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Fusion Protein:ATAD2B-ITSN2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ATAD2B-ITSN2
	FusionPDB ID: 7338
	FusionGDB2.0 ID: 7338
		Hgene	Tgene
	Gene symbol	ATAD2B	ITSN2
	Gene ID	54454	50618
	Gene name	ATPase family AAA domain containing 2B	intersectin 2
	Synonyms	-	PRO2015\|SH3D1B\|SH3P18\|SWA\|SWAP
	Cytomap	2p24.1-p23.3	2p23.3
	Type of gene	protein-coding	protein-coding
	Description	ATPase family AAA domain-containing protein 2B	intersectin-2SH3 domain-containing protein 1BSH3P18-like WASP-associated protein
	Modification date	20200313	20200313
	UniProtAcc	Q9ULI0 Main function of 5'-partner protein:	Q9NZM3 Main function of 5'-partner protein: FUNCTION: Adapter protein that may provide indirect link between the endocytic membrane traffic and the actin assembly machinery. May regulate the formation of clathrin-coated vesicles (CCPs). Seems to be involved in CCPs maturation including invagination or budding. Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR). Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000269\|PubMed:19458185, ECO:0000269\|PubMed:22648170, ECO:0000269\|PubMed:23999003}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000238789, ENST00000474583,	ENST00000406921, ENST00000407704, ENST00000355123, ENST00000361999,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 7 X 4=196	9 X 15 X 5=675
	# samples	7	15
	** MAII score	log2(7/196*10)=-1.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/675*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ATAD2B [Title/Abstract] AND ITSN2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ATAD2B [Title/Abstract] AND ITSN2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ATAD2B(24021008)-ITSN2(24426652), # samples:1
Anticipated loss of major functional domain due to fusion event.	ATAD2B-ITSN2 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. ATAD2B-ITSN2 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. ATAD2B-ITSN2 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. ATAD2B-ITSN2 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	ITSN2	GO:1903861	positive regulation of dendrite extension	23999003

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:24021008/chr2:24426652)
- 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 ATAD2B (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 ITSN2 (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)
ENST00000238789	ATAD2B	chr2	24021008	-	ENST00000361999	ITSN2	chr2	24426652	-	3904	2984	272	3052	926
ENST00000238789	ATAD2B	chr2	24021008	-	ENST00000355123	ITSN2	chr2	24426652	-	3904	2984	272	3052	926

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
ENST00000238789	ENST00000361999	ATAD2B	chr2	24021008	-	ITSN2	chr2	24426652	-	0.002021466	0.9979785
ENST00000238789	ENST00000355123	ATAD2B	chr2	24021008	-	ITSN2	chr2	24426652	-	0.002021466	0.9979785

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 ATAD2B-ITSN2

+/-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
ATAD2B	chr2	24021008	ITSN2	chr2	24426652	2984	904	STSETMYSELPEEISWVVLKFQWQKF

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Potential FusionNeoAntigen Information of ATAD2B-ITSN2 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.

