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Fusion Protein:KCNN1-SLC27A1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: KCNN1-SLC27A1
	FusionPDB ID: 41521
	FusionGDB2.0 ID: 41521
		Hgene	Tgene
	Gene symbol	KCNN1	SLC27A1
	Gene ID	3780	376497
	Gene name	potassium calcium-activated channel subfamily N member 1	solute carrier family 27 member 1
	Synonyms	KCa2.1\|SK1\|SKCA1\|hSK1	ACSVL5\|FATP\|FATP-1\|FATP1
	Cytomap	19p13.11	19p13.11
	Type of gene	protein-coding	protein-coding
	Description	small conductance calcium-activated potassium channel protein 1potassium channel, calcium activated intermediate/small conductance subfamily N alpha, member 1potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1small	long-chain fatty acid transport protein 1fatty acid transport protein 1solute carrier family 27 (fatty acid transporter), member 1
	Modification date	20200313	20200327
	UniProtAcc	Q92952 Main function of 5'-partner protein: FUNCTION: Forms a voltage-independent potassium channel activated by intracellular calcium. Activation is followed by membrane hyperpolarization. Thought to regulate neuronal excitability by contributing to the slow component of synaptic afterhyperpolarization. The channel is blocked by apamin (By similarity). {ECO:0000250}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000222249, ENST00000594192,	ENST00000598424, ENST00000252595, ENST00000442725, ENST00000598848,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 6 X 3=90	5 X 5 X 4=100
	# samples	5	5
	** MAII score	log2(5/90*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: KCNN1 [Title/Abstract] AND SLC27A1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: KCNN1 [Title/Abstract] AND SLC27A1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	KCNN1(18100627)-SLC27A1(17594691), # samples:2
Anticipated loss of major functional domain due to fusion event.	KCNN1-SLC27A1 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. KCNN1-SLC27A1 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. KCNN1-SLC27A1 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. KCNN1-SLC27A1 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:18100627/chr19:17594691)
- 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 KCNN1 (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 SLC27A1 (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)
ENST00000222249	KCNN1	chr19	18100627	+	ENST00000442725	SLC27A1	chr19	17597372	+	3288	1514	1527	3287	586
ENST00000222249	KCNN1	chr19	18100627	+	ENST00000252595	SLC27A1	chr19	17597372	+	4844	1514	1527	3287	586
ENST00000222249	KCNN1	chr19	18100652	-	ENST00000442725	SLC27A1	chr19	17597372	+	3391	1617	226	3390	1055
ENST00000222249	KCNN1	chr19	18100652	-	ENST00000252595	SLC27A1	chr19	17597372	+	4947	1617	226	3390	1054

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
ENST00000222249	ENST00000442725	KCNN1	chr19	18100627	+	SLC27A1	chr19	17597372	+	0.014827379	0.9851726
ENST00000222249	ENST00000252595	KCNN1	chr19	18100627	+	SLC27A1	chr19	17597372	+	0.007895961	0.99210405
ENST00000222249	ENST00000442725	KCNN1	chr19	18100652	-	SLC27A1	chr19	17597372	+	0.002830887	0.9971691
ENST00000222249	ENST00000252595	KCNN1	chr19	18100652	-	SLC27A1	chr19	17597372	+	0.001323994	0.998676

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 KCNN1-SLC27A1

+/-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
KCNN1	chr19	18100652	SLC27A1	chr19	17597372	1617	464	RKHQRKFLQAIHHGLSVLIRVRLELR

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Potential FusionNeoAntigen Information of KCNN1-SLC27A1 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.

