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Fusion Protein:PTDSS1-NIPAL2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTDSS1-NIPAL2
	FusionPDB ID: 69889
	FusionGDB2.0 ID: 69889
		Hgene	Tgene
	Gene symbol	PTDSS1	NIPAL2
	Gene ID	9791	79815
	Gene name	phosphatidylserine synthase 1	NIPA like domain containing 2
	Synonyms	LMHD\|PSS1\|PSSA	NPAL2
	Cytomap	8q22.1	8q22.2
	Type of gene	protein-coding	protein-coding
	Description	phosphatidylserine synthase 1PSS-1ptdSer synthase 1serine-exchange enzyme I	NIPA-like protein 2
	Modification date	20200313	20200313
	UniProtAcc	.	Q9H841 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000518776, ENST00000517309, ENST00000455950, ENST00000522072,	ENST00000341166, ENST00000430223, ENST00000520545,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 5 X 4=100	8 X 7 X 8=448
	# samples	5	11
	** MAII score	log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(11/448*10)=-2.02599520853294 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PTDSS1 [Title/Abstract] AND NIPAL2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PTDSS1 [Title/Abstract] AND NIPAL2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTDSS1(97299374)-NIPAL2(99266315), # samples:2
Anticipated loss of major functional domain due to fusion event.

* 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/chr8:97299374/chr8:99266315)
- 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 PTDSS1 (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 NIPAL2 (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)

ENST00000517309

PTDSS1

chr8

97299374

ENST00000430223

NIPAL2

chr8

99266315

4929

767

179

1783

534

ENST00000517309

PTDSS1

chr8

97299374

ENST00000341166

NIPAL2

chr8

99266315

4957

767

179

1738

519

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
ENST00000517309	ENST00000430223	PTDSS1	chr8	97299374	+	NIPAL2	chr8	99266315	-	0.001033806	0.9989662
ENST00000517309	ENST00000341166	PTDSS1	chr8	97299374	+	NIPAL2	chr8	99266315	-	0.001330806	0.99866927

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 PTDSS1-NIPAL2

+/-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
PTDSS1	chr8	97299374	NIPAL2	chr8	99266315	767	196	PNLRYATREADVMIHLFGVLLAILGN

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Potential FusionNeoAntigen Information of PTDSS1-NIPAL2 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.

