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Fusion Protein:PREX1-PFDN4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PREX1-PFDN4
	FusionPDB ID: 68535
	FusionGDB2.0 ID: 68535
		Hgene	Tgene
	Gene symbol	PREX1	PFDN4
	Gene ID	57580	5203
	Gene name	phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1	prefoldin subunit 4
	Synonyms	P-REX1	C1\|PFD4
	Cytomap	20q13.13	20q13.2
	Type of gene	protein-coding	protein-coding
	Description	phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 proteinPIP3 dependent Rac exchange factor 1ptdIns(3,4,5)-dependent Rac exchanger 1	prefoldin subunit 4prefoldin 4protein C-1
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000371941, ENST00000396220, ENST00000496915,	ENST00000487129, ENST00000371419,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 8 X 5=360	7 X 6 X 5=210
	# samples	10	9
	** MAII score	log2(10/360*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/210*10)=-1.22239242133645 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PREX1 [Title/Abstract] AND PFDN4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PREX1 [Title/Abstract] AND PFDN4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PREX1(47444179)-PFDN4(52830890), # samples:1
Anticipated loss of major functional domain due to fusion event.	PREX1-PFDN4 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. PREX1-PFDN4 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:47444179/chr20:52830890)
- 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 PREX1 (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 PFDN4 (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)

ENST00000371941

PREX1

chr20

47444179

ENST00000371419

PFDN4

chr20

52830890

1426

242

622

199

ENST00000396220

PREX1

chr20

47444179

ENST00000371419

PFDN4

chr20

52830890

1426

242

622

199

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
ENST00000371941	ENST00000371419	PREX1	chr20	47444179	-	PFDN4	chr20	52830890	+	0.000642102	0.9993579
ENST00000396220	ENST00000371419	PREX1	chr20	47444179	-	PFDN4	chr20	52830890	+	0.000642102	0.9993579

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 PREX1-PFDN4

+/-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
PREX1	chr20	47444179	PFDN4	chr20	52830890	242	73	ERDYVGTLRFLQSAAEDVNVTFEDQQ

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Potential FusionNeoAntigen Information of PREX1-PFDN4 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.

PREX1-PFDN4_47444179_52830890.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)
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-A02:22	FLQSAAEDV	0.9797	0.7035	9	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-A02:27	FLQSAAEDV	0.9618	0.728	9	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B08:09	TLRFLQSAA	0.9467	0.9452	6	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-A02:19	FLQSAAEDV	0.8949	0.5987	9	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B35:08	SAAEDVNVTF	0.9982	0.8976	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B35:01	SAAEDVNVTF	0.9952	0.9255	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B15:16	SAAEDVNVTF	0.994	0.7933	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B57:03	SAAEDVNVTF	0.9856	0.991	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B58:02	QSAAEDVNVTF	0.9993	0.9795	11	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B57:03	QSAAEDVNVTF	0.9981	0.9886	11	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B58:01	QSAAEDVNVTF	0.997	0.9743	11	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-A02:19	FLQSAAEDVNV	0.9761	0.6825	9	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B73:01	LRFLQSAA	0.9987	0.9504	7	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-A02:02	FLQSAAEDV	0.9797	0.6426	9	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C05:09	SAAEDVNVTF	0.9996	0.9373	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C08:15	SAAEDVNVTF	0.9995	0.9676	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C12:12	SAAEDVNVTF	0.9982	0.9014	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B15:31	SAAEDVNVTF	0.9942	0.9262	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C03:14	SAAEDVNVTF	0.9929	0.9766	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C03:02	SAAEDVNVTF	0.9998	0.9768	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C05:01	SAAEDVNVTF	0.9996	0.9373	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C08:02	SAAEDVNVTF	0.9995	0.9676	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C12:02	SAAEDVNVTF	0.9995	0.9627	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B35:11	SAAEDVNVTF	0.9985	0.9387	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B15:11	SAAEDVNVTF	0.9983	0.9127	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B15:08	SAAEDVNVTF	0.9983	0.9052	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B35:43	SAAEDVNVTF	0.9982	0.9099	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C16:04	SAAEDVNVTF	0.9982	0.9741	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B57:02	SAAEDVNVTF	0.9982	0.9049	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B35:77	SAAEDVNVTF	0.9952	0.9255	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B35:23	SAAEDVNVTF	0.995	0.9182	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C02:02	SAAEDVNVTF	0.9893	0.9735	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-C02:10	SAAEDVNVTF	0.9893	0.9735	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B35:13	SAAEDVNVTF	0.9747	0.9098	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-A25:01	SAAEDVNVTF	0.8575	0.6919	12	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B57:04	QSAAEDVNVTF	0.9999	0.8496	11	22
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	HLA-B57:02	QSAAEDVNVTF	0.9993	0.9158	11	22