ATAD2B-ITSN2_24021008_24426652.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)
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:01	EEISWVVL	0.9976	0.9254	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:03	SELPEEISW	0.9997	0.982	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B47:01	SELPEEISW	0.978	0.7577	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:02	LPEEISWVV	0.9728	0.9787	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:04	LPEEISWVV	0.9728	0.9787	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:02	LPEEISWVV	0.9723	0.7037	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:01	LPEEISWVV	0.9633	0.7205	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:03	LPEEISWVV	0.953	0.8553	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:01	SELPEEISW	0.9436	0.9029	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:08	LPEEISWVV	0.9412	0.8074	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B13:01	SELPEEISW	0.9352	0.9678	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:01	LPEEISWVV	0.9278	0.8989	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B53:01	LPEEISWVV	0.8838	0.6125	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A02:19	ELPEEISWV	0.5218	0.5717	8	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B82:01	LPEEISWVV	0.3011	0.5475	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B38:01	MYSELPEEI	0.2297	0.9234	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:03	EEISWVVLKF	0.999	0.9718	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B57:01	YSELPEEISW	0.9978	0.9908	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B58:01	YSELPEEISW	0.9942	0.965	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:01	EEISWVVLKF	0.9921	0.8141	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B58:02	YSELPEEISW	0.992	0.9513	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:03	LPEEISWVVL	0.978	0.9586	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:08	LPEEISWVVL	0.9772	0.9193	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:03	YSELPEEISW	0.9689	0.9807	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B15:17	YSELPEEISW	0.9675	0.9681	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:04	LPEEISWVVL	0.9493	0.9857	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:02	LPEEISWVVL	0.9493	0.9857	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B15:16	YSELPEEISW	0.8941	0.7538	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B57:03	YSELPEEISW	0.8721	0.9714	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:03	SELPEEISWV	0.8265	0.9788	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:02	SELPEEISWV	0.7982	0.5077	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A02:38	SELPEEISWV	0.4848	0.7693	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B57:01	MYSELPEEISW	0.9999	0.986	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B58:01	MYSELPEEISW	0.9986	0.9622	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B57:03	MYSELPEEISW	0.9975	0.9859	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:03	MYSELPEEISW	0.9973	0.9809	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:05	MYSELPEEISW	0.9906	0.5291	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A24:14	MYSELPEEISW	0.9901	0.5433	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B58:01	YSELPEEISWV	0.8886	0.9748	6	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C05:09	YSELPEEI	1	0.9715	6	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C08:15	YSELPEEI	0.9997	0.9755	6	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:08	LPEEISWV	0.9676	0.6338	9	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B54:01	LPEEISWVV	0.9984	0.582	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B78:01	LPEEISWVV	0.9819	0.79	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:12	LPEEISWVV	0.9728	0.9787	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:07	LPEEISWVV	0.9636	0.978	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B56:04	LPEEISWVV	0.9425	0.5978	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:08	LPEEISWVV	0.9171	0.5976	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:10	SELPEEISW	0.8876	0.7022	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A02:05	ELPEEISWV	0.8317	0.6823	8	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C04:10	MYSELPEEI	0.8177	0.8288	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C04:07	MYSELPEEI	0.797	0.8142	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:05	MYSELPEEI	0.7184	0.9688	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A02:07	ELPEEISWV	0.7039	0.7328	8	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B39:10	LPEEISWVV	0.5955	0.9755	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:10	MYSELPEEI	0.577	0.963	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:67	MYSELPEEI	0.5443	0.9543	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:80	MYSELPEEI	0.5443	0.9543	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C04:14	MYSELPEEI	0.5412	0.8878	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:13	MYSELPEEI	0.5142	0.9457	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:29	MYSELPEEI	0.5097	0.9633	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:19	MYSELPEEI	0.5059	0.7638	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:27	MYSELPEEI	0.4797	0.9648	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:95	MYSELPEEI	0.4408	0.7893	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C12:16	MYSELPEEI	0.1813	0.9774	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:12	LPEEISWVVL	0.9493	0.9857	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B07:12	LPEEISWVVL	0.9223	0.6829	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B39:10	LPEEISWVVL	0.8991	0.9761	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:10	SELPEEISWV	0.8488	0.7662	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:09	YSELPEEISW	0.8316	0.5171	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A02:07	SELPEEISWV	0.7425	0.7052	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:10	YSELPEEISW	0.6159	0.688	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:10	MYSELPEEISW	0.8902	0.5181	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A02:07	YSELPEEISWV	0.8591	0.7925	6	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C05:01	YSELPEEI	1	0.9715	6	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C08:02	YSELPEEI	0.9997	0.9755	6	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B40:04	EEISWVVL	0.9995	0.6247	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:07	EEISWVVL	0.9982	0.8898	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:04	EEISWVVL	0.9982	0.9305	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:08	EEISWVVL	0.9976	0.8525	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:05	EEISWVVL	0.9976	0.9254	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:06	EEISWVVL	0.997	0.9343	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:03	EEISWVVL	0.9949	0.9186	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:14	LPEEISWV	0.9914	0.719	9	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:11	EEISWVVL	0.9914	0.8947	11	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:13	LPEEISWV	0.9872	0.5143	9	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:29	LPEEISWV	0.984	0.5002	9	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:21	