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Fusion Protein:CDC42BPA-KCNK1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CDC42BPA-KCNK1
	FusionPDB ID: 14838
	FusionGDB2.0 ID: 14838
		Hgene	Tgene
	Gene symbol	CDC42BPA	KCNK1
	Gene ID	8476	3775
	Gene name	CDC42 binding protein kinase alpha	potassium two pore domain channel subfamily K member 1
	Synonyms	MRCK\|MRCKA\|PK428	DPK\|HOHO\|K2P1\|K2p1.1\|KCNO1\|TWIK-1\|TWIK1
	Cytomap	1q42.13	1q42.2
	Type of gene	protein-coding	protein-coding
	Description	serine/threonine-protein kinase MRCK alphaCDC42 binding protein kinase alpha (DMPK-like)CDC42 binding protein kinase betamyotonic dystrophy kinase-related CDC42-binding protein kinase alphamyotonic dystrophy protein kinase-like alphaser-thr protein k	potassium channel subfamily K member 1inward rectifying potassium channel protein TWIK-1potassium channel K2P1potassium channel KCNO1potassium channel, two pore domain subfamily K, member 1potassium inwardly-rectifying channel, subfamily K, member 1
	Modification date	20200313	20200320
	UniProtAcc	Q5VT25 Main function of 5'-partner protein: FUNCTION: Serine/threonine-protein kinase which is an important downstream effector of CDC42 and plays a role in the regulation of cytoskeleton reorganization and cell migration (PubMed:15723050, PubMed:9418861, PubMed:9092543). Regulates actin cytoskeletal reorganization via phosphorylation of PPP1R12C and MYL9/MLC2 (PubMed:21457715). In concert with MYO18A and LURAP1, is involved in modulating lamellar actomyosin retrograde flow that is crucial to cell protrusion and migration (PubMed:18854160). Phosphorylates: PPP1R12A, LIMK1 and LIMK2 (PubMed:11340065, PubMed:11399775). May play a role in TFRC-mediated iron uptake (PubMed:20188707). In concert with FAM89B/LRAP25 mediates the targeting of LIMK1 to the lamellipodium resulting in its activation and subsequent phosphorylation of CFL1 which is important for lamellipodial F-actin regulation (By similarity). Triggers the formation of an extrusion apical actin ring required for epithelial extrusion of apoptotic cells (PubMed:29162624). {ECO:0000250\|UniProtKB:Q3UU96, ECO:0000269\|PubMed:11340065, ECO:0000269\|PubMed:11399775, ECO:0000269\|PubMed:15723050, ECO:0000269\|PubMed:18854160, ECO:0000269\|PubMed:20188707, ECO:0000269\|PubMed:21457715, ECO:0000269\|PubMed:29162624, ECO:0000269\|PubMed:9092543, ECO:0000269\|PubMed:9418861}.	Q96T54 Main function of 5'-partner protein: FUNCTION: Outward rectifying potassium channel. Produces rapidly activating and non-inactivating outward rectifier K(+) currents.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000334218, ENST00000366764, ENST00000366765, ENST00000366766, ENST00000366767, ENST00000366769, ENST00000535525, ENST00000488131,	ENST00000366620, ENST00000472190, ENST00000366621,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 12 X 9=1512	6 X 3 X 5=90
	# samples	15	6
	** MAII score	log2(15/1512*10)=-3.33342373372519 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/90*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CDC42BPA [Title/Abstract] AND KCNK1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CDC42BPA [Title/Abstract] AND KCNK1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CDC42BPA(227259909)-KCNK1(233802341), # samples:1
Anticipated loss of major functional domain due to fusion event.	CDC42BPA-KCNK1 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. CDC42BPA-KCNK1 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. CDC42BPA-KCNK1 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. CDC42BPA-KCNK1 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	CDC42BPA	GO:0006468	protein phosphorylation	9092543
Hgene	CDC42BPA	GO:0031532	actin cytoskeleton reorganization	9418861
Tgene	KCNK1	GO:0035725	sodium ion transmembrane transport	21653227
Tgene	KCNK1	GO:0071805	potassium ion transmembrane transport	21653227\|22282804