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Potential FusionNeoAntigen Information of PREX1-PFDN4 in HLA II

PREX1-PFDN4_47444179_52830890.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)
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0403	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0403	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0405	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0405	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0411	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0411	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0411	DYVGTLRFLQSAAED	2	17
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0415	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0417	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0424	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0424	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0427	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0429	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0429	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0430	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0430	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0436	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0439	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0439	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0441	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0441	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0442	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0445	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0445	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0446	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0446	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0448	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0448	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0449	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0449	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0450	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0450	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0451	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0452	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0452	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0453	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0457	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0457	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0458	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0459	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0460	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0460	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0465	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0467	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0467	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0471	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0471	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0477	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0477	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0478	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0479	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0480	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0482	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0483	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0483	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0484	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0484	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0485	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0485	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0486	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0487	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0488	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0488	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0489	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0489	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0491	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0491	YVGTLRFLQSAAEDV	3	18
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0491	DYVGTLRFLQSAAED	2	17
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0701	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0701	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0701	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0703	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0703	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0703	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0704	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0704	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0704	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0705	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0705	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0705	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0706	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0706	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0707	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0707	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0707	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0708	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0708	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0708	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0709	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0709	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0711	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0711	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0711	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0712	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0712	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0712	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0713	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0713	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0713	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0714	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0714	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0714	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0715	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0715	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0715	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0716	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0716	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0716	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0717	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0717	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0717	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0719	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0719	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0719	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0802	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0809	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0821	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0824	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0829	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0832	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0837	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0901	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0901	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0901	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0904	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0904	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0904	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0905	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0905	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0905	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0907	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0907	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0907	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0908	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0909	TLRFLQSAAEDVNVT	6	21
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0909	GTLRFLQSAAEDVNV	5	20
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-0909	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1002	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1101	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1105	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1108	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1109	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1110	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1112	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1115	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1119	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1124	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1127	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1128	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1129	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1131	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1132	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1133	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1137	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1139	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1145	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1149	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1151	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1153	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1161	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1162	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1164	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1166	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1172	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1173	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1174	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1175	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1180	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1181	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1187	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1190	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1191	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1193	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1194	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1195	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1196	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1305	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1307	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1314	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1321	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1326	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1330	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1337	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1347	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1350	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1356	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1360	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1362	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1382	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1385	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1410	VGTLRFLQSAAEDVN	4	19
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1414	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1427	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1436	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1442	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1444	ERDYVGTLRFLQSAA	0	15
PREX1-PFDN4	chr20	47444179	chr20	52830890	242	DRB1-1453	ERDYVGTLRFLQSAA	0	15

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Fusion breakpoint peptide structures of PREX1-PFDN4

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
9492	TLRFLQSAAEDVNV	PREX1	PFDN4	chr20	47444179	chr20	52830890	242

