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Fusion Protein:ADAM19-PITPNA

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ADAM19-PITPNA
	FusionPDB ID: 1989
	FusionGDB2.0 ID: 1989
		Hgene	Tgene
	Gene symbol	ADAM19	PITPNA
	Gene ID	8728	5306
	Gene name	ADAM metallopeptidase domain 19	phosphatidylinositol transfer protein alpha
	Synonyms	FKSG34\|MADDAM\|MLTNB	HEL-S-36\|PI-TPalpha\|PITPN\|VIB1A
	Cytomap	5q33.3	17p13.3
	Type of gene	protein-coding	protein-coding
	Description	disintegrin and metalloproteinase domain-containing protein 19a disintegrin and metalloproteinase domain 19 (meltrin beta)metalloprotease and disintegrin dendritic antigen markermetalloprotease-disintegrin meltrin beta	phosphatidylinositol transfer protein alpha isoformPI-TP-alphaepididymis secretory protein Li 36ptdIns transfer protein alphaptdInsTP alpha
	Modification date	20200313	20200313
	UniProtAcc	Q9H013 Main function of 5'-partner protein: FUNCTION: Participates in the proteolytic processing of beta-type neuregulin isoforms which are involved in neurogenesis and synaptogenesis, suggesting a regulatory role in glial cell. Also cleaves alpha-2 macroglobulin. May be involved in osteoblast differentiation and/or osteoblast activity in bone (By similarity). {ECO:0000250}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000430702, ENST00000257527, ENST00000394020, ENST00000517905,	ENST00000313486, ENST00000539476,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	4 X 5 X 4=80	11 X 12 X 9=1188
	# samples	4	15
	** MAII score	log2(4/80*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/1188*10)=-2.98550043030489 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ADAM19 [Title/Abstract] AND PITPNA [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ADAM19 [Title/Abstract] AND PITPNA [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ADAM19(156997903)-PITPNA(1442246), # samples:1
Anticipated loss of major functional domain due to fusion event.	ADAM19-PITPNA 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. ADAM19-PITPNA 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	ADAM19	GO:0010628	positive regulation of gene expression	19727588
Hgene	ADAM19	GO:2000049	positive regulation of cell-cell adhesion mediated by cadherin	19727588
Tgene	PITPNA	GO:0015914	phospholipid transport	16274224\|22822086

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:156997903/chr17:1442246)
- 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 ADAM19 (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 PITPNA (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)
ENST00000394020	ADAM19	chr5	156997903	-	ENST00000313486	PITPNA	chr17	1442246	-	3534	250	22	690	222
ENST00000394020	ADAM19	chr5	156997903	-	ENST00000539476	PITPNA	chr17	1442246	-	3259	250	22	690	222
ENST00000257527	ADAM19	chr5	156997903	-	ENST00000313486	PITPNA	chr17	1442246	-	3543	259	37	699	220
ENST00000257527	ADAM19	chr5	156997903	-	ENST00000539476	PITPNA	chr17	1442246	-	3268	259	37	699	220
ENST00000517905	ADAM19	chr5	156997903	-	ENST00000313486	PITPNA	chr17	1442246	-	3509	225	3	665	220
ENST00000517905	ADAM19	chr5	156997903	-	ENST00000539476	PITPNA	chr17	1442246	-	3234	225	3	665	220

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
ENST00000394020	ENST00000313486	ADAM19	chr5	156997903	-	PITPNA	chr17	1442246	-	0.002646359	0.9973537
ENST00000394020	ENST00000539476	ADAM19	chr5	156997903	-	PITPNA	chr17	1442246	-	0.003192491	0.9968076
ENST00000257527	ENST00000313486	ADAM19	chr5	156997903	-	PITPNA	chr17	1442246	-	0.001956228	0.9980438
ENST00000257527	ENST00000539476	ADAM19	chr5	156997903	-	PITPNA	chr17	1442246	-	0.002343048	0.99765694
ENST00000517905	ENST00000313486	ADAM19	chr5	156997903	-	PITPNA	chr17	1442246	-	0.001908557	0.9980914
ENST00000517905	ENST00000539476	ADAM19	chr5	156997903	-	PITPNA	chr17	1442246	-	0.002280137	0.9977198

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 ADAM19-PITPNA

+/-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
ADAM19	chr5	156997903	PITPNA	chr17	1442246	225	34	ARLCLLAFALQPLRPRAAREPGWTRG
ADAM19	chr5	156997903	PITPNA	chr17	1442246	250	76	PQWKTSESPVREKVHKLEPEAWKHVE
ADAM19	chr5	156997903	PITPNA	chr17	1442246	259	34	ARLCLLAFALQPLRPRAAREPGWTRG

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Potential FusionNeoAntigen Information of ADAM19-PITPNA 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.