LPEEISWV	0.9803	0.6591	9	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:09	LPEEISWV	0.9752	0.6981	9	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:05	LPEEISWV	0.9696	0.5011	9	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:26	SELPEEISW	0.9997	0.982	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:07	SELPEEISW	0.9997	0.982	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:13	SELPEEISW	0.9997	0.982	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A25:01	EISWVVLKF	0.9986	0.9451	12	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:22	LPEEISWVV	0.9824	0.6168	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B78:02	LPEEISWVV	0.977	0.8404	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:09	LPEEISWVV	0.9728	0.9787	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:09	LPEEISWVV	0.9667	0.7043	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:14	LPEEISWVV	0.9665	0.6964	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:13	LPEEISWVV	0.9631	0.5518	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A68:02	ELPEEISWV	0.9628	0.8977	8	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:06	LPEEISWVV	0.9608	0.6754	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B51:21	LPEEISWVV	0.9593	0.6446	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:13	LPEEISWVV	0.9509	0.8577	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:08	SELPEEISW	0.9508	0.9448	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:05	SELPEEISW	0.9436	0.9029	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B56:02	LPEEISWVV	0.9425	0.5978	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:04	SELPEEISW	0.9419	0.9084	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:23	LPEEISWVV	0.9365	0.9033	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B55:04	LPEEISWVV	0.9354	0.6575	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:77	LPEEISWVV	0.9278	0.8989	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:06	EEISWVVLK	0.916	0.8836	11	20
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B15:13	EISWVVLKF	0.8881	0.5746	12	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:11	SELPEEISW	0.8861	0.9101	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B40:04	SELPEEISW	0.882	0.7886	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-A69:01	ELPEEISWV	0.8809	0.8837	8	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:06	SELPEEISW	0.869	0.9226	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:03	SELPEEISW	0.8467	0.9011	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C04:01	MYSELPEEI	0.797	0.8142	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:24	LPEEISWVV	0.794	0.9052	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B67:01	LPEEISWVV	0.765	0.835	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C18:01	MYSELPEEI	0.7581	0.8194	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B53:02	LPEEISWVV	0.7344	0.6372	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C04:04	MYSELPEEI	0.6849	0.8803	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C03:67	MYSELPEEI	0.6723	0.9875	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:17	MYSELPEEI	0.5547	0.9765	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:02	MYSELPEEI	0.5443	0.9543	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C14:02	MYSELPEEI	0.4782	0.9598	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C14:03	MYSELPEEI	0.4782	0.9598	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:01	MYSELPEEI	0.456	0.7756	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:04	MYSELPEEI	0.418	0.9182	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C06:06	MYSELPEEI	0.3822	0.9872	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C07:22	MYSELPEEI	0.3579	0.8492	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C06:17	MYSELPEEI	0.3069	0.9938	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C06:02	MYSELPEEI	0.3069	0.9938	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B82:02	LPEEISWVV	0.3011	0.5475	9	18
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B15:13	SELPEEISW	0.2686	0.8197	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B41:03	SELPEEISW	0.2419	0.6341	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B38:05	MYSELPEEI	0.2297	0.9234	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:28	SELPEEISW	0.2184	0.9796	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:20	SELPEEISW	0.1888	0.981	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B48:02	SELPEEISW	0.1742	0.9794	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B15:24	SELPEEISW	0.1584	0.982	7	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-C06:08	MYSELPEEI	0.0983	0.9895	5	14
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:13	EEISWVVLKF	0.999	0.9718	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:07	EEISWVVLKF	0.999	0.9718	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:26	EEISWVVLKF	0.999	0.9718	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B57:10	YSELPEEISW	0.9978	0.9908	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:04	EEISWVVLKF	0.9956	0.8316	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B57:04	YSELPEEISW	0.9952	0.7474	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:08	EEISWVVLKF	0.9925	0.7695	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:06	EEISWVVLKF	0.9923	0.8227	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:05	EEISWVVLKF	0.9921	0.8141	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:11	EEISWVVLKF	0.99	0.8016	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B18:03	EEISWVVLKF	0.9886	0.8064	11	21
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B58:06	YSELPEEISW	0.9837	0.8459	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:13	LPEEISWVVL	0.9751	0.9624	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:26	YSELPEEISW	0.9689	0.9807	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:07	YSELPEEISW	0.9689	0.9807	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:13	YSELPEEISW	0.9689	0.9807	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B57:02	YSELPEEISW	0.965	0.8936	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B35:09	LPEEISWVVL	0.9493	0.9857	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B67:01	LPEEISWVVL	0.9248	0.7752	9	19
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B40:04	SELPEEISWV	0.9041	0.8062	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B15:13	YSELPEEISW	0.8747	0.8249	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:13	SELPEEISWV	0.8265	0.9788	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:26	SELPEEISWV	0.8265	0.9788	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:07	SELPEEISWV	0.8265	0.9788	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:22	SELPEEISWV	0.7982	0.5077	7	17
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B53:02	YSELPEEISW	0.7394	0.6161	6	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B57:10	MYSELPEEISW	0.9999	0.986	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:13	MYSELPEEISW	0.9973	0.9809	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:26	MYSELPEEISW	0.9973	0.9809	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B44:07	MYSELPEEISW	0.9973	0.9809	5	16
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	2984	HLA-B40:04	SELPEEISWVV	0.993	0.8804	7	18

