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Fusion Protein:TM7SF3-KCNC2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TM7SF3-KCNC2
	FusionPDB ID: 91236
	FusionGDB2.0 ID: 91236
		Hgene	Tgene
	Gene symbol	TM7SF3	KCNC2
	Gene ID	51768	3747
	Gene name	transmembrane 7 superfamily member 3	potassium voltage-gated channel subfamily C member 2
	Synonyms	-	KV3.2
	Cytomap	12p11.23	12q21.1
	Type of gene	protein-coding	protein-coding
	Description	transmembrane 7 superfamily member 3seven span transmembrane proteinseven transmembrane protein TM7SF3	potassium voltage-gated channel subfamily C member 2potassium channel, voltage gated Shaw related subfamily C, member 2potassium voltage-gated channel, Shaw-related subfamily, member 2shaw-like potassium channelvoltage-gated potassium channel Kv3.2
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000343028, ENST00000542667,	ENST00000548243, ENST00000298972, ENST00000341669, ENST00000350228, ENST00000393288, ENST00000540018, ENST00000548513, ENST00000549446, ENST00000550433,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 9 X 5=360	15 X 5 X 6=450
	# samples	10	16
	** MAII score	log2(10/360*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(16/450*10)=-1.49185309632967 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: TM7SF3 [Title/Abstract] AND KCNC2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: TM7SF3 [Title/Abstract] AND KCNC2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TM7SF3(27143383)-KCNC2(75445097), # samples:3
Anticipated loss of major functional domain due to fusion event.	TM7SF3-KCNC2 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. TM7SF3-KCNC2 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. TM7SF3-KCNC2 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. TM7SF3-KCNC2 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. TM7SF3-KCNC2 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. TM7SF3-KCNC2 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:27143383/chr12:75445097)
- 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 TM7SF3 (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 KCNC2 (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)
ENST00000343028	TM7SF3	chr12	27148170	-	ENST00000550433	KCNC2	chr12	75445097	-	3139	916	1	2118	705
ENST00000343028	TM7SF3	chr12	27148170	-	ENST00000548513	KCNC2	chr12	75445097	-	3234	916	1	2070	689
ENST00000343028	TM7SF3	chr12	27148170	-	ENST00000549446	KCNC2	chr12	75445097	-	5173	916	1	2145	714
ENST00000343028	TM7SF3	chr12	27148170	-	ENST00000298972	KCNC2	chr12	75445097	-	3195	916	1	2070	689
ENST00000343028	TM7SF3	chr12	27148170	-	ENST00000341669	KCNC2	chr12	75445097	-	3100	916	1	2118	705
ENST00000343028	TM7SF3	chr12	27148170	-	ENST00000350228	KCNC2	chr12	75445097	-	3029	916	1	1905	634
ENST00000343028	TM7SF3	chr12	27148170	-	ENST00000540018	KCNC2	chr12	75445097	-	2125	916	1	1980	659
ENST00000343028	TM7SF3	chr12	27148170	-	ENST00000393288	KCNC2	chr12	75445097	-	2466	916	1	2085	694

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
ENST00000343028	ENST00000550433	TM7SF3	chr12	27148170	-	KCNC2	chr12	75445097	-	0.000296666	0.99970335
ENST00000343028	ENST00000548513	TM7SF3	chr12	27148170	-	KCNC2	chr12	75445097	-	0.000277811	0.9997222
ENST00000343028	ENST00000549446	TM7SF3	chr12	27148170	-	KCNC2	chr12	75445097	-	0.000228424	0.99977154
ENST00000343028	ENST00000298972	TM7SF3	chr12	27148170	-	KCNC2	chr12	75445097	-	0.000289266	0.99971074
ENST00000343028	ENST00000341669	TM7SF3	chr12	27148170	-	KCNC2	chr12	75445097	-	0.000306989	0.99969304
ENST00000343028	ENST00000350228	TM7SF3	chr12	27148170	-	KCNC2	chr12	75445097	-	0.000296172	0.9997038
ENST00000343028	ENST00000540018	TM7SF3	chr12	27148170	-	KCNC2	chr12	75445097	-	0.000934939	0.9990651
ENST00000343028	ENST00000393288	TM7SF3	chr12	27148170	-	KCNC2	chr12	75445097	-	0.00039374	0.9996063

