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Fusion Protein:SPECC1L-RET

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SPECC1L-RET
	FusionPDB ID: 85687
	FusionGDB2.0 ID: 85687
		Hgene	Tgene
	Gene symbol	SPECC1L	RET
	Gene ID	23384	5979
	Gene name	sperm antigen with calponin homology and coiled-coil domains 1 like	ret proto-oncogene
	Synonyms	CYTSA\|GBBB2\|OBLFC1\|TBHS	CDHF12\|CDHR16\|HSCR1\|MEN2A\|MEN2B\|MTC1\|PTC\|RET-ELE1
	Cytomap	22q11.23	10q11.21
	Type of gene	protein-coding	protein-coding
	Description	cytospin-ASPECC1-like proteincytokinesis and spindle organization Arenal carcinoma antigen NY-REN-22	proto-oncogene tyrosine-protein kinase receptor RetRET receptor tyrosine kinasecadherin family member 12cadherin-related family member 16proto-oncogene c-Retrearranged during transfectionret proto-oncogene (multiple endocrine neoplasia and medullary
	Modification date	20200313	20200322
	UniProtAcc	.	RTL1 Main function of 5'-partner protein: 1358
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000314328, ENST00000437398, ENST00000541492, ENST00000416735,	ENST00000340058, ENST00000355710,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	24 X 9 X 16=3456	32 X 31 X 11=10912
	# samples	37	48
	** MAII score	log2(37/3456*10)=-3.22350604164716 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(48/10912*10)=-4.50673733341565 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SPECC1L [Title/Abstract] AND RET [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SPECC1L [Title/Abstract] AND RET [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SPECC1L(24734445)-RET(43612032), # samples:3
Anticipated loss of major functional domain due to fusion event.	SPECC1L-RET 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. SPECC1L-RET 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. SPECC1L-RET 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. SPECC1L-RET 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	SPECC1L	GO:0007155	cell adhesion	21703590
Tgene	RET	GO:0030155	regulation of cell adhesion	21357690
Tgene	RET	GO:0030335	positive regulation of cell migration	20702524
Tgene	RET	GO:0033619	membrane protein proteolysis	21357690
Tgene	RET	GO:0033630	positive regulation of cell adhesion mediated by integrin	20702524
Tgene	RET	GO:0035860	glial cell-derived neurotrophic factor receptor signaling pathway	28953886
Tgene	RET	GO:0043410	positive regulation of MAPK cascade	28846099

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr22:24734445/chr10:43612032)
- 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 SPECC1L (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 RET (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)
ENST00000437398	SPECC1L	chr22	24734445	+	ENST00000355710	RET	chr10	43612032	+	6146	2855	95	4063	1322
ENST00000437398	SPECC1L	chr22	24734445	+	ENST00000340058	RET	chr10	43612032	+	4688	2855	95	3937	1280
ENST00000314328	SPECC1L	chr22	24734445	+	ENST00000355710	RET	chr10	43612032	+	6228	2937	285	4145	1286
ENST00000314328	SPECC1L	chr22	24734445	+	ENST00000340058	RET	chr10	43612032	+	4770	2937	285	4019	1244
ENST00000541492	SPECC1L	chr22	24734445	+	ENST00000355710	RET	chr10	43612032	+	6081	2790	30	3998	1322
ENST00000541492	SPECC1L	chr22	24734445	+	ENST00000340058	RET	chr10	43612032	+	4623	2790	30	3872	1280

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
ENST00000437398	ENST00000355710	SPECC1L	chr22	24734445	+	RET	chr10	43612032	+	0.001359092	0.99864095
ENST00000437398	ENST00000340058	SPECC1L	chr22	24734445	+	RET	chr10	43612032	+	0.004013068	0.9959869
ENST00000314328	ENST00000355710	SPECC1L	chr22	24734445	+	RET	chr10	43612032	+	0.001488268	0.99851173
ENST00000314328	ENST00000340058	SPECC1L	chr22	24734445	+	RET	chr10	43612032	+	0.00423764	0.9957624
ENST00000541492	ENST00000355710	SPECC1L	chr22	24734445	+	RET	chr10	43612032	+	0.001243646	0.9987564
ENST00000541492	ENST00000340058	SPECC1L	chr22	24734445	+	RET	chr10	43612032	+	0.003750178	0.99624985

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 SPECC1L-RET

+/-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
SPECC1L	chr22	24734445	RET	chr10	43612032	2790	920	MKTPPAAAVSPMQEDPKWEFPRKNLV
SPECC1L	chr22	24734445	RET	chr10	43612032	2855	920	MKTPPAAAVSPMQEDPKWEFPRKNLV
SPECC1L	chr22	24734445	RET	chr10	43612032	2937	884	MKTPPAAAVSPMQEDPKWEFPRKNLV

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Potential FusionNeoAntigen Information of SPECC1L-RET 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.

