I\|ARSA1\|ASNA-I\|ASNA1\|TRC40
	Cytomap	11q13.1	19p13.13
	Type of gene	protein-coding	protein-coding
	Description	N-terminal kinase-like proteinSCY1-like protein 1SCY1-like, kinase-like 1coated vesicle-associated kinase of 90 kDalikely ortholog of mouse N-terminal kinase-like proteintelomerase regulation-associated proteintelomerase transcriptional elements-int	ATPase ASNA1arsA arsenite transporter, ATP-binding, homolog 1golgi to ER traffic 3 homologtransmembrane domain recognition complex 40 kDa ATPase subunit
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000270176, ENST00000279270, ENST00000420247, ENST00000524944, ENST00000525364, ENST00000527009, ENST00000533862, ENST00000534462,	ENST00000357332, ENST00000591090,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 8 X 7=448	8 X 8 X 4=256
	# samples	14	10
	** MAII score	log2(14/448*10)=-1.67807190511264 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/256*10)=-1.35614381022528 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SCYL1 [Title/Abstract] AND ASNA1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SCYL1 [Title/Abstract] AND ASNA1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SCYL1(65299154)-ASNA1(12856190), # samples:1
Anticipated loss of major functional domain due to fusion event.	SCYL1-ASNA1 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. SCYL1-ASNA1 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. SCYL1-ASNA1 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. SCYL1-ASNA1 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	SCYL1	GO:0006890	retrograde vesicle-mediated transport, Golgi to ER	18556652
Tgene	ASNA1	GO:0071816	tail-anchored membrane protein insertion into ER membrane	25535373

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:65299154/chr19:12856190)
- 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 SCYL1 (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 ASNA1 (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)
ENST00000525364	SCYL1	chr11	65299154	+	ENST00000591090	ASNA1	chr19	12856190	+	2150	1193	77	1930	617
ENST00000525364	SCYL1	chr11	65299154	+	ENST00000357332	ASNA1	chr19	12856190	+	2150	1193	77	1930	617
ENST00000270176	SCYL1	chr11	65299154	+	ENST00000591090	ASNA1	chr19	12856190	+	2150	1193	77	1930	617
ENST00000270176	SCYL1	chr11	65299154	+	ENST00000357332	ASNA1	chr19	12856190	+	2150	1193	77	1930	617
ENST00000420247	SCYL1	chr11	65299154	+	ENST00000591090	ASNA1	chr19	12856190	+	2142	1185	69	1922	617
ENST00000420247	SCYL1	chr11	65299154	+	ENST00000357332	ASNA1	chr19	12856190	+	2142	1185	69	1922	617
ENST00000533862	SCYL1	chr11	65299154	+	ENST00000591090	ASNA1	chr19	12856190	+	2115	1158	42	1895	617
ENST00000533862	SCYL1	chr11	65299154	+	ENST00000357332	ASNA1	chr19	12856190	+	2115	1158	42	1895	617
ENST00000279270	SCYL1	chr11	65299154	+	ENST00000591090	ASNA1	chr19	12856190	+	2114	1157	41	1894	617
ENST00000279270	SCYL1	chr11	65299154	+	ENST00000357332	ASNA1	chr19	12856190	+	2114	1157	41	1894	617
ENST00000524944	SCYL1	chr11	65299154	+	ENST00000591090	ASNA1	chr19	12856190	+	2106	1149	33	1886	617
ENST00000524944	SCYL1	chr11	65299154	+	ENST00000357332	ASNA1	chr19	12856190	+	2106	1149	33	1886	617
ENST00000527009	SCYL1	chr11	65299154	+	ENST00000591090	ASNA1	chr19	12856190	+	2123	1166	278	1903	541
ENST00000527009	SCYL1	chr11	65299154	+	ENST00000357332	ASNA1	chr19	12856190	+	2123	1166	278	1903	541

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
ENST00000525364	ENST00000591090	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.01145062	0.9885494
ENST00000525364	ENST00000357332	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.01145062	0.9885494
ENST00000270176	ENST00000591090	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.01145062	0.9885494
ENST00000270176	ENST00000357332	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.01145062	0.9885494
ENST00000420247	ENST00000591090	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.011278546	0.98872143
ENST00000420247	ENST00000357332	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.011278546	0.98872143
ENST00000533862	ENST00000591090	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.011236977	0.98876303
ENST00000533862	ENST00000357332	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.011236977	0.98876303
ENST00000279270	ENST00000591090	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.011311387	0.98868865
ENST00000279270	ENST00000357332	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.011311387	0.98868865
ENST00000524944	ENST00000591090	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.011244512	0.9887554
ENST00000524944	ENST00000357332	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.011244512	0.9887554
ENST00000527009	ENST00000591090	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.012783952	0.98721606
ENST00000527009	ENST00000357332	SCYL1	chr11	65299154	+	ASNA1	chr19	12856190	+	0.012783952	0.98721606

