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Fusion Protein:ERBB2-SLC29A3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ERBB2-SLC29A3
	FusionPDB ID: 27191
	FusionGDB2.0 ID: 27191
		Hgene	Tgene
	Gene symbol	ERBB2	SLC29A3
	Gene ID	2064	55315
	Gene name	erb-b2 receptor tyrosine kinase 2	solute carrier family 29 member 3
	Synonyms	CD340\|HER-2\|HER-2/neu\|HER2\|MLN 19\|NEU\|NGL\|TKR1	ENT3\|HCLAP\|HJCD\|PHID
	Cytomap	17q12	10q22.1
	Type of gene	protein-coding	protein-coding
	Description	receptor tyrosine-protein kinase erbB-2c-erb B2/neu proteinherstatinhuman epidermal growth factor receptor 2metastatic lymph node gene 19 proteinneuro/glioblastoma derived oncogene homologneuroblastoma/glioblastoma derived oncogene homologp185erbB2	equilibrative nucleoside transporter 3solute carrier family 29 (equilibrative nucleoside transporter), member 3solute carrier family 29 (nucleoside transporters), member 3
	Modification date	20200329	20200329
	UniProtAcc	P04626 Main function of 5'-partner protein: FUNCTION: Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding. Essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. GP30 is a potential ligand for this receptor. Regulates outgrowth and stabilization of peripheral microtubules (MTs). Upon ERBB2 activation, the MEMO1-RHOA-DIAPH1 signaling pathway elicits the phosphorylation and thus the inhibition of GSK3B at cell membrane. This prevents the phosphorylation of APC and CLASP2, allowing its association with the cell membrane. In turn, membrane-bound APC allows the localization of MACF1 to the cell membrane, which is required for microtubule capture and stabilization. {ECO:0000305}.; FUNCTION: In the nucleus is involved in transcriptional regulation. Associates with the 5'-TCAAATTC-3' sequence in the PTGS2/COX-2 promoter and activates its transcription. Implicated in transcriptional activation of CDKN1A; the function involves STAT3 and SRC. Involved in the transcription of rRNA genes by RNA Pol I and enhances protein synthesis and cell growth. {ECO:0000269\|PubMed:10358079, ECO:0000269\|PubMed:15380516, ECO:0000269\|PubMed:21555369}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000269571, ENST00000406381, ENST00000445658, ENST00000540147, ENST00000541774, ENST00000584450, ENST00000584601, ENST00000540042, ENST00000578199, ENST00000584888,	ENST00000469204, ENST00000373189,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	50 X 44 X 14=30800	3 X 3 X 3=27
	# samples	73	5
	** MAII score	log2(73/30800*10)=-5.39889007670225 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/27*10)=0.888968687611256 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: ERBB2 [Title/Abstract] AND SLC29A3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ERBB2 [Title/Abstract] AND SLC29A3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ERBB2(37883256)-SLC29A3(73121711), # samples:3
Anticipated loss of major functional domain due to fusion event.	ERBB2-SLC29A3 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. ERBB2-SLC29A3 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. ERBB2-SLC29A3 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. ERBB2-SLC29A3 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	ERBB2	GO:0007165	signal transduction	10572067
Hgene	ERBB2	GO:0007166	cell surface receptor signaling pathway	9685399
Hgene	ERBB2	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	7514177
Hgene	ERBB2	GO:0014065	phosphatidylinositol 3-kinase signaling	7556068
Hgene	ERBB2	GO:0018108	peptidyl-tyrosine phosphorylation	12000754
Hgene	ERBB2	GO:0032886	regulation of microtubule-based process	20937854
Hgene	ERBB2	GO:0035556	intracellular signal transduction	19372587
Hgene	ERBB2	GO:0042060	wound healing	12646923
Hgene	ERBB2	GO:0043406	positive regulation of MAP kinase activity	10572067
Hgene	ERBB2	GO:0045785	positive regulation of cell adhesion	7556068
Hgene	ERBB2	GO:0046777	protein autophosphorylation	7556068
Hgene	ERBB2	GO:0050679	positive regulation of epithelial cell proliferation	10572067
Hgene	ERBB2	GO:0071363	cellular response to growth factor stimulus	20010870
Hgene	ERBB2	GO:0090314	positive regulation of protein targeting to membrane	20010870

