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Fusion Protein:CAND1-GNS

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CAND1-GNS
	FusionPDB ID: 12767
	FusionGDB2.0 ID: 12767
		Hgene	Tgene
	Gene symbol	CAND1	GNS
	Gene ID	55832	2799
	Gene name	cullin associated and neddylation dissociated 1	glucosamine (N-acetyl)-6-sulfatase
	Synonyms	TIP120\|TIP120A	G6S
	Cytomap	12q14.3-q15	12q14.3
	Type of gene	protein-coding	protein-coding
	Description	cullin-associated NEDD8-dissociated protein 1TBP-interacting protein of 120 kDa Ap120 CAND1	N-acetylglucosamine-6-sulfataseglucosamine -6-sulfatase
	Modification date	20200327	20200313
	UniProtAcc	Q86VP6 Main function of 5'-partner protein: FUNCTION: Key assembly factor of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complexes that promotes the exchange of the substrate-recognition F-box subunit in SCF complexes, thereby playing a key role in the cellular repertoire of SCF complexes. Acts as a F-box protein exchange factor. The exchange activity of CAND1 is coupled with cycles of neddylation conjugation: in the deneddylated state, cullin-binding CAND1 binds CUL1-RBX1, increasing dissociation of the SCF complex and promoting exchange of the F-box protein. Probably plays a similar role in other cullin-RING E3 ubiquitin ligase complexes. {ECO:0000269\|PubMed:12504025, ECO:0000269\|PubMed:12504026, ECO:0000269\|PubMed:12609982, ECO:0000269\|PubMed:16449638, ECO:0000269\|PubMed:21249194, ECO:0000269\|PubMed:23453757}.	P15586 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000545606, ENST00000539109,	ENST00000258145, ENST00000418919, ENST00000542058, ENST00000543646,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 10 X 7=770	8 X 8 X 4=256
	# samples	11	8
	** MAII score	log2(11/770*10)=-2.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(8/256*10)=-1.67807190511264 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CAND1 [Title/Abstract] AND GNS [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CAND1 [Title/Abstract] AND GNS [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CAND1(67696395)-GNS(65116895), # samples:1
Anticipated loss of major functional domain due to fusion event.	CAND1-GNS 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. CAND1-GNS 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	CAND1	GO:0010265	SCF complex assembly	15537541\|21249194
Hgene	CAND1	GO:0016567	protein ubiquitination	12609982\|15537541\|21249194
Hgene	CAND1	GO:0030154	cell differentiation	10581176
Hgene	CAND1	GO:0043086	negative regulation of catalytic activity	12609982

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:67696395/chr12:65116895)
- 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 CAND1 (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 GNS (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)
ENST00000545606	CAND1	chr12	67696395	+	ENST00000418919	GNS	chr12	65116895	-	5485	1730	437	2188	583
ENST00000545606	CAND1	chr12	67696395	+	ENST00000258145	GNS	chr12	65116895	-	5481	1730	437	2188	583
ENST00000545606	CAND1	chr12	67696395	+	ENST00000543646	GNS	chr12	65116895	-	2468	1730	437	2188	583
ENST00000545606	CAND1	chr12	67696395	+	ENST00000542058	GNS	chr12	65116895	-	2455	1730	437	2188	583

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
ENST00000545606	ENST00000418919	CAND1	chr12	67696395	+	GNS	chr12	65116895	-	0.000822736	0.9991773
ENST00000545606	ENST00000258145	CAND1	chr12	67696395	+	GNS	chr12	65116895	-	0.000826041	0.99917394
ENST00000545606	ENST00000543646	CAND1	chr12	67696395	+	GNS	chr12	65116895	-	0.001760145	0.9982399
ENST00000545606	ENST00000542058	CAND1	chr12	67696395	+	GNS	chr12	65116895	-	0.001796054	0.9982039

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 CAND1-GNS

+/-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
CAND1	chr12	67696395	GNS	chr12	65116895	1730	431	EQGETPLTMLQSQRGASNLTWRSDVL

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Potential FusionNeoAntigen Information of CAND1-GNS 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.