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Potential FusionNeoAntigen Information of ATAD2B-ITSN2 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 ATAD2B-ITSN2

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
10805	YSELPEEISWVVLK	ATAD2B	ITSN2	chr2	24021008	chr2	24426652	2984

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ATAD2B-ITSN2

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	10805	YSELPEEISWVVLK	-7.15543	-7.26883
HLA-B14:02	3BVN	10805	YSELPEEISWVVLK	-4.77435	-5.80965
HLA-B52:01	3W39	10805	YSELPEEISWVVLK	-6.80875	-6.92215
HLA-B52:01	3W39	10805	YSELPEEISWVVLK	-4.20386	-5.23916
HLA-A11:01	4UQ2	10805	YSELPEEISWVVLK	-7.5194	-8.5547
HLA-A11:01	4UQ2	10805	YSELPEEISWVVLK	-6.9601	-7.0735
HLA-A24:02	5HGA	10805	YSELPEEISWVVLK	-7.52403	-7.63743
HLA-A24:02	5HGA	10805	YSELPEEISWVVLK	-5.82433	-6.85963
HLA-B27:05	6PYJ	10805	YSELPEEISWVVLK	-3.28285	-4.31815
HLA-B44:05	3DX8	10805	YSELPEEISWVVLK	-5.91172	-6.94702
HLA-B44:05	3DX8	10805	YSELPEEISWVVLK	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of ATAD2B-ITSN2

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
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	11	19	EEISWVVL	GAAGAGATTTCCTGGGTCGTACTG
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	11	20	EEISWVVLK	GAAGAGATTTCCTGGGTCGTACTGAAA
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	11	21	EEISWVVLKF	GAAGAGATTTCCTGGGTCGTACTGAAATTC
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	12	21	EISWVVLKF	GAGATTTCCTGGGTCGTACTGAAATTC
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	5	14	MYSELPEEI	ATGTACAGTGAACTGCCTGAAGAGATT
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	5	16	MYSELPEEISW	ATGTACAGTGAACTGCCTGAAGAGATTTCCTGG
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	6	14	YSELPEEI	TACAGTGAACTGCCTGAAGAGATT
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	6	16	YSELPEEISW	TACAGTGAACTGCCTGAAGAGATTTCCTGG
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	6	17	YSELPEEISWV	TACAGTGAACTGCCTGAAGAGATTTCCTGGGTC
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	7	16	SELPEEISW	AGTGAACTGCCTGAAGAGATTTCCTGG
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	7	17	SELPEEISWV	AGTGAACTGCCTGAAGAGATTTCCTGGGTC
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	7	18	SELPEEISWVV	AGTGAACTGCCTGAAGAGATTTCCTGGGTCGTA
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	8	17	ELPEEISWV	GAACTGCCTGAAGAGATTTCCTGGGTC
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	9	17	LPEEISWV	CTGCCTGAAGAGATTTCCTGGGTC
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	9	18	LPEEISWVV	CTGCCTGAAGAGATTTCCTGGGTCGTA
ATAD2B-ITSN2	chr2	24021008	chr2	24426652	9	19	LPEEISWVVL	CTGCCTGAAGAGATTTCCTGGGTCGTACTG

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 ATAD2B-ITSN2

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
BRCA	ATAD2B-ITSN2	chr2	24021008	ENST00000238789	chr2	24426652	ENST00000355123	TCGA-LL-A740-01A

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Potential target of CAR-T therapy development for ATAD2B-ITSN2

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 ATAD2B-ITSN2

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 ATAD2B-ITSN2

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)