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PREX1-PFDN4

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	9492	TLRFLQSAAEDVNV	-7.15543	-7.26883
HLA-B14:02	3BVN	9492	TLRFLQSAAEDVNV	-4.77435	-5.80965
HLA-B52:01	3W39	9492	TLRFLQSAAEDVNV	-6.80875	-6.92215
HLA-B52:01	3W39	9492	TLRFLQSAAEDVNV	-4.20386	-5.23916
HLA-A11:01	4UQ2	9492	TLRFLQSAAEDVNV	-7.5194	-8.5547
HLA-A11:01	4UQ2	9492	TLRFLQSAAEDVNV	-6.9601	-7.0735
HLA-A24:02	5HGA	9492	TLRFLQSAAEDVNV	-7.52403	-7.63743
HLA-A24:02	5HGA	9492	TLRFLQSAAEDVNV	-5.82433	-6.85963
HLA-B27:05	6PYJ	9492	TLRFLQSAAEDVNV	-3.28285	-4.31815
HLA-B44:05	3DX8	9492	TLRFLQSAAEDVNV	-5.91172	-6.94702
HLA-B44:05	3DX8	9492	TLRFLQSAAEDVNV	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of PREX1-PFDN4

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
PREX1-PFDN4	chr20	47444179	chr20	52830890	11	22	QSAAEDVNVTF	CAGTCGGCTGCAGAAGATGTCAATGTTACTTTC
PREX1-PFDN4	chr20	47444179	chr20	52830890	12	22	SAAEDVNVTF	TCGGCTGCAGAAGATGTCAATGTTACTTTC
PREX1-PFDN4	chr20	47444179	chr20	52830890	6	15	TLRFLQSAA	ACCTTGCGCTTCTTGCAGTCGGCTGCA
PREX1-PFDN4	chr20	47444179	chr20	52830890	7	15	LRFLQSAA	TTGCGCTTCTTGCAGTCGGCTGCA
PREX1-PFDN4	chr20	47444179	chr20	52830890	9	18	FLQSAAEDV	TTCTTGCAGTCGGCTGCAGAAGATGTC
PREX1-PFDN4	chr20	47444179	chr20	52830890	9	20	FLQSAAEDVNV	TTCTTGCAGTCGGCTGCAGAAGATGTCAATGTT

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
PREX1-PFDN4	chr20	47444179	chr20	52830890	0	15	ERDYVGTLRFLQSAA	GAGAGGGACTACGTGGGCACCTTGCGCTTCTTGCAGTCGGCTGCA
PREX1-PFDN4	chr20	47444179	chr20	52830890	2	17	DYVGTLRFLQSAAED	GACTACGTGGGCACCTTGCGCTTCTTGCAGTCGGCTGCAGAAGAT
PREX1-PFDN4	chr20	47444179	chr20	52830890	3	18	YVGTLRFLQSAAEDV	TACGTGGGCACCTTGCGCTTCTTGCAGTCGGCTGCAGAAGATGTC
PREX1-PFDN4	chr20	47444179	chr20	52830890	4	19	VGTLRFLQSAAEDVN	GTGGGCACCTTGCGCTTCTTGCAGTCGGCTGCAGAAGATGTCAAT
PREX1-PFDN4	chr20	47444179	chr20	52830890	5	20	GTLRFLQSAAEDVNV	GGCACCTTGCGCTTCTTGCAGTCGGCTGCAGAAGATGTCAATGTT
PREX1-PFDN4	chr20	47444179	chr20	52830890	6	21	TLRFLQSAAEDVNVT	ACCTTGCGCTTCTTGCAGTCGGCTGCAGAAGATGTCAATGTTACT

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Information of the samples that have these potential fusion neoantigens of PREX1-PFDN4

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
BRCA	PREX1-PFDN4	chr20	47444179	ENST00000371941	chr20	52830890	ENST00000371419	TCGA-A8-A09D-01A

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Potential target of CAR-T therapy development for PREX1-PFDN4

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 PREX1-PFDN4

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 PREX1-PFDN4

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)