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Fusion Protein:CDKN2A-CAPZB

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CDKN2A-CAPZB
	FusionPDB ID: 15397
	FusionGDB2.0 ID: 15397
		Hgene	Tgene
	Gene symbol	CDKN2A	CAPZB
	Gene ID	1029	832
	Gene name	cyclin dependent kinase inhibitor 2A	capping actin protein of muscle Z-line subunit beta
	Synonyms	ARF\|CDK4I\|CDKN2\|CMM2\|INK4\|INK4A\|MLM\|MTS-1\|MTS1\|P14\|P14ARF\|P16\|P16-INK4A\|P16INK4\|P16INK4A\|P19\|P19ARF\|TP16	CAPB\|CAPPB\|CAPZ
	Cytomap	9p21.3	1p36.13
	Type of gene	protein-coding	protein-coding
	Description	cyclin-dependent kinase inhibitor 2ACDK4 inhibitor p16-INK4alternative reading framecell cycle negative regulator betacyclin-dependent kinase 4 inhibitor Acyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)multiple tumor suppressor 1	F-actin-capping protein subunit betacapZ betacapping actin protein of muscle Z-line beta subunitcapping protein (actin filament) muscle Z-line, betaepididymis secretory sperm binding protein
	Modification date	20200329	20200320
	UniProtAcc	Q96HQ2 Main function of 5'-partner protein:	P47756 Main function of 5'-partner protein: FUNCTION: F-actin-capping proteins bind in a Ca(2+)-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike other capping proteins (such as gelsolin and severin), these proteins do not sever actin filaments. Plays a role in the regulation of cell morphology and cytoskeletal organization. {ECO:0000269\|PubMed:21834987}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000304494, ENST00000446177, ENST00000498124, ENST00000579122, ENST00000361570, ENST00000470819, ENST00000479692, ENST00000494262, ENST00000497750, ENST00000498628, ENST00000530628, ENST00000578845, ENST00000579755,	ENST00000375144, ENST00000482808, ENST00000264202, ENST00000264203, ENST00000375142, ENST00000401084, ENST00000433834,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 9 X 11=1386	23 X 15 X 8=2760
	# samples	17	27
	** MAII score	log2(17/1386*10)=-3.02732060599951 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(27/2760*10)=-3.3536369546147 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CDKN2A [Title/Abstract] AND CAPZB [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CDKN2A [Title/Abstract] AND CAPZB [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CDKN2A(21974677)-CAPZB(19671746), # samples:3
Anticipated loss of major functional domain due to fusion event.	CDKN2A-CAPZB 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. CDKN2A-CAPZB 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	CDKN2A	GO:0000082	G1/S transition of mitotic cell cycle	10208428
Hgene	CDKN2A	GO:0007050	cell cycle arrest	15149599
Hgene	CDKN2A	GO:0008285	negative regulation of cell proliferation	15149599
Hgene	CDKN2A	GO:0030308	negative regulation of cell growth	10208428
Hgene	CDKN2A	GO:0032088	negative regulation of NF-kappaB transcription factor activity	10353611
Hgene	CDKN2A	GO:0042326	negative regulation of phosphorylation	8259215\|10208428
Hgene	CDKN2A	GO:0045736	negative regulation of cyclin-dependent protein serine/threonine kinase activity	7739547\|8259215