CAND1-GNS_67696395_65116895.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)
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B38:01	QRGASNLTW	0.4358	0.9679	12	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:01	SQRGASNLTW	0.999	0.8232	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-A32:13	SQRGASNLTW	0.8337	0.8936	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B57:01	QSQRGASNLTW	1	0.9763	10	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B58:02	QSQRGASNLTW	0.9996	0.9757	10	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B58:01	QSQRGASNLTW	0.999	0.954	10	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B57:03	QSQRGASNLTW	0.9989	0.9885	10	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-A68:24	ETPLTMLQSQR	0.9977	0.861	3	14
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-A68:03	ETPLTMLQSQR	0.9969	0.8594	3	14
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-A68:05	ETPLTMLQSQR	0.9876	0.8621	3	14
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:07	SQRGASNLTW	0.9962	0.7124	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B44:08	SQRGASNLTW	0.9375	0.7976	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-A68:01	ETPLTMLQSQR	0.9977	0.861	3	14
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:73	SQRGASNL	0.9899	0.921	11	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B48:05	SQRGASNL	0.9432	0.5034	11	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B38:05	QRGASNLTW	0.4358	0.9679	12	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:24	SQRGASNLTW	0.9996	0.8912	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:125	SQRGASNLTW	0.999	0.8232	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:34	SQRGASNLTW	0.999	0.8232	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:33	SQRGASNLTW	0.999	0.8232	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:135	SQRGASNLTW	0.999	0.819	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:53	SQRGASNLTW	0.9986	0.8182	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:12	SQRGASNLTW	0.9935	0.7995	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:54	SQRGASNLTW	0.9927	0.7896	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:35	SQRGASNLTW	0.992	0.8513	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:68	SQRGASNLTW	0.9917	0.6451	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:73	LQSQRGASNL	0.9605	0.9664	9	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:30	LQSQRGASNL	0.937	0.9556	9	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B15:13	SQRGASNLTW	0.9312	0.7721	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B48:02	SQRGASNLTW	0.9168	0.7581	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-A32:01	SQRGASNLTW	0.9094	0.9313	11	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B57:10	QSQRGASNLTW	1	0.9763	10	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B57:04	QSQRGASNLTW	0.9998	0.7371	10	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B58:06	QSQRGASNLTW	0.9995	0.9488	10	21
CAND1-GNS	chr12	67696395	chr12	65116895	1730	HLA-B57:02	QSQRGASNLTW	0.999	0.9474	10	21

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Potential FusionNeoAntigen Information of CAND1-GNS in HLA II

CAND1-GNS_67696395_65116895.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)
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0101	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0101	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0102	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0102	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0102	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0102	TPLTMLQSQRGASNL	4	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0105	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0105	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0107	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0107	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0109	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0111	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0113	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0115	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0117	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0119	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0119	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0121	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0121	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0123	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0123	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0123	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0123	TPLTMLQSQRGASNL	4	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0125	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0125	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0127	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0127	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0129	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0131	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0131	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0403	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0403	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0413	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0413	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0415	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0415	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0415	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0415	TPLTMLQSQRGASNL	4	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0419	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0419	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0427	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0427	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0431	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0436	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0436	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0436	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0436	TPLTMLQSQRGASNL	4	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0437	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0437	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0439	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0439	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0440	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0440	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0441	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0441	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0442	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0442	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0442	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0443	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0444	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0444	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0446	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0446	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0447	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0447	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0449	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0449	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0450	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0450	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0451	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0451	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0452	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0452	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0453	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0453	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0453	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0453	TPLTMLQSQRGASNL	4	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0454	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0454	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0455	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0455	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0456	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0456	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0458	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0458	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0458	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0458	TPLTMLQSQRGASNL	4	19
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0459	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0459	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0460	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0460	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0461	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0461	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0465	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0465	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0468	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0468	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0470	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0470	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0471	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0471	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0473	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0473	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0475	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0478	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0478	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0479	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0479	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0479	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0485	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0485	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0488	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0488	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-0831	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1001	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1002	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1002	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1002	QGETPLTMLQSQRGA	1	16
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1003	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1130	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1204	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1204	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1209	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1209	GETPLTMLQSQRGAS	2	17
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1219	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1220	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1221	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1452	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1457	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1601	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1603	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1608	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1615	ETPLTMLQSQRGASN	3	18
CAND1-GNS	chr12	67696395	chr12	65116895	1730	DRB1-1615	GETPLTMLQSQRGAS	2	17