SPECC1L-RET_24734445_43612032.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)
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B44:03	QEDPKWEF	0.9984	0.9817	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:01	QEDPKWEF	0.9974	0.9725	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B53:01	PMQEDPKW	0.9451	0.6683	10	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:01	MQEDPKWEF	0.9879	0.9303	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B45:01	QEDPKWEFP	0.983	0.9661	12	21
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:01	SPMQEDPKW	0.9817	0.8346	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:25	MQEDPKWEF	0.966	0.9685	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B50:02	QEDPKWEFP	0.9645	0.7612	12	21
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:02	MQEDPKWEF	0.9541	0.9766	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:08	SPMQEDPKW	0.9367	0.8139	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B13:01	MQEDPKWEF	0.9312	0.979	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:03	MQEDPKWEF	0.8841	0.9067	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B58:02	SPMQEDPKW	0.8679	0.876	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B47:01	MQEDPKWEF	0.8642	0.6312	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:01	MQEDPKWEF	0.8273	0.9494	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:01	MQEDPKWEF	0.8038	0.9695	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:18	MQEDPKWEF	0.7924	0.8591	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:13	MQEDPKWEF	0.6818	0.966	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B38:01	MQEDPKWEF	0.6725	0.9804	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B38:02	MQEDPKWEF	0.6521	0.9854	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:10	MQEDPKWEF	0.5929	0.7592	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-A32:13	MQEDPKWEF	0.5356	0.9472	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:37	MQEDPKWEF	0.5257	0.7299	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B41:01	QEDPKWEFP	0.3522	0.9679	12	21
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:01	VSPMQEDPKW	0.9995	0.9308	8	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B58:02	VSPMQEDPKW	0.9986	0.8753	8	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B58:01	VSPMQEDPKW	0.997	0.8286	8	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:03	VSPMQEDPKW	0.9933	0.9665	8	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:01	AVSPMQEDPKW	0.9999	0.949	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B58:02	AVSPMQEDPKW	0.9998	0.895	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:08	SPMQEDPKWEF	0.9996	0.8318	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:01	SPMQEDPKWEF	0.9994	0.8145	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B58:01	AVSPMQEDPKW	0.9994	0.8917	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:05	SPMQEDPKWEF	0.9992	0.5904	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:03	AVSPMQEDPKW	0.9976	0.9772	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-A32:13	AVSPMQEDPKW	0.9963	0.9532	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:03	SPMQEDPKWEF	0.9953	0.8078	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:02	SPMQEDPKWEF	0.9843	0.928	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:04	SPMQEDPKWEF	0.9843	0.928	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B13:01	SPMQEDPKWEF	0.943	0.8955	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:08	QEDPKWEF	0.9856	0.9466	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C05:09	MQEDPKWEF	0.9989	0.9126	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C04:07	MQEDPKWEF	0.9988	0.8256	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C04:10	MQEDPKWEF	0.9987	0.8235	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C08:15	MQEDPKWEF	0.9977	0.972	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:21	MQEDPKWEF	0.9517	0.9661	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:05	MQEDPKWEF	0.9437	0.9646	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C03:14	MQEDPKWEF	0.9411	0.9818	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:31	MQEDPKWEF	0.9292	0.9663	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C04:14	MQEDPKWEF	0.9072	0.8439	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C08:03	MQEDPKWEF	0.8817	0.9836	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:09	MQEDPKWEF	0.866	0.7217	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:12	MQEDPKWEF	0.821	0.9717	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:08	MQEDPKWEF	0.7864	0.9197	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:05	MQEDPKWEF	0.6366	0.9635	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B07:12	SPMQEDPKWEF	0.9998	0.5798	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B42:02	SPMQEDPKWEF	0.9912	0.7368	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B42:01	SPMQEDPKWEF	0.9879	0.7332	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:12	SPMQEDPKWEF	0.9843	0.928	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:10	SPMQEDPKWEF	0.9485	0.9281	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B44:13	QEDPKWEF	0.9984	0.9817	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B44:07	QEDPKWEF	0.9984	0.9817	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B44:26	QEDPKWEF	0.9984	0.9817	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:11	QEDPKWEF	0.9982	0.9741	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:06	QEDPKWEF	0.9978	0.9762	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:04	QEDPKWEF	0.9978	0.9757	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:05	QEDPKWEF	0.9974	0.9725	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:08	