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr9:21974677/chr1:19671746)
- 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 CDKN2A (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 CAPZB (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)
ENST00000304494	CDKN2A	chr9	21974677	-	ENST00000401084	CAPZB	chr1	19671746	-	1409	421	124	651	175
ENST00000304494	CDKN2A	chr9	21974677	-	ENST00000264203	CAPZB	chr1	19671746	-	1329	421	124	537	137
ENST00000304494	CDKN2A	chr9	21974677	-	ENST00000375142	CAPZB	chr1	19671746	-	1472	421	786	76	236
ENST00000304494	CDKN2A	chr9	21974677	-	ENST00000433834	CAPZB	chr1	19671746	-	823	421	124	651	175
ENST00000304494	CDKN2A	chr9	21974677	-	ENST00000264202	CAPZB	chr1	19671746	-	667	421	654	76	192
ENST00000579122	CDKN2A	chr9	21974677	-	ENST00000401084	CAPZB	chr1	19671746	-	1169	181	31	411	126
ENST00000579122	CDKN2A	chr9	21974677	-	ENST00000264203	CAPZB	chr1	19671746	-	1089	181	961	623	112
ENST00000579122	CDKN2A	chr9	21974677	-	ENST00000375142	CAPZB	chr1	19671746	-	1232	181	546	1	182
ENST00000579122	CDKN2A	chr9	21974677	-	ENST00000433834	CAPZB	chr1	19671746	-	583	181	31	411	126
ENST00000579122	CDKN2A	chr9	21974677	-	ENST00000264202	CAPZB	chr1	19671746	-	427	181	414	1	138
ENST00000498124	CDKN2A	chr9	21974677	-	ENST00000401084	CAPZB	chr1	19671746	-	1177	189	39	419	126
ENST00000498124	CDKN2A	chr9	21974677	-	ENST00000264203	CAPZB	chr1	19671746	-	1097	189	969	631	112
ENST00000498124	CDKN2A	chr9	21974677	-	ENST00000375142	CAPZB	chr1	19671746	-	1240	189	554	0	185
ENST00000498124	CDKN2A	chr9	21974677	-	ENST00000433834	CAPZB	chr1	19671746	-	591	189	39	419	126
ENST00000498124	CDKN2A	chr9	21974677	-	ENST00000264202	CAPZB	chr1	19671746	-	435	189	422	0	141
ENST00000446177	CDKN2A	chr9	21974677	-	ENST00000401084	CAPZB	chr1	19671746	-	1350	362	65	592	175
ENST00000446177	CDKN2A	chr9	21974677	-	ENST00000264203	CAPZB	chr1	19671746	-	1270	362	65	478	137
ENST00000446177	CDKN2A	chr9	21974677	-	ENST00000375142	CAPZB	chr1	19671746	-	1413	362	727	17	236
ENST00000446177	CDKN2A	chr9	21974677	-	ENST00000433834	CAPZB	chr1	19671746	-	764	362	65	592	175
ENST00000446177	CDKN2A	chr9	21974677	-	ENST00000264202	CAPZB	chr1	19671746	-	608	362	595	17	192
ENST00000304494	CDKN2A	chr9	21974676	-	ENST00000401084	CAPZB	chr1	19671746	-	1409	421	124	651	175
ENST00000304494	CDKN2A	chr9	21974676	-	ENST00000264203	CAPZB	chr1	19671746	-	1329	421	124	537	137
ENST00000304494	CDKN2A	chr9	21974676	-	ENST00000375142	CAPZB	chr1	19671746	-	1472	421	786	76	236
ENST00000304494	CDKN2A	chr9	21974676	-	ENST00000433834	CAPZB	chr1	19671746	-	823	421	124	651	175
ENST00000304494	CDKN2A	chr9	21974676	-	ENST00000264202	CAPZB	chr1	19671746	-	667	421	654	76	192
ENST00000579122	CDKN2A	chr9	21974676	-	ENST00000401084	CAPZB	chr1	19671746	-	1169	181	31	411	126
ENST00000579122	CDKN2A	chr9	21974676	-	ENST00000264203	CAPZB	chr1	19671746	-	1089	181	961	623	112
ENST00000579122	CDKN2A	chr9	21974676	-	ENST00000375142	CAPZB	chr1	19671746	-	1232	181	546	1	182
ENST00000579122	CDKN2A	chr9	21974676	-	ENST00000433834	CAPZB	chr1	19671746	-	583	181	31	411	126
ENST00000579122	CDKN2A	chr9	21974676	-	ENST00000264202	CAPZB	chr1	19671746	-	427	181	414	1	138
ENST00000498124	CDKN2A	chr9	21974676	-	ENST00000401084	CAPZB	chr1	19671746	-	1177	189	39	419	126
ENST00000498124	CDKN2A	chr9	21974676	-	ENST00000264203	CAPZB	chr1	19671746	-	1097	189	969	631	112
ENST00000498124	CDKN2A	chr9	21974676	-	ENST00000375142	CAPZB	chr1	19671746	-	1240	189	554	0	185
ENST00000498124	CDKN2A	chr9	21974676	-	ENST00000433834	CAPZB	chr1	19671746	-	591	189	39	419	126
ENST00000498124	CDKN2A	chr9	21974676	-	ENST00000264202	CAPZB	chr1	19671746	-	435	189	422	0	141
ENST00000446177	CDKN2A	chr9	21974676	-	ENST00000401084	CAPZB	chr1	19671746	-	1350	362	65	592	175
ENST00000446177	CDKN2A	chr9	21974676	-	ENST00000264203	CAPZB	chr1	19671746	-	1270	362	65	478	137
ENST00000446177	CDKN2A	chr9	21974676	-	ENST00000375142	CAPZB	chr1	19671746	-	1413	362	727	17	236
ENST00000446177	CDKN2A	chr9	21974676	-	ENST00000433834	CAPZB	chr1	19671746	-	764	362	65	592	175
ENST00000446177	CDKN2A	chr9	21974676	-	ENST00000264202	CAPZB	chr1	19671746	-	608	362	595	17	192