ADAM19-PITPNA_156997903_1442246.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)
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-B08:09	QPLRPRAA	0.9975	0.8808	10	18
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B14:02	VREKVHKL	0.9936	0.6423	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B14:01	VREKVHKL	0.9936	0.6423	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-B55:01	QPLRPRAA	0.9831	0.7351	10	18
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-B56:01	QPLRPRAA	0.9511	0.8905	10	18
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B45:01	SESPVREKV	0.9995	0.6371	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-A30:08	KVHKLEPEA	0.9955	0.9016	12	21
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B13:01	SESPVREKV	0.9952	0.7884	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:24	LAFALQPLR	0.9929	0.6233	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:03	LAFALQPLR	0.9915	0.6025	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:06	LAFALQPLR	0.9862	0.6952	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B44:03	SESPVREKV	0.9861	0.9085	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:08	LAFALQPLR	0.9747	0.7268	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A02:13	ALQPLRPRA	0.9735	0.8378	8	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:03	FALQPLRPR	0.9734	0.6827	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:05	LAFALQPLR	0.9733	0.634	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-B08:09	LQPLRPRAA	0.9601	0.9075	9	18
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A33:05	FALQPLRPR	0.9601	0.6672	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A33:01	FALQPLRPR	0.9601	0.6672	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:08	FALQPLRPR	0.9587	0.6744	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:05	FALQPLRPR	0.9489	0.6863	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:06	LAFALQPLR	0.9386	0.7647	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A33:05	LAFALQPLR	0.9375	0.5259	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A33:01	LAFALQPLR	0.9375	0.5259	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B41:01	SESPVREKV	0.8889	0.6364	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:02	FALQPLRPR	0.8768	0.9149	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A66:03	FALQPLRPR	0.8688	0.5673	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B45:01	REKVHKLEP	0.8439	0.8686	10	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A34:01	FALQPLRPR	0.8343	0.6622	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A34:05	FALQPLRPR	0.8343	0.6622	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A66:01	FALQPLRPR	0.8149	0.5622	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B18:01	SESPVREKV	0.7565	0.821	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B50:01	SESPVREKV	0.7116	0.5789	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B50:02	REKVHKLEP	0.482	0.6397	10	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B52:01	SESPVREKV	0.4417	0.7188	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B39:13	SESPVREKV	0.3664	0.8253	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B41:01	REKVHKLEP	0.3226	0.9111	10	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B50:01	REKVHKLEP	0.0431	0.8128	10	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B57:01	KVHKLEPEAW	0.9997	0.9963	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B58:02	KVHKLEPEAW	0.9989	0.9919	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B58:01	KVHKLEPEAW	0.9978	0.9939	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B57:03	KVHKLEPEAW	0.9959	0.9985	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:02	AFALQPLRPR	0.9654	0.9209	6	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:06	AFALQPLRPR	0.8559	0.8541	6	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-A32:13	KVHKLEPEAW	0.7564	0.9902	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B35:03	SPVREKVHKL	0.2807	0.7754	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B35:04	SPVREKVHKL	0.1841	0.7134	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B35:02	SPVREKVHKL	0.1841	0.7134	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A74:09	ALQPLRPRAAR	0.982	0.9515	8	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A74:03	ALQPLRPRAAR	0.982	0.9515	8	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A74:11	ALQPLRPRAAR	0.982	0.9515	8	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:02	ALQPLRPRAAR	0.9732	0.9532	8	