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:37883256/chr10:73121711)
- 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 ERBB2 (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 SLC29A3 (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)
ENST00000584601	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121711	+	5298	3866	752	3910	1052
ENST00000406381	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121711	+	5011	3579	510	3623	1037
ENST00000541774	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121711	+	4546	3114	0	3158	1052
ENST00000445658	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121711	+	4026	2594	50	2638	862
ENST00000540147	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121711	+	4829	3397	25	3441	1138
ENST00000584450	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121711	+	4806	3374	2	3418	1138
ENST00000269571	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121711	+	4750	3318	57	3362	1101
ENST00000584601	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121710	+	5298	3866	752	3910	1052
ENST00000406381	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121710	+	5011	3579	510	3623	1037
ENST00000541774	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121710	+	4546	3114	0	3158	1052
ENST00000445658	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121710	+	4026	2594	50	2638	862
ENST00000540147	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121710	+	4829	3397	25	3441	1138
ENST00000584450	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121710	+	4806	3374	2	3418	1138
ENST00000269571	ERBB2	chr17	37883256	+	ENST00000373189	SLC29A3	chr10	73121710	+	4750	3318	57	3362	1101
ENST00000584601	ERBB2	chr17	37883255	+	ENST00000373189	SLC29A3	chr10	73121710	+	5298	3866	752	3910	1052
ENST00000406381	ERBB2	chr17	37883255	+	ENST00000373189	SLC29A3	chr10	73121710	+	5011	3579	510	3623	1037
ENST00000541774	ERBB2	chr17	37883255	+	ENST00000373189	SLC29A3	chr10	73121710	+	4546	3114	0	3158	1052
ENST00000445658	ERBB2	chr17	37883255	+	ENST00000373189	SLC29A3	chr10	73121710	+	4026	2594	50	2638	862
ENST00000540147	ERBB2	chr17	37883255	+	ENST00000373189	SLC29A3	chr10	73121710	+	4829	3397	25	3441	1138
ENST00000584450	ERBB2	chr17	37883255	+	ENST00000373189	SLC29A3	chr10	73121710	+	4806	3374	2	3418	1138
ENST00000269571	ERBB2	chr17	37883255	+	ENST00000373189	SLC29A3	chr10	73121710	+	4750	3318	57	3362	1101

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
ENST00000584601	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121711	+	0.002471897	0.99752814
ENST00000406381	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121711	+	0.001926238	0.9980737
ENST00000541774	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121711	+	0.001173401	0.99882656
ENST00000445658	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121711	+	0.004988879	0.9950111
ENST00000540147	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121711	+	0.001691971	0.99830806
ENST00000584450	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121711	+	0.00170476	0.99829525
ENST00000269571	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121711	+	0.0016029	0.99839705
ENST00000584601	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121710	+	0.002471897	0.99752814
ENST00000406381	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121710	+	0.001926238	0.9980737
ENST00000541774	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121710	+	0.001173401	0.99882656
ENST00000445658	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121710	+	0.004988879	0.9950111
ENST00000540147	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121710	+	0.001691971	0.99830806
ENST00000584450	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121710	+	0.00170476	0.99829525
ENST00000269571	ENST00000373189	ERBB2	chr17	37883256	+	SLC29A3	chr10	73121710	+	0.0016029	0.99839705
ENST00000584601	ENST00000373189	ERBB2	chr17	37883255	+	SLC29A3	chr10	73121710	+	0.002471897	0.99752814
ENST00000406381	ENST00000373189	ERBB2	chr17	37883255	+	SLC29A3	chr10	73121710	+	0.001926238	0.9980737
ENST00000541774	ENST00000373189	ERBB2	chr17	37883255	+	SLC29A3	chr10	73121710	+	0.001173401	0.99882656
ENST00000445658	ENST00000373189	ERBB2	chr17	37883255	+	SLC29A3	chr10	73121710	+	0.004988879	0.9950111
ENST00000540147	ENST00000373189	ERBB2	chr17	37883255	+	SLC29A3	chr10	73121710	+	0.001691971	0.99830806
ENST00000584450	ENST00000373189	ERBB2	chr17	37883255	+	SLC29A3	chr10	73121710	+	0.00170476	0.99829525
ENST00000269571	ENST00000373189	ERBB2	chr17	37883255	+	SLC29A3	chr10	73121710	+	0.0016029	0.99839705

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 ERBB2-SLC29A3

+/-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
ERBB2	chr17	37883255	SLC29A3	chr10	73121710	2594	844	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883255	SLC29A3	chr10	73121710	3114	1034	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883255	SLC29A3	chr10	73121710	3318	1083	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883255	SLC29A3	chr10	73121710	3374	1120	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883255	SLC29A3	chr10	73121710	3397	1120	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883255	SLC29A3	chr10	73121710	3579	1019	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883255	SLC29A3	chr10	73121710	3866	1034	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121710	2594	844	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121710	3114	1034	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121710	3318	1083	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121710	3374	1120	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121710	3397	1120	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121710	3579	1019	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121710	3866	1034	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121711	2594	844	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121711	3114	1034	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121711	3318	1083	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121711	3374	1120	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121711	3397	1120	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121711	3579	1019	PGAGGMVHHRHRSSSTRVLHEACSCG
ERBB2	chr17	37883256	SLC29A3	chr10	73121711	3866	1034	PGAGGMVHHRHRSSSTRVLHEACSCG

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Potential FusionNeoAntigen Information of ERBB2-SLC29A3 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.