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 TM7SF3-KCNC2

+/-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
TM7SF3	chr12	27148170	KCNC2	chr12	75445097	916	303	QRMVSVPQVKASALKFIAFASLFFIL

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Potential FusionNeoAntigen Information of TM7SF3-KCNC2 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.

TM7SF3-KCNC2_27148170_75445097.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)
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:10	VPQVKASAL	0.9997	0.5585	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:02	VPQVKASAL	0.9997	0.5188	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:01	QVKASALKF	0.998	0.7304	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:17	ASALKFIAF	0.9969	0.8081	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:25	ASALKFIAF	0.9967	0.817	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B58:02	ASALKFIAF	0.996	0.8159	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:16	ASALKFIAF	0.9958	0.7164	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B57:03	ASALKFIAF	0.9947	0.9473	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:25	QVKASALKF	0.9935	0.8499	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:17	QVKASALKF	0.99	0.8572	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B08:09	VPQVKASAL	0.9894	0.5565	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:02	QVKASALKF	0.989	0.8668	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:16	QVKASALKF	0.9823	0.8115	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B14:02	VPQVKASAL	0.9755	0.7208	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B14:01	VPQVKASAL	0.9755	0.7208	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:03	VPQVKASAL	0.9401	0.6331	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B08:01	ASALKFIAF	0.93	0.5623	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:01	VPQVKASAL	0.9237	0.5969	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:08	VPQVKASAL	0.9215	0.6169	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-A32:13	ASALKFIAF	0.9018	0.9673	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B58:02	QVKASALKF	0.8103	0.9285	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:02	VPQVKASAL	0.7938	0.7431	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:04	VPQVKASAL	0.7938	0.7431	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-A32:13	QVKASALKF	0.6682	0.9059	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B82:01	VPQVKASAL	0.3859	0.5075	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:02	SVPQVKASAL	0.9887	0.5657	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B82:01	SVPQVKASAL	0.5475	0.5369	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:02	VSVPQVKASAL	0.9864	0.5777	3	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:07	QVKASALKF	0.9983	0.6684	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:12	VPQVKASAL	0.9956	0.6721	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:07	ASALKFIAF	0.9936	0.5666	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B14:03	VPQVKASAL	0.9913	0.7814	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C15:04	ASALKFIAF	0.9902	0.8659	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:04	QVKASALKF	0.9741	0.7968	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C12:12	ASALKFIAF	0.967	0.942	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C03:14	ASALKFIAF	0.9265	0.9692	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C15:04	QVKASALKF	0.8813	0.9211	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:12	VPQVKASAL	0.7938	0.7431	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B39:10	VPQVKASAL	0.7828	0.7187	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B39:09	VPQVKASAL	0.7484	0.5386	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C01:30	VPQVKASAL	0.603	0.9369	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:12	SVPQVKASAL	0.9899	0.7159	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C01:17	SVPQVKASAL	0.9842	0.9588	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C01:30	SVPQVKASAL	0.9774	0.9602	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:04	VSVPQVKASAL	0.99	0.5239	3	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:12	VSVPQVKASAL	0.9898	0.7278	3	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C03:02	SALKFIAF	0.9999	0.9366	11	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C16:01	SALKFIAF	0.9991	0.9598	11	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:09	VPQVKASAL	0.9997	0.5329	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:22	VPQVKASAL	0.9997	0.5188	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B57:04	ASALKFIAF	0.9981	0.6655	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:33	QVKASALKF	0.998	0.7304	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:34	QVKASALKF	