KCNN1-SLC27A1_18100652_17597372.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)
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:01	IHHGLSVL	0.9995	0.9092	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:02	IHHGLSVL	0.9992	0.9551	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:01	HHGLSVLI	0.9991	0.8641	11	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:01	IHHGLSVL	0.9991	0.954	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:10	IHHGLSVL	0.9984	0.5402	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B14:02	IHHGLSVL	0.9983	0.7315	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B14:01	IHHGLSVL	0.9983	0.7315	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:02	HHGLSVLI	0.9972	0.9277	11	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:01	HHGLSVLI	0.9968	0.9384	11	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:18	IHHGLSVL	0.961	0.6692	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:01	IHHGLSVLI	0.9973	0.6696	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:01	IHHGLSVLI	0.9963	0.785	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:06	IHHGLSVLI	0.9962	0.5681	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:02	IHHGLSVLI	0.9962	0.7783	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B52:01	QAIHHGLSV	0.9873	0.7873	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-A02:04	FLQAIHHGL	0.9786	0.5534	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-A02:13	FLQAIHHGL	0.9713	0.5338	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B08:09	QAIHHGLSV	0.9425	0.8676	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-A02:38	FLQAIHHGL	0.9286	0.597	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B08:01	FLQAIHHGL	0.7968	0.796	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:09	IHHGLSVL	0.9997	0.5944	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:12	IHHGLSVL	0.9993	0.9156	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:05	IHHGLSVL	0.999	0.8979	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:05	HHGLSVLI	0.9961	0.8456	11	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B14:03	IHHGLSVL	0.8783	0.8455	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:07	QAIHHGLSV	0.9996	0.9814	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C15:06	QAIHHGLSV	0.9996	0.9452	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C04:06	QAIHHGLSV	0.9995	0.7659	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C15:04	QAIHHGLSV	0.9994	0.9483	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C12:04	QAIHHGLSV	0.9977	0.9903	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:19	QAIHHGLSV	0.9975	0.945	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C06:03	QAIHHGLSV	0.9974	0.9903	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C12:12	QAIHHGLSV	0.9972	0.9492	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:12	IHHGLSVLI	0.997	0.6831	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:05	IHHGLSVLI	0.9957	0.6495	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-A02:05	FLQAIHHGL	0.9935	0.5196	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B78:01	QAIHHGLSV	0.991	0.648	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:08	QAIHHGLSV	0.9907	0.8834	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C02:06	QAIHHGLSV	0.9905	0.9687	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B51:07	QAIHHGLSV	0.9884	0.661	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C08:13	QAIHHGLSV	0.9871	0.9336	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C08:04	QAIHHGLSV	0.9871	0.9336	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:07	FLQAIHHGL	0.9609	0.9711	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C08:03	QAIHHGLSV	0.9398	0.9584	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C04:06	FLQAIHHGL	0.9078	0.5247	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C02:06	FLQAIHHGL	0.7097	0.9486	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:14	QAIHHGLSV	0.6373	0.9698	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C07:13	FLQAIHHGL	0.5049	0.809	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C07:29	FLQAIHHGL	0.432	0.8491	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C01:30	FLQAIHHGL	0.2076	0.8928	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:31	IHHGLSVL	0.9995	0.9106	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:05	IHHGLSVL	0.9991	0.954	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:09	IHHGLSVL	0.997	0.6328	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:05	HHGLSVLI	0.9968	0.9384	11	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:09	HHGLSVLI	0.9882	0.5832	11	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:11	IHHGLSVL	0.8858	0.8225	10	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C15:02	QAIHHGLSV	0.9996	0.8771	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C15:05	QAIHHGLSV	0.9996	0.8947	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C15:09	QAIHHGLSV	0.9994	0.9483	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:17	QAIHHGLSV	0.9975	0.9184	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:05	QAIHHGLSV	0.9973	0.8259	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:31	IHHGLSVLI	0.9973	0.6743	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B38:05	IHHGLSVLI	0.9963	0.785	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C12:03	QAIHHGLSV	0.9961	0.9785	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:06	QAIHHGLSV	0.9942	0.9513	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:03	QAIHHGLSV	0.9938	0.959	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:04	QAIHHGLSV	0.9938	0.959	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C16:04	QAIHHGLSV	0.9938	0.9786	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-A02:03	FLQAIHHGL	0.9935	0.5334	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C02:10	QAIHHGLSV	0.9927	0.9812	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C02:02	QAIHHGLSV	0.9927	0.9812	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:02	QAIHHGLSV	0.9912	0.9638	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B78:02	QAIHHGLSV	0.99	0.668	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:09	IHHGLSVLI	0.9877	0.5219	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C16:02	QAIHHGLSV	0.9863	0.9855	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:73	AIHHGLSVL	0.9818	0.8615	9	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C16:01	QAIHHGLSV	0.9757	0.9703	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:30	AIHHGLSVL	0.9719	0.918	9	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C17:01	QAIHHGLSV	0.969	0.9527	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C12:02	QAIHHGLSV	0.9685	0.9752	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C08:01	QAIHHGLSV	0.9398	0.9584	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B07:13	QAIHHGLSV	0.933	0.7892	8	17
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:67	FLQAIHHGL	0.9246	0.8673	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B08:18	FLQAIHHGL	0.7968	0.796	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:73	FLQAIHHGL	0.7344	0.7312	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B15:30	FLQAIHHGL	0.6404	0.7073	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B39:11	IHHGLSVLI	0.6331	0.5778	10	19
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B08:12	FLQAIHHGL	0.6052	0.8954	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C07:04	FLQAIHHGL	0.5543	0.8421	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C17:01	FLQAIHHGL	0.547	0.6549	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-B07:13	FLQAIHHGL	0.2303	0.7789	6	15
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:03	QAIHHGLSVL	0.9993	0.9711	8	18
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	1617	HLA-C03:04	QAIHHGLSVL	0.9993	0.9711	8	18