ERBB2-SLC29A3_37883255_73121710.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)
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:04	HRSSSTRVL	0.9977	0.7958	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:02	HRSSSTRVL	0.9973	0.6618	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:05	HRSSSTRVL	0.9968	0.9126	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B39:01	HRSSSTRVL	0.9968	0.8822	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B39:06	HRSSSTRVL	0.9962	0.7805	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:05	HRHRSSSTR	0.9957	0.796	8	17
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B14:01	HRSSSTRVL	0.9931	0.665	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B14:02	HRSSSTRVL	0.9931	0.665	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B38:02	HRSSSTRVL	0.9915	0.9505	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B38:01	HRSSSTRVL	0.9907	0.9399	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-A30:08	RSSSTRVLH	0.9877	0.8729	11	20
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B15:10	HRSSSTRVL	0.93	0.5441	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B15:18	HRSSSTRVL	0.6646	0.6697	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B15:37	HRSSSTRVL	0.4562	0.5429	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B38:01	RHRSSSTRVL	0.6709	0.845	9	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B38:02	RHRSSSTRVL	0.67	0.8528	9	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B15:10	RHRSSSTRVL	0.6223	0.5028	9	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B39:09	HRSSSTRVL	0.9977	0.5812	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:95	HRSSSTRVL	0.9976	0.7245	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:05	HRSSSTRVL	0.9973	0.9775	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:14	HRSSSTRVL	0.9966	0.8863	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B39:12	HRSSSTRVL	0.9965	0.8831	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:14	HRHRSSSTR	0.996	0.8011	8	17
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:27	HRSSSTRVL	0.9949	0.9698	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:29	HRSSSTRVL	0.9931	0.9395	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:13	HRSSSTRVL	0.9923	0.961	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B39:05	HRSSSTRVL	0.9914	0.8663	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:46	HRSSSTRVL	0.9732	0.9234	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:19	HRSSSTRVL	0.9301	0.826	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:67	HRSSSTRVL	0.9118	0.9622	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:80	HRSSSTRVL	0.9118	0.9622	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B73:01	HRSSSTRVL	0.9039	0.5092	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:10	HRSSSTRVL	0.9015	0.9746	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:03	HRSSSTRVL	0.8921	0.929	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B14:03	HRSSSTRVL	0.5958	0.8561	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C12:16	HRSSSTRVL	0.0335	0.9741	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C16:02	RSSSTRVL	0.9953	0.9962	11	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C16:01	RSSSTRVL	0.9633	0.9818	11	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:06	HRSSSTRVL	0.9987	0.7856	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:01	HRSSSTRVL	0.9979	0.7073	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:09	HRSSSTRVL	0.9978	0.8919	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:10	HRSSSTRVL	0.9976	0.8926	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:08	HRSSSTRVL	0.9973	0.8451	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B39:31	HRSSSTRVL	0.9969	0.8811	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B39:02	HRSSSTRVL	0.9966	0.9123	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:10	HRHRSSSTR	0.9936	0.8207	8	17
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-A30:01	RSSSTRVLH	0.9908	0.9578	11	20
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B38:05	HRSSSTRVL	0.9907	0.9399	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:17	HRSSSTRVL	0.9863	0.9753	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C06:08	HRSSSTRVL	0.9796	0.9919	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:02	HRSSSTRVL	0.9118	0.9622	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:04	HRSSSTRVL	0.8476	0.9118	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B15:09	HRSSSTRVL	0.8065	0.576	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C07:22	HRSSSTRVL	0.7652	0.7649	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B39:11	HRSSSTRVL	0.6825	0.7111	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C03:67	HRSSSTRVL	0.5183	0.9826	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C06:06	HRSSSTRVL	0.3413	0.991	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C06:02	HRSSSTRVL	0.0544	0.9954	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-C06:17	HRSSSTRVL	0.0544	0.9954	10	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:06	RHRSSSTRVL	0.8885	0.7191	9	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B38:05	RHRSSSTRVL	0.6709	0.845	9	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B15:09	RHRSSSTRVL	0.3047	0.5417	9	19
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	HLA-B27:06	HRHRSSSTRVL	0.9922	0.714	8	19