0.998	0.7304	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:125	QVKASALKF	0.998	0.7304	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:135	QVKASALKF	0.998	0.7218	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:27	QVKASALKF	0.9979	0.769	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:35	QVKASALKF	0.9978	0.7741	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:11	QVKASALKF	0.9978	0.7013	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:08	QVKASALKF	0.9976	0.6824	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C03:02	ASALKFIAF	0.9974	0.9463	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B58:06	ASALKFIAF	0.9967	0.7096	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:50	QVKASALKF	0.9965	0.7771	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:39	ASALKFIAF	0.9961	0.7117	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:24	QVKASALKF	0.9959	0.883	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:39	QVKASALKF	0.9931	0.7841	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B57:02	ASALKFIAF	0.9922	0.8712	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C15:09	ASALKFIAF	0.9902	0.8659	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B58:06	QVKASALKF	0.9885	0.8914	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C03:05	ASALKFIAF	0.9869	0.842	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-A32:01	ASALKFIAF	0.9862	0.9572	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C03:17	ASALKFIAF	0.982	0.9477	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C16:04	ASALKFIAF	0.9818	0.9807	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:13	QVKASALKF	0.9794	0.8653	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-A32:01	QVKASALKF	0.9714	0.9095	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C16:01	ASALKFIAF	0.9338	0.9756	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:13	VPQVKASAL	0.933	0.6443	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B08:18	ASALKFIAF	0.93	0.5623	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:23	VPQVKASAL	0.9254	0.613	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:77	VPQVKASAL	0.9237	0.5969	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C12:02	ASALKFIAF	0.9141	0.9733	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:12	QVKASALKF	0.9107	0.803	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C15:09	QVKASALKF	0.8813	0.9211	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-A25:01	QVKASALKF	0.8707	0.8466	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B08:12	VPQVKASAL	0.8443	0.5375	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:20	QVKASALKF	0.8309	0.8413	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:24	VPQVKASAL	0.8226	0.6271	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:11	VPQVKASAL	0.8045	0.6782	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:09	VPQVKASAL	0.7938	0.7431	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B67:01	VPQVKASAL	0.763	0.6499	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C16:02	ASALKFIAF	0.6979	0.9886	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C02:10	ASALKFIAF	0.5939	0.962	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C02:02	ASALKFIAF	0.5939	0.962	10	19
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C02:02	QVKASALKF	0.4999	0.9634	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C02:10	QVKASALKF	0.4999	0.9634	7	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B82:02	VPQVKASAL	0.3859	0.5075	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B35:43	VPQVKASAL	0.0642	0.5585	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:08	VPQVKASAL	0.05	0.5544	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B15:11	VPQVKASAL	0.0401	0.5585	5	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:09	SVPQVKASAL	0.9893	0.5662	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:22	SVPQVKASAL	0.9887	0.5657	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C01:02	SVPQVKASAL	0.9835	0.9557	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-C01:03	SVPQVKASAL	0.9834	0.9661	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B08:12	SVPQVKASAL	0.9065	0.5647	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B67:01	SVPQVKASAL	0.6418	0.7175	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B82:02	SVPQVKASAL	0.5475	0.5369	4	14
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:09	VPQVKASALKF	0.9993	0.5682	5	16
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	916	HLA-B07:22	VSVPQVKASAL	0.9864	0.5777	3	14

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Potential FusionNeoAntigen Information of TM7SF3-KCNC2 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 TM7SF3-KCNC2

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
6929	PQVKASALKFIAFA	TM7SF3	KCNC2	chr12	27148170	chr12	75445097	916

