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Fusion Protein:ACP6-ATP4A

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ACP6-ATP4A
	FusionPDB ID: 1430
	FusionGDB2.0 ID: 1430
		Hgene	Tgene
	Gene symbol	ACP6	ATP4A
	Gene ID	51205	495
	Gene name	acid phosphatase 6, lysophosphatidic	ATPase H+/K+ transporting subunit alpha
	Synonyms	ACPL1\|LPAP\|PACPL1	ATP6A
	Cytomap	1q21.2	19q13.12
	Type of gene	protein-coding	protein-coding
	Description	lysophosphatidic acid phosphatase type 6acid phosphatase-like protein 1	potassium-transporting ATPase alpha chain 1ATPase H+/K+ transporting alpha subunitATPase, H+/K+ exchanging, alpha polypeptideATPase, H+/K+ transporting, alpha polypeptideepididymis secretory sperm binding proteingastric H+/K+ ATPase alpha subunitgas
	Modification date	20200313	20200313
	UniProtAcc	Q9NPH0 Main function of 5'-partner protein: FUNCTION: Hydrolyzes lysophosphatidic acid (LPA) containing a medium length fatty acid chain to the corresponding monoacylglycerol. Has highest activity with lysophosphatidic acid containing myristate (C14:0), monounsaturated oleate (C18:1) or palmitate (C16:0), and lower activity with C18:0 and C6:0 lysophosphatidic acid. {ECO:0000269\|PubMed:10506173, ECO:0000269\|PubMed:23807634}.	P20648 Main function of 5'-partner protein: FUNCTION: Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000460583, ENST00000369238, ENST00000392988,	ENST00000262623,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 6 X 6=288	2 X 2 X 2=8
	# samples	8	3
	** MAII score	log2(8/288*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/8*10)=1.90689059560852
Fusion gene context	PubMed: ACP6 [Title/Abstract] AND ATP4A [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ACP6 [Title/Abstract] AND ATP4A [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ACP6(147120047)-ATP4A(36042482), # samples:1
Anticipated loss of major functional domain due to fusion event.	ACP6-ATP4A 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. ACP6-ATP4A 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. ACP6-ATP4A 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. ACP6-ATP4A 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	ACP6	GO:2001311	lysobisphosphatidic acid metabolic process	23807634

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:147120047/chr19:36042482)
- 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 ACP6 (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 ATP4A (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)

ENST00000369238

ACP6

chr1

147120047

ENST00000262623

ATP4A

chr19

36042482

2520

1591

358

1947

529

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
ENST00000369238	ENST00000262623	ACP6	chr1	147120047	-	ATP4A	chr19	36042482	-	0.009173281	0.9908268

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 ACP6-ATP4A

+/-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
ACP6	chr1	147120047	ATP4A	chr19	36042482	1591	411	SKEWFVQLYYHGKTFGQRLYQQYTCY

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Potential FusionNeoAntigen Information of ACP6-ATP4A 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.