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Fusion breakpoint peptide structures of CAND1-GNS

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
5731	LTMLQSQRGASNLT	CAND1	GNS	chr12	67696395	chr12	65116895	1730

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CAND1-GNS

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	5731	LTMLQSQRGASNLT	-7.15543	-7.26883
HLA-B14:02	3BVN	5731	LTMLQSQRGASNLT	-4.77435	-5.80965
HLA-B52:01	3W39	5731	LTMLQSQRGASNLT	-6.80875	-6.92215
HLA-B52:01	3W39	5731	LTMLQSQRGASNLT	-4.20386	-5.23916
HLA-A11:01	4UQ2	5731	LTMLQSQRGASNLT	-7.5194	-8.5547
HLA-A11:01	4UQ2	5731	LTMLQSQRGASNLT	-6.9601	-7.0735
HLA-A24:02	5HGA	5731	LTMLQSQRGASNLT	-7.52403	-7.63743
HLA-A24:02	5HGA	5731	LTMLQSQRGASNLT	-5.82433	-6.85963
HLA-B27:05	6PYJ	5731	LTMLQSQRGASNLT	-3.28285	-4.31815
HLA-B44:05	3DX8	5731	LTMLQSQRGASNLT	-5.91172	-6.94702
HLA-B44:05	3DX8	5731	LTMLQSQRGASNLT	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of CAND1-GNS

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
CAND1-GNS	chr12	67696395	chr12	65116895	10	21	QSQRGASNLTW	CAGAGTCAGAGAGGTGCCAGTAACTTGACCTGG
CAND1-GNS	chr12	67696395	chr12	65116895	11	19	SQRGASNL	AGTCAGAGAGGTGCCAGTAACTTG
CAND1-GNS	chr12	67696395	chr12	65116895	11	21	SQRGASNLTW	AGTCAGAGAGGTGCCAGTAACTTGACCTGG
CAND1-GNS	chr12	67696395	chr12	65116895	12	21	QRGASNLTW	CAGAGAGGTGCCAGTAACTTGACCTGG
CAND1-GNS	chr12	67696395	chr12	65116895	3	14	ETPLTMLQSQR	GAAACACCTTTAACAATGCTTCAGAGTCAGAGA
CAND1-GNS	chr12	67696395	chr12	65116895	9	19	LQSQRGASNL	CTTCAGAGTCAGAGAGGTGCCAGTAACTTG

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
CAND1-GNS	chr12	67696395	chr12	65116895	1	16	QGETPLTMLQSQRGA	CAGGGAGAAACACCTTTAACAATGCTTCAGAGTCAGAGAGGTGCC
CAND1-GNS	chr12	67696395	chr12	65116895	2	17	GETPLTMLQSQRGAS	GGAGAAACACCTTTAACAATGCTTCAGAGTCAGAGAGGTGCCAGT
CAND1-GNS	chr12	67696395	chr12	65116895	3	18	ETPLTMLQSQRGASN	GAAACACCTTTAACAATGCTTCAGAGTCAGAGAGGTGCCAGTAAC
CAND1-GNS	chr12	67696395	chr12	65116895	4	19	TPLTMLQSQRGASNL	ACACCTTTAACAATGCTTCAGAGTCAGAGAGGTGCCAGTAACTTG

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Information of the samples that have these potential fusion neoantigens of CAND1-GNS

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
N/A	CAND1-GNS	chr12	67696395	ENST00000545606	chr12	65116895	ENST00000258145	BQ434418

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Potential target of CAR-T therapy development for CAND1-GNS

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 CAND1-GNS

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 CAND1-GNS

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)