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TM7SF3-KCNC2

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	6929	PQVKASALKFIAFA	-7.15543	-7.26883
HLA-B14:02	3BVN	6929	PQVKASALKFIAFA	-4.77435	-5.80965
HLA-B52:01	3W39	6929	PQVKASALKFIAFA	-6.80875	-6.92215
HLA-B52:01	3W39	6929	PQVKASALKFIAFA	-4.20386	-5.23916
HLA-A11:01	4UQ2	6929	PQVKASALKFIAFA	-7.5194	-8.5547
HLA-A11:01	4UQ2	6929	PQVKASALKFIAFA	-6.9601	-7.0735
HLA-A24:02	5HGA	6929	PQVKASALKFIAFA	-7.52403	-7.63743
HLA-A24:02	5HGA	6929	PQVKASALKFIAFA	-5.82433	-6.85963
HLA-B27:05	6PYJ	6929	PQVKASALKFIAFA	-3.28285	-4.31815
HLA-B44:05	3DX8	6929	PQVKASALKFIAFA	-5.91172	-6.94702
HLA-B44:05	3DX8	6929	PQVKASALKFIAFA	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of TM7SF3-KCNC2

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
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	10	19	ASALKFIAF	GCTCTCAAGTTTATTGCTTTTGCTTCT
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	11	19	SALKFIAF	CTCAAGTTTATTGCTTTTGCTTCT
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	3	14	VSVPQVKASAL	GTGCCCCAGGTGAAGGCCAGTGCTCTCAAGTTT
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	4	14	SVPQVKASAL	CCCCAGGTGAAGGCCAGTGCTCTCAAGTTT
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	5	14	VPQVKASAL	CAGGTGAAGGCCAGTGCTCTCAAGTTT
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	5	16	VPQVKASALKF	CAGGTGAAGGCCAGTGCTCTCAAGTTTATTGCT
TM7SF3-KCNC2	chr12	27148170	chr12	75445097	7	16	QVKASALKF	AAGGCCAGTGCTCTCAAGTTTATTGCT

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 TM7SF3-KCNC2

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
SARC	TM7SF3-KCNC2	chr12	27148170	ENST00000343028	chr12	75445097	ENST00000298972	TCGA-RN-AAAQ-01A

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Potential target of CAR-T therapy development for TM7SF3-KCNC2

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

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000298972

230_250

599.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000298972

284_303

599.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000298972

314_334

599.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000298972

346_368

599.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000298972

382_402

599.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000298972

453_473

599.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000341669

230_250

630.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000341669

284_303

630.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000341669

314_334

630.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000341669

346_368

630.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000341669

382_402

630.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000341669

453_473

630.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000350228

230_250

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000350228

284_303

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000350228

314_334

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000350228

346_368

543.6666666666666

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000350228

382_402

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000350228

453_473

543.6666666666666

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000393288

230_250

619.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000393288

284_303

619.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000393288

314_334

619.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000393288

346_368

619.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000393288

382_402

619.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000393288

453_473

619.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000540018

230_250

584.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000540018

284_303

584.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000540018

314_334

584.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000540018

346_368

584.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000540018

382_402

584.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000540018

453_473

584.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000548513

230_250

477.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000548513

284_303

477.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000548513

314_334

477.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000548513

346_368

477.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000548513

382_402

477.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000548513

453_473

477.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000549446

230_250

639.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000549446

284_303

639.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000549446

314_334

639.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000549446

346_368

639.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000549446

382_402

639.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000549446

453_473

639.0

Transmembrane

Helical%3B Name%3DSegment S6

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000550433

230_250

630.0

Transmembrane

Helical%3B Name%3DSegment S1

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000550433

284_303

630.0

Transmembrane

Helical%3B Name%3DSegment S2

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000550433

314_334

630.0

Transmembrane

Helical%3B Name%3DSegment S3

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000550433

346_368

630.0

Transmembrane

Helical%3B Voltage-sensor%3B Name%3DSegment S4

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000550433

382_402

630.0

Transmembrane

Helical%3B Name%3DSegment S5

Tgene

KCNC2

chr12:27148170

chr12:75445097

ENST00000550433

453_473

630.0

Transmembrane

Helical%3B Name%3DSegment S6

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 TM7SF3-KCNC2

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 TM7SF3-KCNC2

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)