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
ENST00000304494	ENST00000401084	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.01974465	0.98025537
ENST00000304494	ENST00000264203	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.3950649	0.60493517
ENST00000304494	ENST00000375142	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.019539258	0.9804607
ENST00000304494	ENST00000433834	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.012351234	0.9876488
ENST00000304494	ENST00000264202	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.007798152	0.9922018
ENST00000579122	ENST00000401084	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.010844709	0.98915535
ENST00000579122	ENST00000264203	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.210111	0.789889
ENST00000579122	ENST00000375142	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.005771158	0.99422884
ENST00000579122	ENST00000433834	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.003662412	0.99633765
ENST00000579122	ENST00000264202	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.005403562	0.9945964
ENST00000498124	ENST00000401084	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.006321932	0.99367803
ENST00000498124	ENST00000264203	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.12249864	0.8775014
ENST00000498124	ENST00000375142	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.00555213	0.9944478
ENST00000498124	ENST00000433834	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.003002173	0.99699783
ENST00000498124	ENST00000264202	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.004709014	0.995291
ENST00000446177	ENST00000401084	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.010657227	0.9893428
ENST00000446177	ENST00000264203	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.20956732	0.79043275
ENST00000446177	ENST00000375142	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.011179291	0.9888207
ENST00000446177	ENST00000433834	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.007552621	0.9924474
ENST00000446177	ENST00000264202	CDKN2A	chr9	21974677	-	CAPZB	chr1	19671746	-	0.005750045	0.99424994
ENST00000304494	ENST00000401084	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.01974465	0.98025537
ENST00000304494	ENST00000264203	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.3950649	0.60493517
ENST00000304494	ENST00000375142	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.019539258	0.9804607
ENST00000304494	ENST00000433834	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.012351234	0.9876488
ENST00000304494	ENST00000264202	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.007798152	0.9922018
ENST00000579122	ENST00000401084	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.010844709	0.98915535
ENST00000579122	ENST00000264203	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.210111	0.789889
ENST00000579122	ENST00000375142	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.005771158	0.99422884
ENST00000579122	ENST00000433834	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.003662412	0.99633765
ENST00000579122	ENST00000264202	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.005403562	0.9945964
ENST00000498124	ENST00000401084	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.006321932	0.99367803
ENST00000498124	ENST00000264203	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.12249864	0.8775014
ENST00000498124	ENST00000375142	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.00555213	0.9944478
ENST00000498124	ENST00000433834	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.003002173	0.99699783
ENST00000498124	ENST00000264202	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.004709014	0.995291
ENST00000446177	ENST00000401084	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.010657227	0.9893428
ENST00000446177	ENST00000264203	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.20956732	0.79043275
ENST00000446177	ENST00000375142	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.011179291	0.9888207
ENST00000446177	ENST00000433834	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.007552621	0.9924474
ENST00000446177	ENST00000264202	CDKN2A	chr9	21974676	-	CAPZB	chr1	19671746	-	0.005750045	0.99424994