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Potential FusionNeoAntigen Information of ERBB2-SLC29A3 in HLA II

ERBB2-SLC29A3_37883255_73121710.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)
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	3318	DRB1-1155	AGGMVHHRHRSSSTR	2	17

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Fusion breakpoint peptide structures of ERBB2-SLC29A3

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
9977	VHHRHRSSSTRVLH	ERBB2	SLC29A3	chr17	37883255	chr10	73121710	3318

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ERBB2-SLC29A3

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	9977	VHHRHRSSSTRVLH	-7.9962	-8.1096
HLA-B14:02	3BVN	9977	VHHRHRSSSTRVLH	-5.70842	-6.74372
HLA-B52:01	3W39	9977	VHHRHRSSSTRVLH	-6.83737	-6.95077
HLA-B52:01	3W39	9977	VHHRHRSSSTRVLH	-4.4836	-5.5189
HLA-A11:01	4UQ2	9977	VHHRHRSSSTRVLH	-10.0067	-10.1201
HLA-A11:01	4UQ2	9977	VHHRHRSSSTRVLH	-9.03915	-10.0745
HLA-A24:02	5HGA	9977	VHHRHRSSSTRVLH	-6.56204	-6.67544
HLA-A24:02	5HGA	9977	VHHRHRSSSTRVLH	-5.42271	-6.45801
HLA-B44:05	3DX8	9977	VHHRHRSSSTRVLH	-7.85648	-8.89178
HLA-B44:05	3DX8	9977	VHHRHRSSSTRVLH	-5.3978	-5.5112
HLA-A02:01	6TDR	9977	VHHRHRSSSTRVLH	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of ERBB2-SLC29A3

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
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	10	19	HRSSSTRVL	TCTACCAGGGTACTACATGAGGCCTGT
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	11	19	RSSSTRVL	ACCAGGGTACTACATGAGGCCTGT
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	11	20	RSSSTRVLH	ACCAGGGTACTACATGAGGCCTGTTCT
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	8	17	HRHRSSSTR	AGCTCATCTACCAGGGTACTACATGAG
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	8	19	HRHRSSSTRVL	AGCTCATCTACCAGGGTACTACATGAGGCCTGT
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	9	19	RHRSSSTRVL	TCATCTACCAGGGTACTACATGAGGCCTGT

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
ERBB2-SLC29A3	chr17	37883255	chr10	73121710	2	17	AGGMVHHRHRSSSTR	GTCCACCACAGGCACCGCAGCTCATCTACCAGGGTACTACATGAG

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Information of the samples that have these potential fusion neoantigens of ERBB2-SLC29A3

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	ERBB2-SLC29A3	chr17	37883255	ENST00000269571	chr10	73121710	ENST00000373189	TCGA-AR-A254-01A

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Potential target of CAR-T therapy development for ERBB2-SLC29A3

Predicted 3D structure. We used RoseTTAFold.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

ERBB2

chr17:37883255

chr10:73121710

ENST00000269571

653_675

1053

1256.0

Transmembrane

Helical

Hgene

ERBB2

chr17:37883255

chr10:73121710

ENST00000541774

653_675

1038

1241.0

Transmembrane

Helical

Hgene

ERBB2

chr17:37883256

chr10:73121710

ENST00000269571

653_675

1053

1256.0

Transmembrane

Helical

Hgene

ERBB2

chr17:37883256

chr10:73121710

ENST00000541774

653_675

1038

1241.0

Transmembrane

Helical

Hgene

ERBB2

chr17:37883256

chr10:73121711

ENST00000269571

653_675

1053

1256.0

Transmembrane

Helical

Hgene

ERBB2

chr17:37883256

chr10:73121711

ENST00000541774

653_675

1038

1241.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883255

chr10:73121710

ENST00000373189

306_326

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883255

chr10:73121710

ENST00000373189

338_358

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883255

chr10:73121710

ENST00000373189

378_398

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883255

chr10:73121710

ENST00000373189

416_436

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883255

chr10:73121710

ENST00000373189

455_475

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121710

ENST00000373189

306_326

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121710

ENST00000373189

338_358

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121710

ENST00000373189

378_398

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121710

ENST00000373189

416_436

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121710

ENST00000373189

455_475

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121711

ENST00000373189

306_326

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121711

ENST00000373189

338_358

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121711

ENST00000373189

378_398

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121711

ENST00000373189

416_436

476.0

Transmembrane

Helical

Tgene

SLC29A3

chr17:37883256

chr10:73121711

ENST00000373189

455_475

476.0

Transmembrane

Helical

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to ERBB2-SLC29A3

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 ERBB2-SLC29A3

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)