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:227259909/chr1:233802341)
- 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 CDC42BPA (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 KCNK1 (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)
ENST00000366767	CDC42BPA	chr1	227259909	-	ENST00000366621	KCNK1	chr1	233802341	+	4222	2584	0	3239	1079
ENST00000366769	CDC42BPA	chr1	227259909	-	ENST00000366621	KCNK1	chr1	233802341	+	5757	4119	1292	4774	1160
ENST00000366764	CDC42BPA	chr1	227259909	-	ENST00000366621	KCNK1	chr1	233802341	+	5408	3770	943	4425	1160
ENST00000334218	CDC42BPA	chr1	227259909	-	ENST00000366621	KCNK1	chr1	233802341	+	5408	3770	943	4425	1160
ENST00000366766	CDC42BPA	chr1	227259909	-	ENST00000366621	KCNK1	chr1	233802341	+	5408	3770	943	4425	1160
ENST00000535525	CDC42BPA	chr1	227259909	-	ENST00000366621	KCNK1	chr1	233802341	+	4492	2854	27	3509	1160
ENST00000366765	CDC42BPA	chr1	227259909	-	ENST00000366621	KCNK1	chr1	233802341	+	4997	3359	532	4014	1160

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
ENST00000366767	ENST00000366621	CDC42BPA	chr1	227259909	-	KCNK1	chr1	233802341	+	0.000234584	0.99976546
ENST00000366769	ENST00000366621	CDC42BPA	chr1	227259909	-	KCNK1	chr1	233802341	+	0.001314693	0.9986853
ENST00000366764	ENST00000366621	CDC42BPA	chr1	227259909	-	KCNK1	chr1	233802341	+	0.000897317	0.9991027
ENST00000334218	ENST00000366621	CDC42BPA	chr1	227259909	-	KCNK1	chr1	233802341	+	0.000897317	0.9991027
ENST00000366766	ENST00000366621	CDC42BPA	chr1	227259909	-	KCNK1	chr1	233802341	+	0.000897317	0.9991027
ENST00000535525	ENST00000366621	CDC42BPA	chr1	227259909	-	KCNK1	chr1	233802341	+	0.000508189	0.9994918
ENST00000366765	ENST00000366621	CDC42BPA	chr1	227259909	-	KCNK1	chr1	233802341	+	0.000564189	0.99943584

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 CDC42BPA-KCNK1

+/-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
CDC42BPA	chr1	227259909	KCNK1	chr1	233802341	2584	861	QLIKDTEELRSEKGYGHTVPLSDGGK
CDC42BPA	chr1	227259909	KCNK1	chr1	233802341	2854	942	QLIKDTEELRSEKGYGHTVPLSDGGK
CDC42BPA	chr1	227259909	KCNK1	chr1	233802341	3359	942	QLIKDTEELRSEKGYGHTVPLSDGGK
CDC42BPA	chr1	227259909	KCNK1	chr1	233802341	3770	942	QLIKDTEELRSEKGYGHTVPLSDGGK
CDC42BPA	chr1	227259909	KCNK1	chr1	233802341	4119	942	QLIKDTEELRSEKGYGHTVPLSDGGK

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Potential FusionNeoAntigen Information of CDC42BPA-KCNK1 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.