PTDSS1-NIPAL2_97299374_99266315.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)
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B13:01	READVMIHL	0.9989	0.929	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B50:02	READVMIHL	0.9969	0.5145	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B47:01	READVMIHL	0.9952	0.6091	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:08	EADVMIHLF	0.9933	0.6862	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:03	READVMIHL	0.9895	0.9466	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:01	EADVMIHLF	0.9814	0.6457	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B45:01	READVMIHL	0.974	0.7349	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:03	EADVMIHLF	0.956	0.6937	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B38:02	READVMIHL	0.9347	0.9396	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B39:13	READVMIHL	0.9323	0.9266	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-A30:08	ATREADVMI	0.9264	0.8258	5	14
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B38:01	READVMIHL	0.9177	0.9356	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:01	READVMIHL	0.8937	0.8958	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:04	EADVMIHLF	0.8163	0.7572	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:02	EADVMIHLF	0.8163	0.7572	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B41:01	READVMIHL	0.5198	0.8454	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B50:01	READVMIHL	0.4847	0.6184	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B52:01	READVMIHL	0.0491	0.7308	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B47:01	READVMIHLF	0.9999	0.5092	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:03	READVMIHLF	0.9996	0.9291	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B27:04	TREADVMIHL	0.9986	0.7612	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B27:02	TREADVMIHL	0.9984	0.531	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B27:05	TREADVMIHL	0.9982	0.8267	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B13:01	READVMIHLF	0.9964	0.8591	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B39:13	READVMIHLF	0.9469	0.9115	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:01	READVMIHLF	0.9249	0.8749	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:03	ATREADVMIHL	0.7408	0.9452	5	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:15	EADVMIHL	1	0.9407	8	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C05:09	EADVMIHL	1	0.896	8	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:03	EADVMIHL	0.995	0.9513	8	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B40:06	READVMIHL	0.9998	0.6474	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C05:09	EADVMIHLF	0.9997	0.8563	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C04:07	EADVMIHLF	0.9997	0.621	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C04:10	EADVMIHLF	0.9997	0.5777	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:15	EADVMIHLF	0.9993	0.916	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B15:31	EADVMIHLF	0.984	0.6079	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B39:05	READVMIHL	0.9361	0.839	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B39:08	READVMIHL	0.9229	0.8367	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:04	EADVMIHLF	0.8409	0.8439	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:13	EADVMIHLF	0.8409	0.8439	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:12	EADVMIHLF	0.8163	0.7572	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C04:06	EADVMIHLF	0.7853	0.6339	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:03	EADVMIHLF	0.7293	0.9248	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C04:14	EADVMIHLF	0.554	0.5689	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C07:95	TREADVMIHL	0.9949	0.7037	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B39:08	READVMIHLF	0.9806	0.8124	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B27:03	TREADVMIHL	0.9279	0.8465	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:10	ATREADVMIHL	0.7733	0.5188	5	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:02	EADVMIHL	1	0.9407	8	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C05:01	EADVMIHL	1	0.896	8	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C04:03	EADVMIHL	1	0.7648	8	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:01	EADVMIHL	0.995	0.9513	8	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C05:01	EADVMIHLF	0.9997	0.8563	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C04:03	EADVMIHLF	0.9997	0.6868	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C04:01	EADVMIHLF	0.9997	0.621	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B40:04	READVMIHL	0.9996	0.6829	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C18:01	EADVMIHLF	0.9995	0.6952	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:02	EADVMIHLF	0.9993	0.916	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-A68:02	DVMIHLFGV	0.999	0.5657	10	19
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-A69:01	DVMIHLFGV	0.9975	0.5706	10	19
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:26	READVMIHL	0.9895	0.9466	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:13	READVMIHL	0.9895	0.9466	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:07	READVMIHL	0.9895	0.9466	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:77	EADVMIHLF	0.9814	0.6457	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:23	EADVMIHLF	0.9807	0.63	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:20	EADVMIHLF	0.9796	0.7536	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-A25:01	EADVMIHLF	0.9662	0.8322	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:11	EADVMIHLF	0.9517	0.77	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:24	EADVMIHLF	0.9495	0.6246	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B39:02	READVMIHL	0.935	0.9254	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B39:31	READVMIHL	0.931	0.8616	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:11	READVMIHL	0.9255	0.9064	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B38:05	READVMIHL	0.9177	0.9356	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B39:11	READVMIHL	0.8967	0.7156	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:05	READVMIHL	0.8937	0.8958	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:08	READVMIHL	0.8912	0.8837	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B15:13	EADVMIHLF	0.889	0.537	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:06	READVMIHL	0.8724	0.9069	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:03	READVMIHL	0.8222	0.8921	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:09	EADVMIHLF	0.8163	0.7572	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:04	EADVMIHLF	0.7834	0.7687	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C08:01	EADVMIHLF	0.7293	0.9248	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B41:03	READVMIHL	0.725	0.6209	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B57:02	EADVMIHLF	0.7216	0.7072	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:07	EADVMIHLF	0.6368	0.7044	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B48:02	READVMIHL	0.6289	0.9297	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:08	EADVMIHLF	0.5389	0.6479	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B50:05	READVMIHL	0.4847	0.6184	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B50:04	READVMIHL	0.4847	0.6184	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:43	EADVMIHLF	0.2702	0.7056	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B15:08	EADVMIHLF	0.2668	0.6989	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B15:11	EADVMIHLF	0.2369	0.6891	8	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B15:54	READVMIHL	0.1937	0.8853	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B15:53	READVMIHL	0.0889	0.8968	7	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:26	READVMIHLF	0.9996	0.9291	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:07	READVMIHLF	0.9996	0.9291	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:13	READVMIHLF	0.9996	0.9291	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B27:09	TREADVMIHL	0.9988	0.7941	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B27:06	TREADVMIHL	0.9985	0.7935	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B27:08	TREADVMIHL	0.9984	0.7061	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B40:04	READVMIHLF	0.9973	0.6348	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:11	READVMIHLF	0.9964	0.8945	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C07:22	TREADVMIHL	0.993	0.6901	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C06:08	TREADVMIHL	0.988	0.9765	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B15:53	READVMIHLF	0.9729	0.8697	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B48:02	READVMIHLF	0.9669	0.8918	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B15:54	READVMIHLF	0.9655	0.8488	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B41:03	READVMIHLF	0.9642	0.5871	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B35:28	READVMIHLF	0.9526	0.9017	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B57:02	READVMIHLF	0.9508	0.8785	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C06:02	TREADVMIHL	0.9335	0.9858	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-C06:17	TREADVMIHL	0.9335	0.9858	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:08	READVMIHLF	0.9273	0.8346	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:05	READVMIHLF	0.9249	0.8749	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B18:03	READVMIHLF	0.9148	0.8674	7	17
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B40:04	TREADVMIHL	0.6736	0.7557	6	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B41:03	ATREADVMIHL	0.8031	0.652	5	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B40:04	ATREADVMIHL	0.7782	0.7761	5	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:26	ATREADVMIHL	0.7408	0.9452	5	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:07	ATREADVMIHL	0.7408	0.9452	5	16
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	HLA-B44:13	ATREADVMIHL	0.7408	0.9452	5	16