QEDPKWEF	0.9971	0.9682	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B40:04	QEDPKWEF	0.9969	0.7816	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:03	QEDPKWEF	0.9955	0.9695	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B53:02	PMQEDPKW	0.9547	0.6364	10	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B41:03	QEDPKWEF	0.9352	0.8382	12	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C05:01	MQEDPKWEF	0.9989	0.9126	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C04:03	MQEDPKWEF	0.9989	0.8405	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C04:01	MQEDPKWEF	0.9988	0.8256	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C18:01	MQEDPKWEF	0.998	0.8219	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C08:02	MQEDPKWEF	0.9977	0.972	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:33	MQEDPKWEF	0.9879	0.9303	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:125	MQEDPKWEF	0.9879	0.9303	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:34	MQEDPKWEF	0.9879	0.9303	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:27	MQEDPKWEF	0.9876	0.9299	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:50	MQEDPKWEF	0.9873	0.9313	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:135	MQEDPKWEF	0.9871	0.9307	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:24	MQEDPKWEF	0.9819	0.9386	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:77	SPMQEDPKW	0.9817	0.8346	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:23	SPMQEDPKW	0.9793	0.8253	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:12	MQEDPKWEF	0.9757	0.9064	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:17	SPMQEDPKW	0.9756	0.6702	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:30	SPMQEDPKW	0.9756	0.6702	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C07:17	MQEDPKWEF	0.9688	0.9757	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:39	MQEDPKWEF	0.9628	0.9266	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:13	SPMQEDPKW	0.9593	0.7276	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:28	MQEDPKWEF	0.9468	0.9797	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:20	MQEDPKWEF	0.9467	0.978	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:53	MQEDPKWEF	0.9448	0.9158	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C04:04	MQEDPKWEF	0.9212	0.8042	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:24	SPMQEDPKW	0.9204	0.8578	9	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:20	MQEDPKWEF	0.9094	0.9835	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:11	MQEDPKWEF	0.9063	0.9521	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:04	MQEDPKWEF	0.8905	0.9584	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-C08:01	MQEDPKWEF	0.8817	0.9836	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B48:02	MQEDPKWEF	0.8625	0.9756	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:06	MQEDPKWEF	0.8597	0.9546	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:13	MQEDPKWEF	0.8563	0.7529	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:07	MQEDPKWEF	0.8546	0.9135	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:73	MQEDPKWEF	0.8521	0.9719	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:02	MQEDPKWEF	0.8495	0.9684	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:31	MQEDPKWEF	0.8483	0.9689	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:05	MQEDPKWEF	0.8273	0.9494	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:54	MQEDPKWEF	0.8253	0.9018	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:68	MQEDPKWEF	0.8202	0.7182	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:08	MQEDPKWEF	0.818	0.9328	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B18:03	MQEDPKWEF	0.7974	0.9466	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B39:11	MQEDPKWEF	0.7415	0.9078	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:30	MQEDPKWEF	0.7405	0.97	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B38:05	MQEDPKWEF	0.6725	0.9804	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:09	MQEDPKWEF	0.2209	0.9399	11	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:10	VSPMQEDPKW	0.9995	0.9308	8	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:04	VSPMQEDPKW	0.9982	0.6676	8	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B58:06	VSPMQEDPKW	0.9973	0.8163	8	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:02	VSPMQEDPKW	0.9858	0.8853	8	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:04	AVSPMQEDPKW	0.9999	0.6759	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:10	AVSPMQEDPKW	0.9999	0.949	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B58:06	AVSPMQEDPKW	0.9998	0.8521	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B57:02	AVSPMQEDPKW	0.9996	0.9134	7	18
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:30	SPMQEDPKWEF	0.9994	0.678	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:17	SPMQEDPKWEF	0.9994	0.678	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:77	SPMQEDPKWEF	0.9994	0.8145	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:23	SPMQEDPKWEF	0.9993	0.8127	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:08	SPMQEDPKWEF	0.999	0.8167	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:43	SPMQEDPKWEF	0.999	0.819	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B15:11	SPMQEDPKWEF	0.999	0.825	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:11	SPMQEDPKWEF	0.9982	0.8475	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:24	SPMQEDPKWEF	0.994	0.8642	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B35:09	SPMQEDPKWEF	0.9843	0.928	9	20
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	HLA-B67:01	SPMQEDPKWEF	0.9599	0.8817	9	20