ACP6-ATP4A_147120047_36042482.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)
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:17	KTFGQRLY	0.9981	0.8673	12	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B58:02	KTFGQRLY	0.9975	0.8752	12	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:16	KTFGQRLY	0.9959	0.7325	12	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:01	QLYYHGKTF	0.9935	0.6738	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:25	QLYYHGKTF	0.9383	0.7389	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:02	QLYYHGKTF	0.9197	0.7626	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A30:08	KTFGQRLYQ	0.9125	0.8444	12	21
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A32:13	QLYYHGKTF	0.6699	0.6298	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:03	GKTFGQRLY	0.1775	0.709	11	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B13:01	QLYYHGKTF	0.0112	0.6882	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B39:01	YHGKTFGQRL	0.9959	0.9092	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B39:24	YHGKTFGQRL	0.9956	0.7748	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B38:02	YHGKTFGQRL	0.9704	0.9598	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B38:01	YHGKTFGQRL	0.9703	0.9549	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:10	YHGKTFGQRL	0.963	0.703	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A31:02	YYHGKTFGQR	0.9485	0.7148	8	18
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:25	VQLYYHGKTF	0.8769	0.7189	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:37	YHGKTFGQRL	0.8216	0.7056	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A24:23	YYHGKTFGQRL	0.9995	0.725	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B57:01	KTFGQRLYQQY	0.9995	0.9668	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A24:25	YYHGKTFGQRL	0.9988	0.7082	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A24:20	YYHGKTFGQRL	0.9986	0.707	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A24:31	YYHGKTFGQRL	0.9982	0.7033	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B58:02	KTFGQRLYQQY	0.9972	0.9094	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:17	KTFGQRLYQQY	0.9971	0.9213	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A23:04	YYHGKTFGQRL	0.9957	0.5325	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:16	KTFGQRLYQQY	0.9952	0.865	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A31:02	LYYHGKTFGQR	0.995	0.7662	7	18
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A80:01	KTFGQRLYQQY	0.9932	0.5471	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B58:01	KTFGQRLYQQY	0.9924	0.9008	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:18	YHGKTFGQRLY	0.9917	0.6468	9	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A24:10	YYHGKTFGQRL	0.9874	0.7223	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A30:08	KTFGQRLYQQY	0.9654	0.9284	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A32:13	KTFGQRLYQQY	0.9608	0.9694	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A74:09	KTFGQRLYQQY	0.9501	0.6125	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A74:11	KTFGQRLYQQY	0.9501	0.6125	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A74:03	KTFGQRLYQQY	0.9501	0.6125	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C15:04	KTFGQRLY	0.9951	0.8086	12	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C07:80	LYYHGKTF	0.9865	0.7909	7	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C07:67	LYYHGKTF	0.9865	0.7909	7	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C07:10	LYYHGKTF	0.9853	0.9123	7	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:04	QLYYHGKTF	0.9635	0.671	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:21	QLYYHGKTF	0.9201	0.7218	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:05	QLYYHGKTF	0.6418	0.6105	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:31	QLYYHGKTF	0.6366	0.6299	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:04	VQLYYHGKTF	0.9778	0.5043	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B39:05	YHGKTFGQRL	0.9754	0.9042	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A24:02	YYHGKTFGQRL	0.9986	0.707	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:07	KTFGQRLYQQY	0.9979	0.7701	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A31:01	LYYHGKTFGQR	0.9961	0.7502	7	18
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C15:04	KTFGQRLYQQY	0.9938	0.8411	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C07:29	YYHGKTFGQRL	0.9459	0.9298	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B58:06	KTFGQRLY	0.9979	0.7767	12	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C15:09	KTFGQRLY	0.9951	0.8086	12	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C07:17	LYYHGKTF	0.9881	0.9112	7	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C07:02	LYYHGKTF	0.9865	0.7909	7	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C06:06	LYYHGKTF	0.9467	0.9229	7	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C14:02	LYYHGKTF	0.9437	0.8101	7	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C14:03	LYYHGKTF	0.9437	0.8101	7	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C16:02	KTFGQRLY	0.9265	0.9702	12	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:135	QLYYHGKTF	0.9936	0.6777	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:33	QLYYHGKTF	0.9935	0.6738	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:34	QLYYHGKTF	0.9935	0.6738	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:125	QLYYHGKTF	0.9935	0.6738	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:27	QLYYHGKTF	0.9933	0.7114	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:24	QLYYHGKTF	0.9903	0.6133	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:50	QLYYHGKTF	0.9899	0.6884	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:35	QLYYHGKTF	0.9884	0.5331	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:12	QLYYHGKTF	0.9698	0.6659	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:39	QLYYHGKTF	0.9443	0.5805	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:53	QLYYHGKTF	0.9417	0.5979	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A30:01	KTFGQRLYQ	0.921	0.9349	12	21
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:54	QLYYHGKTF	0.8745	0.5443	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A32:01	QLYYHGKTF	0.8523	0.6184	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:13	QLYYHGKTF	0.8224	0.6128	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:73	QLYYHGKTF	0.7527	0.6089	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:20	QLYYHGKTF	0.6552	0.714	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B35:28	QLYYHGKTF	0.5759	0.713	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B35:20	QLYYHGKTF	0.5671	0.7452	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:30	QLYYHGKTF	0.5498	0.5878	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B08:12	QLYYHGKTF	0.496	0.6173	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C03:02	QLYYHGKTF	0.4363	0.8952	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C03:67	QLYYHGKTF	0.4322	0.9399	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B48:02	QLYYHGKTF	0.2348	0.6781	6	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:54	GKTFGQRLY	0.0095	0.7907	11	20
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:24	VQLYYHGKTF	0.9908	0.5582	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:135	VQLYYHGKTF	0.9907	0.5212	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:27	VQLYYHGKTF	0.9906	0.5818	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:50	VQLYYHGKTF	0.9796	0.5243	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B38:05	YHGKTFGQRL	0.9703	0.9549	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:12	VQLYYHGKTF	0.9595	0.5634	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:39	VQLYYHGKTF	0.8868	0.5382	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:09	YHGKTFGQRL	0.8571	0.7739	9	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B48:02	VQLYYHGKTF	0.8484	0.655	5	15
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B57:10	KTFGQRLYQQY	0.9995	0.9668	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A24:03	YYHGKTFGQRL	0.9995	0.725	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B57:04	KTFGQRLYQQY	0.9993	0.7193	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:135	KTFGQRLYQQY	0.9987	0.9384	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B58:06	KTFGQRLYQQY	0.9979	0.8424	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-B15:35	KTFGQRLYQQY	0.9972	0.9093	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C15:09	KTFGQRLYQQY	0.9938	0.8411	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A32:01	KTFGQRLYQQY	0.9897	0.9643	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A30:01	KTFGQRLYQQY	0.9686	0.9585	12	23
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C14:03	YYHGKTFGQRL	0.9573	0.9565	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-C14:02	YYHGKTFGQRL	0.9573	0.9565	8	19
ACP6-ATP4A	chr1	147120047	chr19	36042482	1591	HLA-A74:01	KTFGQRLYQQY	0.9501	0.6125	12	23