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 SCYL1-ASNA1

+/-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
SCYL1	chr11	65299154	ASNA1	chr19	12856190	1149	371	SSTDRAMRIRLLQQEIDPSLGVAELP
SCYL1	chr11	65299154	ASNA1	chr19	12856190	1157	371	SSTDRAMRIRLLQQEIDPSLGVAELP
SCYL1	chr11	65299154	ASNA1	chr19	12856190	1158	371	SSTDRAMRIRLLQQEIDPSLGVAELP
SCYL1	chr11	65299154	ASNA1	chr19	12856190	1166	295	SSTDRAMRIRLLQQEIDPSLGVAELP
SCYL1	chr11	65299154	ASNA1	chr19	12856190	1185	371	SSTDRAMRIRLLQQEIDPSLGVAELP
SCYL1	chr11	65299154	ASNA1	chr19	12856190	1193	371	SSTDRAMRIRLLQQEIDPSLGVAELP

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Potential FusionNeoAntigen Information of SCYL1-ASNA1 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.

SCYL1-ASNA1_65299154_12856190.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)
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:13	QQEIDPSL	0.9738	0.9403	12	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A30:08	RIRLLQQEI	0.9876	0.8611	7	16
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B48:01	LQQEIDPSL	0.9749	0.5054	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:01	LQQEIDPSL	0.9293	0.9753	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:24	LQQEIDPSL	0.9273	0.5781	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:13	LQQEIDPSL	0.889	0.9635	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B38:01	LQQEIDPSL	0.8538	0.978	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B38:02	LQQEIDPSL	0.8413	0.9842	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:22	LQQEIDPSL	0.8412	0.7498	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:21	LQQEIDPSL	0.8017	0.7973	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:60	LQQEIDPSL	0.7984	0.6055	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:30	LQQEIDPSL	0.7963	0.6762	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:67	LQQEIDPSL	0.7963	0.6762	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:24	LQQEIDPSL	0.7963	0.6762	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:10	LQQEIDPSL	0.7298	0.765	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:04	LQQEIDPSL	0.6894	0.6697	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B13:01	LQQEIDPSL	0.6698	0.9866	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B13:02	LQQEIDPSL	0.6681	0.6648	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:29	LQQEIDPSL	0.6504	0.6834	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:37	LQQEIDPSL	0.6143	0.738	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:03	LQQEIDPSL	0.5959	0.8803	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:16	LQQEIDPSL	0.5352	0.7063	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B47:01	LQQEIDPSL	0.4533	0.8382	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B13:02	RIRLLQQEI	0.2348	0.8033	7	16
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:19	LQQEIDPSL	0.1655	0.6881	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B52:01	LQQEIDPSL	0.1085	0.964	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:22	LLQQEIDPSL	0.9591	0.8551	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:30	LLQQEIDPSL	0.8757	0.77	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:24	LLQQEIDPSL	0.8757	0.77	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:67	LLQQEIDPSL	0.8757	0.77	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:60	LLQQEIDPSL	0.8706	0.7277	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B45:01	QQEIDPSLGV	0.8585	0.992	12	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:04	LLQQEIDPSL	0.8386	0.7332	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B50:02	QQEIDPSLGV	0.8267	0.8131	12	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:16	LLQQEIDPSL	0.8136	0.7613	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:29	LLQQEIDPSL	0.7322	0.7751	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:21	QQEIDPSLGV	0.7153	0.8546	12	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:19	LLQQEIDPSL	0.6361	0.7691	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B13:02	QQEIDPSLGV	0.5866	0.9337	12	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:60	RLLQQEIDPSL	0.9939	0.733	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:30	RLLQQEIDPSL	0.9932	0.7439	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:67	RLLQQEIDPSL	0.9932	0.7439	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:24	RLLQQEIDPSL	0.9932	0.7439	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:11	RLLQQEIDPSL	0.9919	0.7701	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:16	RLLQQEIDPSL	0.9912	0.6843	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:17	RLLQQEIDPSL	0.9896	0.6058	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:21	RLLQQEIDPSL	0.9894	0.833	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:04	RLLQQEIDPSL	0.9861	0.7858	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:27	RLLQQEIDPSL	0.9851	0.7511	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:21	LQQEIDPSLGV	0.977	0.8652	11	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B48:01	RLLQQEIDPSL	0.9409	0.7625	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:29	RLLQQEIDPSL	0.9166	0.7436	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:20	RLLQQEIDPSL	0.9124	0.7502	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:35	RLLQQEIDPSL	0.9015	0.7588	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B13:02	RLLQQEIDPSL	0.8915	0.8609	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B13:02	LQQEIDPSLGV	0.874	0.9678	11	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B13:01	RLLQQEIDPSL	0.7513	0.9924	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:13	RLLQQEIDPSL	0.6337	0.9844	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:08	QQEIDPSL	0.9792	0.9356	12	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:09	LQQEIDPSL	0.9464	0.7077	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:04	LQQEIDPSL	0.9125	0.9312	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:08	LQQEIDPSL	0.9066	0.941	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-C08:03	LQQEIDPSL	0.9	0.9841	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:02	LQQEIDPSL	0.8568	0.501	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:05	LQQEIDPSL	0.8561	0.6628	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:05	LQQEIDPSL	0.8454	0.9726	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:01	LQQEIDPSL	0.7963	0.6762	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B14:03	LQQEIDPSL	0.603	0.7783	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:05	LQQEIDPSL	0.4961	0.9631	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B51:07	LQQEIDPSL	0.0784	0.854	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:02	LLQQEIDPSL	0.963	0.7051	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:01	LLQQEIDPSL	0.8757	0.77	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:05	QQEIDPSLGV	0.8225	0.832	12	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B44:10	QQEIDPSLGV	0.4868	0.8459	12	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:01	RLLQQEIDPSL	0.9932	0.7439	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:02	RLLQQEIDPSL	0.9924	0.6291	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:08	RLLQQEIDPSL	0.8498	0.9776	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B48:03	RLLQQEIDPSL	0.7077	0.6844	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:02	QQEIDPSL	0.9883	0.9416	12	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:11	QQEIDPSL	0.9798	0.9122	12	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A30:01	RIRLLQQEI	0.9885	0.9459	7	16
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:73	LQQEIDPSL	0.9753	0.9422	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:02	LQQEIDPSL	0.951	0.9645	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:31	LQQEIDPSL	0.9406	0.9764	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:30	LQQEIDPSL	0.9026	0.9014	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-C08:01	LQQEIDPSL	0.9	0.9841	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:11	LQQEIDPSL	0.8748	0.9339	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B38:05	LQQEIDPSL	0.8538	0.978	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:53	LQQEIDPSL	0.8126	0.9107	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:54	LQQEIDPSL	0.8102	0.9004	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:14	LQQEIDPSL	0.8067	0.7506	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:06	LQQEIDPSL	0.8017	0.7973	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B35:13	LQQEIDPSL	0.6704	0.9678	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B48:02	LQQEIDPSL	0.6022	0.9737	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:09	LQQEIDPSL	0.5405	0.8542	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B35:20	LQQEIDPSL	0.5333	0.9805	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:20	LQQEIDPSL	0.5014	0.9775	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B35:28	LQQEIDPSL	0.4906	0.9776	11	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:14	QQEIDPSLGV	0.727	0.8183	12	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:06	QQEIDPSLGV	0.7153	0.8546	12	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B40:21	LLQQEIDPSL	0.3077	0.5408	10	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B15:73	RLLQQEIDPSL	0.9968	0.9846	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:14	RLLQQEIDPSL	0.9901	0.7783	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:06	RLLQQEIDPSL	0.9894	0.833	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:14	LQQEIDPSLGV	0.9796	0.8645	11	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-A02:06	LQQEIDPSLGV	0.977	0.8652	11	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B39:02	RLLQQEIDPSL	0.808	0.9831	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B40:21	RLLQQEIDPSL	0.8034	0.7715	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B40:12	RLLQQEIDPSL	0.7077	0.6844	9	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	HLA-B40:49	RLLQQEIDPSL	0.6768	0.6248	9	20