CDC42BPA-KCNK1_227259909_233802341.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)
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:03	EELRSEKGY	0.9988	0.9305	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B45:01	SEKGYGHTV	0.9984	0.8957	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B50:02	SEKGYGHTV	0.9982	0.794	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:01	EELRSEKGY	0.9917	0.6934	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-A30:08	KGYGHTVPL	0.8921	0.8423	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:03	SEKGYGHTV	0.8097	0.9415	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B41:01	SEKGYGHTV	0.7888	0.6732	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B07:10	KGYGHTVPL	0.7488	0.5143	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B47:01	SEKGYGHTV	0.6946	0.5304	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B48:01	KGYGHTVPL	0.5036	0.8615	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B50:01	SEKGYGHTV	0.3794	0.8597	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:01	SEKGYGHTV	0.3362	0.7944	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B39:13	SEKGYGHTV	0.2471	0.7238	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B52:01	SEKGYGHTV	0.0268	0.9846	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:03	TEELRSEKGY	0.9972	0.9378	5	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B45:01	SEKGYGHTVP	0.9795	0.9271	10	20
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B50:02	SEKGYGHTVP	0.9604	0.7962	10	20
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B50:01	SEKGYGHTVP	0.9414	0.8379	10	20
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B41:01	SEKGYGHTVP	0.9099	0.7412	10	20
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B48:01	SEKGYGHTVPL	0.9969	0.6371	10	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:05	SEKGYGHTVPL	0.9781	0.5149	10	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B39:13	SEKGYGHTVPL	0.975	0.8437	10	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B40:06	SEKGYGHTV	0.999	0.8463	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C03:08	KGYGHTVPL	0.9937	0.962	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C15:06	KGYGHTVPL	0.9926	0.9572	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C03:19	KGYGHTVPL	0.9915	0.995	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:10	SEKGYGHTV	0.986	0.7258	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C07:29	KGYGHTVPL	0.7903	0.9488	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B39:08	SEKGYGHTV	0.4732	0.6804	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B51:07	SEKGYGHTV	0.011	0.9709	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B40:06	SEKGYGHTVP	0.9825	0.8936	10	20
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:26	EELRSEKGY	0.9988	0.9305	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:07	EELRSEKGY	0.9988	0.9305	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:13	EELRSEKGY	0.9988	0.9305	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B40:04	SEKGYGHTV	0.9965	0.846	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C15:02	KGYGHTVPL	0.9938	0.9411	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C03:05	KGYGHTVPL	0.993	0.9588	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:08	EELRSEKGY	0.9924	0.5493	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:04	EELRSEKGY	0.9924	0.7205	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C15:05	KGYGHTVPL	0.9923	0.9482	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C03:17	KGYGHTVPL	0.9918	0.9828	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:05	EELRSEKGY	0.9917	0.6934	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:06	EELRSEKGY	0.9903	0.7001	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C03:67	KGYGHTVPL	0.9838	0.9906	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C03:03	KGYGHTVPL	0.9835	0.9939	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C03:04	KGYGHTVPL	0.9835	0.9939	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:03	EELRSEKGY	0.9707	0.6815	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:11	EELRSEKGY	0.9626	0.6722	6	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:26	SEKGYGHTV	0.8097	0.9415	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:13	SEKGYGHTV	0.8097	0.9415	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:07	SEKGYGHTV	0.8097	0.9415	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B07:13	KGYGHTVPL	0.6845	0.859	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:11	SEKGYGHTV	0.5323	0.6914	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C17:01	KGYGHTVPL	0.5282	0.9823	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B50:05	SEKGYGHTV	0.3794	0.8597	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B50:04	SEKGYGHTV	0.3794	0.8597	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:08	SEKGYGHTV	0.3737	0.752	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:05	SEKGYGHTV	0.3362	0.7944	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:03	SEKGYGHTV	0.3354	0.777	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B18:06	SEKGYGHTV	0.3	0.8281	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-C01:02	KGYGHTVPL	0.2539	0.9531	12	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B39:02	SEKGYGHTV	0.1945	0.7389	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B15:53	SEKGYGHTV	0.027	0.8559	10	19
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:26	TEELRSEKGY	0.9972	0.9378	5	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:07	TEELRSEKGY	0.9972	0.9378	5	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B44:13	TEELRSEKGY	0.9972	0.9378	5	15
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B50:04	SEKGYGHTVP	0.9414	0.8379	10	20
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B50:05	SEKGYGHTVP	0.9414	0.8379	10	20
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B40:04	SEKGYGHTVPL	0.9963	0.7893	10	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B39:02	SEKGYGHTVPL	0.9884	0.8628	10	21
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	HLA-B41:03	SEKGYGHTVPL	0.9606	0.5699	10	21

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Potential FusionNeoAntigen Information of CDC42BPA-KCNK1 in HLA II