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 CDKN2A-CAPZB

+/-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
CDKN2A	chr9	21974676	CAPZB	chr1	19671746	181	49	LPNAPNSYGRRPIQMEKDETVSDCSP
CDKN2A	chr9	21974676	CAPZB	chr1	19671746	189	49	LPNAPNSYGRRPIQMEKDETVSDCSP
CDKN2A	chr9	21974676	CAPZB	chr1	19671746	362	98	LPNAPNSYGRRPIQMEKDETVSDCSP
CDKN2A	chr9	21974676	CAPZB	chr1	19671746	421	98	LPNAPNSYGRRPIQMEKDETVSDCSP
CDKN2A	chr9	21974677	CAPZB	chr1	19671746	181	49	LPNAPNSYGRRPIQMEKDETVSDCSP
CDKN2A	chr9	21974677	CAPZB	chr1	19671746	189	49	LPNAPNSYGRRPIQMEKDETVSDCSP
CDKN2A	chr9	21974677	CAPZB	chr1	19671746	362	98	LPNAPNSYGRRPIQMEKDETVSDCSP
CDKN2A	chr9	21974677	CAPZB	chr1	19671746	421	98	LPNAPNSYGRRPIQMEKDETVSDCSP

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Potential FusionNeoAntigen Information of CDKN2A-CAPZB 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.

CDKN2A-CAPZB_21974676_19671746.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)
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:05	GRRPIQMEK	0.9972	0.6626	8	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:04	GRRPIQMEK	0.9863	0.7629	8	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:22	IQMEKDETV	0.9639	0.6	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:21	IQMEKDETV	0.9168	0.6262	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:11	IQMEKDETV	0.902	0.5047	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B13:02	IQMEKDETV	0.8605	0.5252	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:04	IQMEKDETV	0.8382	0.7337	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:27	IQMEKDETV	0.8172	0.5528	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:13	IQMEKDETV	0.768	0.6492	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B13:01	IQMEKDETV	0.6759	0.9294	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B38:01	IQMEKDETV	0.4371	0.9501	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B39:13	IQMEKDETV	0.3943	0.9288	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B52:01	IQMEKDETV	0.0689	0.9811	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B13:02	RPIQMEKDETV	0.9064	0.6731	10	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:14	RRPIQMEK	0.9993	0.6622	9	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:14	GRRPIQMEK	0.9927	0.6569	8	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:05	IQMEKDETV	0.9605	0.6012	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:03	GRRPIQMEK	0.8746	0.6789	8	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:80	SYGRRPIQM	0.6425	0.851	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:67	SYGRRPIQM	0.6425	0.851	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:05	SYGRRPIQM	0.6318	0.8586	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:10	SYGRRPIQM	0.6302	0.8464	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:29	SYGRRPIQM	0.5877	0.7719	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:46	SYGRRPIQM	0.5854	0.6958	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B39:08	IQMEKDETV	0.5608	0.9161	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:27	SYGRRPIQM	0.5566	0.8494	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:13	SYGRRPIQM	0.524	0.8253	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B39:09	IQMEKDETV	0.5012	0.7827	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B39:05	IQMEKDETV	0.3291	0.9149	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B51:07	IQMEKDETV	0.0557	0.9513	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:14	YGRRPIQMEK	0.9594	0.6563	7	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:10	RRPIQMEK	0.9996	0.8479	9	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A30:01	RRPIQMEK	0.9737	0.8526	9	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:10	GRRPIQMEK	0.9965	0.8423	8	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:08	GRRPIQMEK	0.9952	0.5856	8	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:03	IQMEKDETV	0.9621	0.6675	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:14	IQMEKDETV	0.9178	0.5376	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A02:06	IQMEKDETV	0.9168	0.6262	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B15:73	IQMEKDETV	0.8617	0.9574	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B15:30	IQMEKDETV	0.7574	0.855	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:17	SYGRRPIQM	0.6808	0.8981	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:02	SYGRRPIQM	0.6425	0.851	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A30:01	GRRPIQMEK	0.6005	0.8126	8	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B39:11	IQMEKDETV	0.5282	0.9167	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:04	SYGRRPIQM	0.5129	0.9021	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B39:02	IQMEKDETV	0.4761	0.9329	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B38:05	IQMEKDETV	0.4371	0.9501	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C06:06	SYGRRPIQM	0.3797	0.9846	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C07:04	IQMEKDETV	0.3536	0.939	12	21
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C14:03	SYGRRPIQM	0.2568	0.93	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C14:02	SYGRRPIQM	0.2568	0.93	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-C18:01	SYGRRPIQM	0.2078	0.8432	6	15
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:10	YGRRPIQMEK	0.9795	0.8684	7	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-A30:01	SYGRRPIQMEK	0.9895	0.7725	6	17
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	HLA-B27:10	SYGRRPIQMEK	0.9803	0.768	6	17