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Potential FusionNeoAntigen Information of ACP6-ATP4A 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 ACP6-ATP4A

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
7408	QLYYHGKTFGQRLY	ACP6	ATP4A	chr1	147120047	chr19	36042482	1591

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ACP6-ATP4A

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	7408	QLYYHGKTFGQRLY	-8.62545	-8.73885
HLA-B14:02	3BVN	7408	QLYYHGKTFGQRLY	-3.26321	-4.29851
HLA-B52:01	3W39	7408	QLYYHGKTFGQRLY	-6.23413	-6.34753
HLA-B52:01	3W39	7408	QLYYHGKTFGQRLY	-4.55402	-5.58932
HLA-A24:02	5HGA	7408	QLYYHGKTFGQRLY	-8.62578	-8.73918
HLA-A24:02	5HGA	7408	QLYYHGKTFGQRLY	-6.438	-7.4733
HLA-B44:05	3DX8	7408	QLYYHGKTFGQRLY	-5.68484	-5.79824
HLA-B44:05	3DX8	7408	QLYYHGKTFGQRLY	-3.64855	-4.68385
HLA-A02:01	6TDR	7408	QLYYHGKTFGQRLY	-5.14764	-6.18294

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Vaccine Design for the FusionNeoAntigens of ACP6-ATP4A

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
ACP6-ATP4A	chr1	147120047	chr19	36042482	11	20	GKTFGQRLY	GGGAAGACATTCGGGCAGCGCCTGTAC
ACP6-ATP4A	chr1	147120047	chr19	36042482	12	20	KTFGQRLY	AAGACATTCGGGCAGCGCCTGTAC
ACP6-ATP4A	chr1	147120047	chr19	36042482	12	21	KTFGQRLYQ	AAGACATTCGGGCAGCGCCTGTACCAG
ACP6-ATP4A	chr1	147120047	chr19	36042482	12	23	KTFGQRLYQQY	AAGACATTCGGGCAGCGCCTGTACCAGCAGTAC
ACP6-ATP4A	chr1	147120047	chr19	36042482	5	15	VQLYYHGKTF	GTGCAGCTCTATTACCACGGGAAGACATTC
ACP6-ATP4A	chr1	147120047	chr19	36042482	6	15	QLYYHGKTF	CAGCTCTATTACCACGGGAAGACATTC
ACP6-ATP4A	chr1	147120047	chr19	36042482	7	15	LYYHGKTF	CTCTATTACCACGGGAAGACATTC
ACP6-ATP4A	chr1	147120047	chr19	36042482	7	18	LYYHGKTFGQR	CTCTATTACCACGGGAAGACATTCGGGCAGCGC
ACP6-ATP4A	chr1	147120047	chr19	36042482	8	18	YYHGKTFGQR	TATTACCACGGGAAGACATTCGGGCAGCGC
ACP6-ATP4A	chr1	147120047	chr19	36042482	8	19	YYHGKTFGQRL	TATTACCACGGGAAGACATTCGGGCAGCGCCTG
ACP6-ATP4A	chr1	147120047	chr19	36042482	9	19	YHGKTFGQRL	TACCACGGGAAGACATTCGGGCAGCGCCTG
ACP6-ATP4A	chr1	147120047	chr19	36042482	9	20	YHGKTFGQRLY	TACCACGGGAAGACATTCGGGCAGCGCCTGTAC

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 ACP6-ATP4A

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
Non-Cancer	ACP6-ATP4A	chr1	147120047	ENST00000369238	chr19	36042482	ENST00000262623	131Nd

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Potential target of CAR-T therapy development for ACP6-ATP4A

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

ATP4A

chr1:147120047

chr19:36042482

ENST00000262623

930_949

1036.0

Transmembrane

Helical

Tgene

ATP4A

chr1:147120047

chr19:36042482

ENST00000262623

964_982

1036.0

Transmembrane

Helical

Tgene

ATP4A

chr1:147120047

chr19:36042482

ENST00000262623

998_1018

1036.0

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 ACP6-ATP4A

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 ACP6-ATP4A

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)