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Potential FusionNeoAntigen Information of PTDSS1-NIPAL2 in HLA II

PTDSS1-NIPAL2_97299374_99266315.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)
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	DRB1-1303	PNLRYATREADVMIH	0	15
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	DRB1-13101	PNLRYATREADVMIH	0	15
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	DRB1-1310	PNLRYATREADVMIH	0	15
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	DRB1-1358	PNLRYATREADVMIH	0	15
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	DRB1-1381	PNLRYATREADVMIH	0	15
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	DRB1-1389	PNLRYATREADVMIH	0	15
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	DRB1-1390	PNLRYATREADVMIH	0	15
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	767	DRB1-1395	PNLRYATREADVMIH	0	15

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Fusion breakpoint peptide structures of PTDSS1-NIPAL2

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
9593	TREADVMIHLFGVL	PTDSS1	NIPAL2	chr8	97299374	chr8	99266315	767

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTDSS1-NIPAL2

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	9593	TREADVMIHLFGVL	-7.15543	-7.26883
HLA-B14:02	3BVN	9593	TREADVMIHLFGVL	-4.77435	-5.80965
HLA-B52:01	3W39	9593	TREADVMIHLFGVL	-6.80875	-6.92215
HLA-B52:01	3W39	9593	TREADVMIHLFGVL	-4.20386	-5.23916
HLA-A11:01	4UQ2	9593	TREADVMIHLFGVL	-7.5194	-8.5547
HLA-A11:01	4UQ2	9593	TREADVMIHLFGVL	-6.9601	-7.0735
HLA-A24:02	5HGA	9593	TREADVMIHLFGVL	-7.52403	-7.63743
HLA-A24:02	5HGA	9593	TREADVMIHLFGVL	-5.82433	-6.85963
HLA-B27:05	6PYJ	9593	TREADVMIHLFGVL	-3.28285	-4.31815
HLA-B44:05	3DX8	9593	TREADVMIHLFGVL	-5.91172	-6.94702
HLA-B44:05	3DX8	9593	TREADVMIHLFGVL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of PTDSS1-NIPAL2

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
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	10	19	DVMIHLFGV	GATGTCATGATTCACCTTTTTGGAGTT
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	5	14	ATREADVMI	GCCACAAGGGAAGCAGATGTCATGATT
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	5	16	ATREADVMIHL	GCCACAAGGGAAGCAGATGTCATGATTCACCTT
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	6	16	TREADVMIHL	ACAAGGGAAGCAGATGTCATGATTCACCTT
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	7	16	READVMIHL	AGGGAAGCAGATGTCATGATTCACCTT
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	7	17	READVMIHLF	AGGGAAGCAGATGTCATGATTCACCTTTTT
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	8	16	EADVMIHL	GAAGCAGATGTCATGATTCACCTT
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	8	17	EADVMIHLF	GAAGCAGATGTCATGATTCACCTTTTT

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
PTDSS1-NIPAL2	chr8	97299374	chr8	99266315	0	15	PNLRYATREADVMIH	CCAAATCTTCGATACGCCACAAGGGAAGCAGATGTCATGATTCAC

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Information of the samples that have these potential fusion neoantigens of PTDSS1-NIPAL2

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	PTDSS1-NIPAL2	chr8	97299374	ENST00000517309	chr8	99266315	ENST00000341166	TCGA-BT-A2LD-01A

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Potential target of CAR-T therapy development for PTDSS1-NIPAL2

Predicted 3D structure. We used RoseTTAFold.

358_PTDSS1-NIPAL2_a41b4_pred.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

PTDSS1

chr8:97299374

chr8:99266315

ENST00000517309

103_123

147

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97299374

chr8:99266315

ENST00000517309

36_56

147

474.0

Transmembrane

Helical

Hgene

PTDSS1

chr8:97299374

chr8:99266315

ENST00000517309

73_93

147

474.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

110_130

369.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

144_164

369.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

177_197

369.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

209_229

369.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

243_263

369.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

278_298

369.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

306_326

369.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

46_66

369.0

Transmembrane

Helical

Tgene

NIPAL2

chr8:97299374

chr8:99266315

ENST00000341166

88_108

369.0

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
PTDSS1	chr8	97299374	ENST00000517309	NIPAL2	chr8	99266315	ENST00000341166
PTDSS1	chr8	97299374	ENST00000517309	NIPAL2	chr8	99266315	ENST00000430223

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Related Drugs to PTDSS1-NIPAL2

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 PTDSS1-NIPAL2

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)