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:06	ALQPLRPRAAR	0.9626	0.9251	8	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C07:95	VREKVHKL	0.998	0.724	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C07:05	VREKVHKL	0.9979	0.9588	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C07:27	VREKVHKL	0.995	0.961	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C07:13	VREKVHKL	0.9884	0.9532	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B39:12	VREKVHKL	0.9751	0.8774	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B14:03	VREKVHKL	0.8712	0.8001	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C12:16	VREKVHKL	0.8381	0.952	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A68:01	LAFALQPLR	0.9929	0.6233	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B40:06	REKVHKLEP	0.9712	0.7134	10	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A33:03	FALQPLRPR	0.953	0.5736	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:01	FALQPLRPR	0.8997	0.8996	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B39:08	SESPVREKV	0.7312	0.6576	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B51:07	SESPVREKV	0.467	0.5033	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:01	AFALQPLRPR	0.9641	0.9073	6	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B07:12	SPVREKVHKL	0.9203	0.5542	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B35:12	SPVREKVHKL	0.1841	0.7134	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B39:10	SPVREKVHKL	0.1571	0.7955	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B40:06	REKVHKLEPEA	0.9983	0.7704	10	21
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A31:01	ALQPLRPRAAR	0.9826	0.9475	8	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C07:01	VREKVHKL	0.9985	0.7032	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C07:22	VREKVHKL	0.9935	0.7356	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-B56:05	QPLRPRAA	0.9884	0.8575	10	18
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C07:04	VREKVHKL	0.9825	0.9422	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C06:08	VREKVHKL	0.975	0.9862	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-B55:02	QPLRPRAA	0.9559	0.8858	10	18
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C06:06	VREKVHKL	0.9171	0.9913	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C06:17	VREKVHKL	0.8759	0.9915	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-C06:02	VREKVHKL	0.8759	0.9915	9	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B40:04	SESPVREKV	0.9976	0.6658	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B44:07	SESPVREKV	0.9861	0.9085	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B44:26	SESPVREKV	0.9861	0.9085	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B44:13	SESPVREKV	0.9861	0.9085	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A66:02	FALQPLRPR	0.8907	0.5671	7	16
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B18:05	SESPVREKV	0.7565	0.821	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B50:04	SESPVREKV	0.7116	0.5789	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B50:05	SESPVREKV	0.7116	0.5789	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B18:06	SESPVREKV	0.6823	0.8304	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B18:03	SESPVREKV	0.6747	0.814	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B18:11	SESPVREKV	0.6533	0.7775	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B39:02	SESPVREKV	0.3276	0.8276	5	14
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B50:04	REKVHKLEP	0.0431	0.8128	10	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B50:05	REKVHKLEP	0.0431	0.8128	10	19
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B57:10	KVHKLEPEAW	0.9997	0.9963	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B58:06	KVHKLEPEAW	0.9981	0.9822	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B57:04	KVHKLEPEAW	0.998	0.9725	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B15:24	KVHKLEPEAW	0.9821	0.9912	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-A32:01	KVHKLEPEAW	0.9752	0.9946	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B57:02	KVHKLEPEAW	0.9687	0.9857	12	22
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B08:12	SPVREKVHKL	0.551	0.5316	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B35:09	SPVREKVHKL	0.1841	0.7134	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	HLA-B67:01	SPVREKVHKL	0.1571	0.5916	7	17
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	HLA-A74:01	ALQPLRPRAAR	0.982	0.9515	8	19