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Potential FusionNeoAntigen Information of KCNN1-SLC27A1 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 KCNN1-SLC27A1

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
2455	FLQAIHHGLSVLIR	KCNN1	SLC27A1	chr19	18100652	chr19	17597372	1617

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KCNN1-SLC27A1

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	2455	FLQAIHHGLSVLIR	-7.15543	-7.26883
HLA-B14:02	3BVN	2455	FLQAIHHGLSVLIR	-4.77435	-5.80965
HLA-B52:01	3W39	2455	FLQAIHHGLSVLIR	-6.80875	-6.92215
HLA-B52:01	3W39	2455	FLQAIHHGLSVLIR	-4.20386	-5.23916
HLA-A11:01	4UQ2	2455	FLQAIHHGLSVLIR	-7.5194	-8.5547
HLA-A11:01	4UQ2	2455	FLQAIHHGLSVLIR	-6.9601	-7.0735
HLA-A24:02	5HGA	2455	FLQAIHHGLSVLIR	-7.52403	-7.63743
HLA-A24:02	5HGA	2455	FLQAIHHGLSVLIR	-5.82433	-6.85963
HLA-B27:05	6PYJ	2455	FLQAIHHGLSVLIR	-3.28285	-4.31815
HLA-B44:05	3DX8	2455	FLQAIHHGLSVLIR	-5.91172	-6.94702
HLA-B44:05	3DX8	2455	FLQAIHHGLSVLIR	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of KCNN1-SLC27A1

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
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	10	18	IHHGLSVL	CATCCATCACGGTCTCTCTGTGCT
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	10	19	IHHGLSVLI	CATCCATCACGGTCTCTCTGTGCTGAT
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	11	19	HHGLSVLI	CCATCACGGTCTCTCTGTGCTGAT
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	6	15	FLQAIHHGL	GTTCCTCCAAGCCATCCATCACGGTCT
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	8	17	QAIHHGLSV	CCAAGCCATCCATCACGGTCTCTCTGT
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	8	18	QAIHHGLSVL	CCAAGCCATCCATCACGGTCTCTCTGTGCT
KCNN1-SLC27A1	chr19	18100652	chr19	17597372	9	18	AIHHGLSVL	AGCCATCCATCACGGTCTCTCTGTGCT

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 KCNN1-SLC27A1

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
OV	KCNN1-SLC27A1	chr19	18100652	ENST00000222249	chr19	17597372	ENST00000252595	TCGA-25-1329-01A

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Potential target of CAR-T therapy development for KCNN1-SLC27A1

Predicted 3D structure. We used RoseTTAFold.

242_KCNN1-SLC27A1_t000_.e2e.pdb

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

KCNN1

chr19:18100652

chr19:17597372

ENST00000222249

317_337

432

544.0

Intramembrane

Pore-forming%3B Name%3DSegment H5

Hgene

KCNN1

chr19:18100652

chr19:17597372

ENST00000222249

111_131

432

544.0

Transmembrane

Helical%3B Name%3DSegment S1

Hgene

KCNN1

chr19:18100652

chr19:17597372

ENST00000222249

140_160

432

544.0

Transmembrane

Helical%3B Name%3DSegment S2

Hgene

KCNN1

chr19:18100652

chr19:17597372

ENST00000222249

179_199

432

544.0

Transmembrane

Helical%3B Name%3DSegment S3

Hgene

KCNN1

chr19:18100652

chr19:17597372

ENST00000222249

228_248

432

544.0

Transmembrane

Helical%3B Name%3DSegment S4

Hgene

KCNN1

chr19:18100652

chr19:17597372

ENST00000222249

277_297

432

544.0

Transmembrane

Helical%3B Name%3DSegment S5

Hgene

KCNN1

chr19:18100652

chr19:17597372

ENST00000222249

346_366

432

544.0

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
KCNN1	chr19	18100627	ENST00000222249	SLC27A1	chr19	17597372	ENST00000252595
KCNN1	chr19	18100652	ENST00000222249	SLC27A1	chr19	17597372	ENST00000252595
KCNN1	chr19	18100652	ENST00000222249	SLC27A1	chr19	17597372	ENST00000442725

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Related Drugs to KCNN1-SLC27A1

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 KCNN1-SLC27A1

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)