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Potential FusionNeoAntigen Information of SCYL1-ASNA1 in HLA II

SCYL1-ASNA1_65299154_12856190.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)
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0101	RIRLLQQEIDPSLGV	7	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0101	MRIRLLQQEIDPSLG	6	21
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0101	AMRIRLLQQEIDPSL	5	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0101	IRLLQQEIDPSLGVA	8	23
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0101	RAMRIRLLQQEIDPS	4	19
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0103	RIRLLQQEIDPSLGV	7	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0103	MRIRLLQQEIDPSLG	6	21
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0103	AMRIRLLQQEIDPSL	5	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0103	IRLLQQEIDPSLGVA	8	23
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0103	RAMRIRLLQQEIDPS	4	19
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0104	RIRLLQQEIDPSLGV	7	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0104	MRIRLLQQEIDPSLG	6	21
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0104	AMRIRLLQQEIDPSL	5	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0104	IRLLQQEIDPSLGVA	8	23
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0104	RAMRIRLLQQEIDPS	4	19
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0106	RIRLLQQEIDPSLGV	7	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0106	MRIRLLQQEIDPSLG	6	21
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0106	AMRIRLLQQEIDPSL	5	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0106	IRLLQQEIDPSLGVA	8	23
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0106	RAMRIRLLQQEIDPS	4	19
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0107	RIRLLQQEIDPSLGV	7	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0107	MRIRLLQQEIDPSLG	6	21
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0107	AMRIRLLQQEIDPSL	5	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0107	IRLLQQEIDPSLGVA	8	23
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0107	RAMRIRLLQQEIDPS	4	19
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0108	RIRLLQQEIDPSLGV	7	22
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0108	MRIRLLQQEIDPSLG	6	21
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0108	AMRIRLLQQEIDPSL	5	20
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0108	IRLLQQEIDPSLGVA	8	23
SCYL1-ASNA1	chr11	65299154	chr19	12856190	1193	DRB4-0108	RAMRIRLLQQEIDPS	4	19