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Potential FusionNeoAntigen Information of CDKN2A-CAPZB in HLA II

CDKN2A-CAPZB_21974676_19671746.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)
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	DRB1-0422	GRRPIQMEKDETVSD	8	23
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	DRB1-1410	GRRPIQMEKDETVSD	8	23
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	DRB1-1523	GRRPIQMEKDETVSD	8	23
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	DRB1-1525	GRRPIQMEKDETVSD	8	23
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	DRB1-1525	RRPIQMEKDETVSDC	9	24
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	421	DRB1-1525	YGRRPIQMEKDETVS	7	22

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Fusion breakpoint peptide structures of CDKN2A-CAPZB

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
9196	SYGRRPIQMEKDET	CDKN2A	CAPZB	chr9	21974676	chr1	19671746	421

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDKN2A-CAPZB

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	9196	SYGRRPIQMEKDET	-7.9962	-8.1096
HLA-B14:02	3BVN	9196	SYGRRPIQMEKDET	-5.70842	-6.74372
HLA-B52:01	3W39	9196	SYGRRPIQMEKDET	-6.83737	-6.95077
HLA-B52:01	3W39	9196	SYGRRPIQMEKDET	-4.4836	-5.5189
HLA-A11:01	4UQ2	9196	SYGRRPIQMEKDET	-10.0067	-10.1201
HLA-A11:01	4UQ2	9196	SYGRRPIQMEKDET	-9.03915	-10.0745
HLA-A24:02	5HGA	9196	SYGRRPIQMEKDET	-6.56204	-6.67544
HLA-A24:02	5HGA	9196	SYGRRPIQMEKDET	-5.42271	-6.45801
HLA-B44:05	3DX8	9196	SYGRRPIQMEKDET	-7.85648	-8.89178
HLA-B44:05	3DX8	9196	SYGRRPIQMEKDET	-5.3978	-5.5112
HLA-A02:01	6TDR	9196	SYGRRPIQMEKDET	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of CDKN2A-CAPZB

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
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	10	21	RPIQMEKDETV	CCGATCCAGATGGAGAAGGATGAAACTGTGAGT
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	12	21	IQMEKDETV	CAGATGGAGAAGGATGAAACTGTGAGT
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	6	15	SYGRRPIQM	TACGGTCGGAGGCCGATCCAGATGGAG
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	6	17	SYGRRPIQMEK	TACGGTCGGAGGCCGATCCAGATGGAGAAGGAT
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	7	17	YGRRPIQMEK	GGTCGGAGGCCGATCCAGATGGAGAAGGAT
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	8	17	GRRPIQMEK	CGGAGGCCGATCCAGATGGAGAAGGAT
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	9	17	RRPIQMEK	AGGCCGATCCAGATGGAGAAGGAT

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
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	7	22	YGRRPIQMEKDETVS	GGTCGGAGGCCGATCCAGATGGAGAAGGATGAAACTGTGAGTGAC
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	8	23	GRRPIQMEKDETVSD	CGGAGGCCGATCCAGATGGAGAAGGATGAAACTGTGAGTGACTGC
CDKN2A-CAPZB	chr9	21974676	chr1	19671746	9	24	RRPIQMEKDETVSDC	AGGCCGATCCAGATGGAGAAGGATGAAACTGTGAGTGACTGCTCC

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Information of the samples that have these potential fusion neoantigens of CDKN2A-CAPZB

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
BLCA	CDKN2A-CAPZB	chr9	21974676	ENST00000304494	chr1	19671746	ENST00000264203	TCGA-E7-A6MD

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Potential target of CAR-T therapy development for CDKN2A-CAPZB

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 CDKN2A-CAPZB

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 CDKN2A-CAPZB

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)