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Potential FusionNeoAntigen Information of SPECC1L-RET in HLA II

SPECC1L-RET_24734445_43612032.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)
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0301	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0301	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0305	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0307	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0310	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0310	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0310	SPMQEDPKWEFPRKN	9	24
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0310	AAVSPMQEDPKWEFP	6	21
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0313	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0313	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0315	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0315	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0318	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0318	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0320	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0320	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0322	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0322	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0324	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0326	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0328	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0328	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0330	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0330	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0332	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0332	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0334	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0334	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0336	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0336	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0342	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0344	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0344	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0346	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0346	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0348	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0348	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0350	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0350	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0352	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0352	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0354	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-0354	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-1107	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-1476	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-1476	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-1479	VSPMQEDPKWEFPRK	8	23
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB1-1479	AVSPMQEDPKWEFPR	7	22
SPECC1L-RET	chr22	24734445	chr10	43612032	2937	DRB3-0114	VSPMQEDPKWEFPRK	8	23

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Fusion breakpoint peptide structures of SPECC1L-RET

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
80	AAVSPMQEDPKWEF	SPECC1L	RET	chr22	24734445	chr10	43612032	2937

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SPECC1L-RET

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	80	AAVSPMQEDPKWEF	-6.35143	-7.38673
HLA-B14:02	3BVN	80	AAVSPMQEDPKWEF	-5.20162	-5.31502
HLA-B52:01	3W39	80	AAVSPMQEDPKWEF	-6.03049	-6.14389
HLA-B52:01	3W39	80	AAVSPMQEDPKWEF	-5.12323	-6.15853
HLA-A24:02	5HGA	80	AAVSPMQEDPKWEF	-9.81198	-9.92538
HLA-A24:02	5HGA	80	AAVSPMQEDPKWEF	-7.16433	-8.19963
HLA-B44:05	3DX8	80	AAVSPMQEDPKWEF	-6.46131	-6.57471
HLA-B44:05	3DX8	80	AAVSPMQEDPKWEF	-3.08576	-4.12106
HLA-A02:01	6TDR	80	AAVSPMQEDPKWEF	-5.03933	-5.15273

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Vaccine Design for the FusionNeoAntigens of SPECC1L-RET

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
SPECC1L-RET	chr22	24734445	chr10	43612032	10	18	PMQEDPKW	CCTATGCAGGAGGATCCAAAGTGG
SPECC1L-RET	chr22	24734445	chr10	43612032	11	20	MQEDPKWEF	ATGCAGGAGGATCCAAAGTGGGAATTC
SPECC1L-RET	chr22	24734445	chr10	43612032	12	20	QEDPKWEF	CAGGAGGATCCAAAGTGGGAATTC
SPECC1L-RET	chr22	24734445	chr10	43612032	12	21	QEDPKWEFP	CAGGAGGATCCAAAGTGGGAATTCCCT
SPECC1L-RET	chr22	24734445	chr10	43612032	7	18	AVSPMQEDPKW	GCTGTGTCCCCTATGCAGGAGGATCCAAAGTGG
SPECC1L-RET	chr22	24734445	chr10	43612032	8	18	VSPMQEDPKW	GTGTCCCCTATGCAGGAGGATCCAAAGTGG
SPECC1L-RET	chr22	24734445	chr10	43612032	9	18	SPMQEDPKW	TCCCCTATGCAGGAGGATCCAAAGTGG
SPECC1L-RET	chr22	24734445	chr10	43612032	9	20	SPMQEDPKWEF	TCCCCTATGCAGGAGGATCCAAAGTGGGAATTC

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
SPECC1L-RET	chr22	24734445	chr10	43612032	6	21	AAVSPMQEDPKWEFP	GCAGCTGTGTCCCCTATGCAGGAGGATCCAAAGTGGGAATTCCCT
SPECC1L-RET	chr22	24734445	chr10	43612032	7	22	AVSPMQEDPKWEFPR	GCTGTGTCCCCTATGCAGGAGGATCCAAAGTGGGAATTCCCTCGG
SPECC1L-RET	chr22	24734445	chr10	43612032	8	23	VSPMQEDPKWEFPRK	GTGTCCCCTATGCAGGAGGATCCAAAGTGGGAATTCCCTCGGAAG
SPECC1L-RET	chr22	24734445	chr10	43612032	9	24	SPMQEDPKWEFPRKN	TCCCCTATGCAGGAGGATCCAAAGTGGGAATTCCCTCGGAAGAAC