CDC42BPA-KCNK1_227259909_233802341.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)
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0417	EKGYGHTVPLSDGGK	11	26
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0469	EKGYGHTVPLSDGGK	11	26
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0480	EKGYGHTVPLSDGGK	11	26
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0486	EKGYGHTVPLSDGGK	11	26
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0706	EKGYGHTVPLSDGGK	11	26
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0903	EKGYGHTVPLSDGGK	11	26
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0903	SEKGYGHTVPLSDGG	10	25
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0908	EKGYGHTVPLSDGGK	11	26
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	3770	DRB1-0908	SEKGYGHTVPLSDGG	10	25

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Fusion breakpoint peptide structures of CDC42BPA-KCNK1

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
1685	EELRSEKGYGHTVP	CDC42BPA	KCNK1	chr1	227259909	chr1	233802341	3770

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDC42BPA-KCNK1

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	1685	EELRSEKGYGHTVP	-6.35143	-7.38673
HLA-B14:02	3BVN	1685	EELRSEKGYGHTVP	-5.20162	-5.31502
HLA-B52:01	3W39	1685	EELRSEKGYGHTVP	-6.03049	-6.14389
HLA-B52:01	3W39	1685	EELRSEKGYGHTVP	-5.12323	-6.15853
HLA-A24:02	5HGA	1685	EELRSEKGYGHTVP	-9.81198	-9.92538
HLA-A24:02	5HGA	1685	EELRSEKGYGHTVP	-7.16433	-8.19963
HLA-B44:05	3DX8	1685	EELRSEKGYGHTVP	-6.46131	-6.57471
HLA-B44:05	3DX8	1685	EELRSEKGYGHTVP	-3.08576	-4.12106
HLA-A02:01	6TDR	1685	EELRSEKGYGHTVP	-5.03933	-5.15273

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Vaccine Design for the FusionNeoAntigens of CDC42BPA-KCNK1

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
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	10	19	SEKGYGHTV	CTGAAAAGGGTTATGGCCACACCGTGC
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	10	20	SEKGYGHTVP	CTGAAAAGGGTTATGGCCACACCGTGCCCT
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	10	21	SEKGYGHTVPL	CTGAAAAGGGTTATGGCCACACCGTGCCCTTGT
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	12	21	KGYGHTVPL	AGGGTTATGGCCACACCGTGCCCTTGT
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	5	15	TEELRSEKGY	CTGAAGAGCTTAGATCTGAAAAGGGTTATG
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	6	15	EELRSEKGY	AAGAGCTTAGATCTGAAAAGGGTTATG

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
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	10	25	SEKGYGHTVPLSDGG	CTGAAAAGGGTTATGGCCACACCGTGCCCTTGTCAGATGGAGGTA
CDC42BPA-KCNK1	chr1	227259909	chr1	233802341	11	26	EKGYGHTVPLSDGGK	AAAAGGGTTATGGCCACACCGTGCCCTTGTCAGATGGAGGTAAGG

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Information of the samples that have these potential fusion neoantigens of CDC42BPA-KCNK1

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
STAD	CDC42BPA-KCNK1	chr1	227259909	ENST00000334218	chr1	233802341	ENST00000366621	TCGA-CD-5799-01A

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Potential target of CAR-T therapy development for CDC42BPA-KCNK1

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

KCNK1

chr1:227259909

chr1:233802341

ENST00000366621

212_224

337.0

Intramembrane

Helical%3B Name%3DPore helix 2

Tgene

KCNK1

chr1:227259909

chr1:233802341

ENST00000366621

225_231

337.0

Intramembrane

Ontology_term=ECO:0000269

Tgene

KCNK1

chr1:227259909

chr1:233802341

ENST00000366621

133_156

337.0

Transmembrane

Helical

Tgene

KCNK1

chr1:227259909

chr1:233802341

ENST00000366621

182_202

337.0

Transmembrane

Helical

Tgene

KCNK1

chr1:227259909

chr1:233802341

ENST00000366621

244_267

337.0

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 CDC42BPA-KCNK1

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 CDC42BPA-KCNK1

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)