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Fusion breakpoint peptide structures of SCYL1-ASNA1

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
6003	MRIRLLQQEIDPSL	SCYL1	ASNA1	chr11	65299154	chr19	12856190	1193

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SCYL1-ASNA1

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	6003	MRIRLLQQEIDPSL	-7.9962	-8.1096
HLA-B14:02	3BVN	6003	MRIRLLQQEIDPSL	-5.70842	-6.74372
HLA-B52:01	3W39	6003	MRIRLLQQEIDPSL	-6.83737	-6.95077
HLA-B52:01	3W39	6003	MRIRLLQQEIDPSL	-4.4836	-5.5189
HLA-A11:01	4UQ2	6003	MRIRLLQQEIDPSL	-10.0067	-10.1201
HLA-A11:01	4UQ2	6003	MRIRLLQQEIDPSL	-9.03915	-10.0745
HLA-A24:02	5HGA	6003	MRIRLLQQEIDPSL	-6.56204	-6.67544
HLA-A24:02	5HGA	6003	MRIRLLQQEIDPSL	-5.42271	-6.45801
HLA-B44:05	3DX8	6003	MRIRLLQQEIDPSL	-7.85648	-8.89178
HLA-B44:05	3DX8	6003	MRIRLLQQEIDPSL	-5.3978	-5.5112
HLA-A02:01	6TDR	6003	MRIRLLQQEIDPSL	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of SCYL1-ASNA1

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
SCYL1-ASNA1	chr11	65299154	chr19	12856190	10	20	LLQQEIDPSL	CTGCAGCAGGAGATTGACCCCAGCCTGGGC
SCYL1-ASNA1	chr11	65299154	chr19	12856190	11	20	LQQEIDPSL	CAGCAGGAGATTGACCCCAGCCTGGGC
SCYL1-ASNA1	chr11	65299154	chr19	12856190	11	22	LQQEIDPSLGV	CAGCAGGAGATTGACCCCAGCCTGGGCGTGGCG
SCYL1-ASNA1	chr11	65299154	chr19	12856190	12	20	QQEIDPSL	CAGGAGATTGACCCCAGCCTGGGC
SCYL1-ASNA1	chr11	65299154	chr19	12856190	12	22	QQEIDPSLGV	CAGGAGATTGACCCCAGCCTGGGCGTGGCG
SCYL1-ASNA1	chr11	65299154	chr19	12856190	7	16	RIRLLQQEI	ATCCGCCTCCTGCAGCAGGAGATTGAC
SCYL1-ASNA1	chr11	65299154	chr19	12856190	9	20	RLLQQEIDPSL	CTCCTGCAGCAGGAGATTGACCCCAGCCTGGGC

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
SCYL1-ASNA1	chr11	65299154	chr19	12856190	4	19	RAMRIRLLQQEIDPS	GCCATGCGCATCCGCCTCCTGCAGCAGGAGATTGACCCCAGCCTG
SCYL1-ASNA1	chr11	65299154	chr19	12856190	5	20	AMRIRLLQQEIDPSL	ATGCGCATCCGCCTCCTGCAGCAGGAGATTGACCCCAGCCTGGGC
SCYL1-ASNA1	chr11	65299154	chr19	12856190	6	21	MRIRLLQQEIDPSLG	CGCATCCGCCTCCTGCAGCAGGAGATTGACCCCAGCCTGGGCGTG
SCYL1-ASNA1	chr11	65299154	chr19	12856190	7	22	RIRLLQQEIDPSLGV	ATCCGCCTCCTGCAGCAGGAGATTGACCCCAGCCTGGGCGTGGCG
SCYL1-ASNA1	chr11	65299154	chr19	12856190	8	23	IRLLQQEIDPSLGVA	CGCCTCCTGCAGCAGGAGATTGACCCCAGCCTGGGCGTGGCGGAG

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Information of the samples that have these potential fusion neoantigens of SCYL1-ASNA1

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
OV	SCYL1-ASNA1	chr11	65299154	ENST00000270176	chr19	12856190	ENST00000357332	TCGA-13-0801

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Potential target of CAR-T therapy development for SCYL1-ASNA1

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 SCYL1-ASNA1

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 SCYL1-ASNA1

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)