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Potential FusionNeoAntigen Information of ADAM19-PITPNA in HLA II

ADAM19-PITPNA_156997903_1442246.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)
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	DRB1-0123	AFALQPLRPRAAREP	6	21
ADAM19-PITPNA	chr5	156997903	chr17	1442246	259	DRB1-0123	LAFALQPLRPRAARE	5	20
ADAM19-PITPNA	chr5	156997903	chr17	1442246	250	DRB5-0112	PQWKTSESPVREKVH	0	15

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Fusion breakpoint peptide structures of ADAM19-PITPNA

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
185	AFALQPLRPRAARE	ADAM19	PITPNA	chr5	156997903	chr17	1442246	259

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
2138	ESPVREKVHKLEPE	ADAM19	PITPNA	chr5	156997903	chr17	1442246	250

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ADAM19-PITPNA

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	185	AFALQPLRPRAARE	-7.9962	-8.1096
HLA-B14:02	3BVN	185	AFALQPLRPRAARE	-5.70842	-6.74372
HLA-B52:01	3W39	185	AFALQPLRPRAARE	-6.83737	-6.95077
HLA-B52:01	3W39	185	AFALQPLRPRAARE	-4.4836	-5.5189
HLA-A11:01	4UQ2	185	AFALQPLRPRAARE	-10.0067	-10.1201
HLA-A11:01	4UQ2	185	AFALQPLRPRAARE	-9.03915	-10.0745
HLA-A24:02	5HGA	185	AFALQPLRPRAARE	-6.56204	-6.67544
HLA-A24:02	5HGA	185	AFALQPLRPRAARE	-5.42271	-6.45801
HLA-B44:05	3DX8	185	AFALQPLRPRAARE	-7.85648	-8.89178
HLA-B44:05	3DX8	185	AFALQPLRPRAARE	-5.3978	-5.5112
HLA-A02:01	6TDR	185	AFALQPLRPRAARE	-3.37154	-4.40684
HLA-B14:02	3BVN	2138	ESPVREKVHKLEPE	-6.18902	-6.30242
HLA-B14:02	3BVN	2138	ESPVREKVHKLEPE	-5.51674	-6.55204
HLA-B52:01	3W39	2138	ESPVREKVHKLEPE	-6.26372	-6.37712
HLA-B52:01	3W39	2138	ESPVREKVHKLEPE	-2.88933	-3.92463
HLA-A11:01	4UQ2	2138	ESPVREKVHKLEPE	-8.95966	-9.99496
HLA-A24:02	5HGA	2138	ESPVREKVHKLEPE	-7.97421	-8.08761
HLA-A24:02	5HGA	2138	ESPVREKVHKLEPE	-4.46014	-5.49544
HLA-B44:05	3DX8	2138	ESPVREKVHKLEPE	-4.21738	-4.33078
HLA-B44:05	3DX8	2138	ESPVREKVHKLEPE	-3.79801	-4.83331
HLA-A02:01	6TDR	2138	ESPVREKVHKLEPE	-6.07498	-7.11028

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Vaccine Design for the FusionNeoAntigens of ADAM19-PITPNA

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
ADAM19-PITPNA	chr5	156997903	chr17	1442246	10	18	QPLRPRAA	AGAGAAAAGGTGCATAAGCTGGAG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	10	19	REKVHKLEP	AGAGAAAAGGTGCATAAGCTGGAGCCT
ADAM19-PITPNA	chr5	156997903	chr17	1442246	10	21	REKVHKLEPEA	AGAGAAAAGGTGCATAAGCTGGAGCCTGAGGCG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	12	21	KVHKLEPEA	AAGGTGCATAAGCTGGAGCCTGAGGCG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	12	22	KVHKLEPEAW	AAGGTGCATAAGCTGGAGCCTGAGGCGTGG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	5	14	LAFALQPLR	TCAGAAAGCCCCGTGAGAGAAAAGGTG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	5	14	SESPVREKV	TCAGAAAGCCCCGTGAGAGAAAAGGTG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	6	16	AFALQPLRPR	GAAAGCCCCGTGAGAGAAAAGGTGCATAAG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	7	16	FALQPLRPR	AGCCCCGTGAGAGAAAAGGTGCATAAG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	7	17	SPVREKVHKL	AGCCCCGTGAGAGAAAAGGTGCATAAGCTG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	8	17	ALQPLRPRA	CCCGTGAGAGAAAAGGTGCATAAGCTG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	8	19	ALQPLRPRAAR	CCCGTGAGAGAAAAGGTGCATAAGCTGGAGCCT
ADAM19-PITPNA	chr5	156997903	chr17	1442246	9	17	VREKVHKL	GTGAGAGAAAAGGTGCATAAGCTG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	9	18	LQPLRPRAA	GTGAGAGAAAAGGTGCATAAGCTGGAG

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
ADAM19-PITPNA	chr5	156997903	chr17	1442246	0	15	PQWKTSESPVREKVH	CCTCAGTGGAAGACTTCAGAAAGCCCCGTGAGAGAAAAGGTGCAT
ADAM19-PITPNA	chr5	156997903	chr17	1442246	5	20	LAFALQPLRPRAARE	TCAGAAAGCCCCGTGAGAGAAAAGGTGCATAAGCTGGAGCCTGAG
ADAM19-PITPNA	chr5	156997903	chr17	1442246	6	21	AFALQPLRPRAAREP	GAAAGCCCCGTGAGAGAAAAGGTGCATAAGCTGGAGCCTGAGGCG

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Information of the samples that have these potential fusion neoantigens of ADAM19-PITPNA

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
GBM	ADAM19-PITPNA	chr5	156997903	ENST00000257527	chr17	1442246	ENST00000313486	TCGA-14-0790-01B
GBM	ADAM19-PITPNA	chr5	156997903	ENST00000394020	chr17	1442246	ENST00000313486	TCGA-14-0790-01B

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Potential target of CAR-T therapy development for ADAM19-PITPNA

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 ADAM19-PITPNA

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 ADAM19-PITPNA

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)