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Information of the samples that have these potential fusion neoantigens of SPECC1L-RET

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
THCA	SPECC1L-RET	chr22	24734445	ENST00000314328	chr10	43612032	ENST00000340058	TCGA-CE-A485-01A

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Potential target of CAR-T therapy development for SPECC1L-RET

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 SPECC1L-RET

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 SPECC1L-RET

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
Tgene	RET	C1833921	Familial medullary thyroid carcinoma	23	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	RET	C3888239	HIRSCHSPRUNG DISEASE, SUSCEPTIBILITY TO, 1	16	GENOMICS_ENGLAND;UNIPROT
Tgene	RET	C0025268	Multiple Endocrine Neoplasia Type 2a	15	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	RET	C1708353	Hereditary Paraganglioma-Pheochromocytoma Syndrome	12	CLINGEN
Tgene	RET	C0025269	Multiple Endocrine Neoplasia Type 2b	10	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Tgene	RET	C0238463	Papillary thyroid carcinoma	3	CTD_human;ORPHANET
Tgene	RET	C1275808	Congenital central hypoventilation	3	CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	RET	C1859049	CCHS WITH HIRSCHSPRUNG DISEASE	3	CTD_human;ORPHANET
Tgene	RET	C0009402	Colorectal Carcinoma	2	CTD_human;UNIPROT
Tgene	RET	C0009404	Colorectal Neoplasms	2	CTD_human
Tgene	RET	C0019569	Hirschsprung Disease	2	CTD_human
Tgene	RET	C0027662	Multiple Endocrine Neoplasia	2	CTD_human;GENOMICS_ENGLAND
Tgene	RET	C0085758	Aganglionosis, Colonic	2	CTD_human
Tgene	RET	C0266294	Unilateral agenesis of kidney	2	ORPHANET
Tgene	RET	C1257840	Aganglionosis, Rectosigmoid Colon	2	CTD_human
Tgene	RET	C3661523	Congenital Intestinal Aganglionosis	2	CTD_human
Tgene	RET	C0006413	Burkitt Lymphoma	1	CTD_human
Tgene	RET	C0031511	Pheochromocytoma	1	CGI;CTD_human;GENOMICS_ENGLAND;UNIPROT
Tgene	RET	C0038220	Status Epilepticus	1	CTD_human
Tgene	RET	C0040136	Thyroid Neoplasm	1	CGI;CTD_human
Tgene	RET	C0151468	Thyroid Gland Follicular Adenoma	1	CTD_human
Tgene	RET	C0206693	Medullary carcinoma	1	CTD_human
Tgene	RET	C0238462	Medullary carcinoma of thyroid	1	CGI;CTD_human
Tgene	RET	C0270823	Petit mal status	1	CTD_human
Tgene	RET	C0311335	Grand Mal Status Epilepticus	1	CTD_human
Tgene	RET	C0343640	African Burkitt's lymphoma	1	CTD_human
Tgene	RET	C0393734	Complex Partial Status Epilepticus	1	CTD_human
Tgene	RET	C0549473	Thyroid carcinoma	1	CGI;CTD_human;UNIPROT
Tgene	RET	C0740340	Amyloidosis, Familial	1	CTD_human
Tgene	RET	C0751522	Status Epilepticus, Subclinical	1	CTD_human
Tgene	RET	C0751523	Non-Convulsive Status Epilepticus	1	CTD_human
Tgene	RET	C0751524	Simple Partial Status Epilepticus	1	CTD_human
Tgene	RET	C1257877	Pheochromocytoma, Extra-Adrenal	1	CTD_human
Tgene	RET	C1609433	Congenital absence of kidneys syndrome	1	CTD_human;GENOMICS_ENGLAND;ORPHANET
Tgene	RET	C3501843	Nonmedullary Thyroid Carcinoma	1	CTD_human
Tgene	RET	C3501844	Familial Nonmedullary Thyroid Cancer	1	CTD_human
Tgene	RET	C4721444	Burkitt Leukemia	1	CTD_human

	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)