Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:PHF20-RPN2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PHF20-RPN2
	FusionPDB ID: 64825
	FusionGDB2.0 ID: 64825
		Hgene	Tgene
	Gene symbol	PHF20	RPN2
	Gene ID	51230	6185
	Gene name	PHD finger protein 20	ribophorin II
	Synonyms	C20orf104\|GLEA2\|HCA58\|NZF\|TDRD20A\|TZP	RIBIIR\|RPN-II\|RPNII\|SWP1
	Cytomap	20q11.22-q11.23	20q11.23
	Type of gene	protein-coding	protein-coding
	Description	PHD finger protein 20glioma-expressed antigen 2hepatocellular carcinoma-associated antigen 58novel zinc finger proteintranscription factor TZPtudor domain containing 20A	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunitoligosaccharyltransferase complex subunit (non-catalytic)ribophorin-2
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000439301, ENST00000374012, ENST00000481202,	ENST00000237530, ENST00000373622, ENST00000470352,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	19 X 17 X 11=3553	12 X 13 X 9=1404
	# samples	29	17
	** MAII score	log2(29/3553*10)=-3.61491288331629 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(17/1404*10)=-3.04593628416686 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PHF20 [Title/Abstract] AND RPN2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PHF20 [Title/Abstract] AND RPN2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PHF20(34528969)-RPN2(35812583), # samples:3
Anticipated loss of major functional domain due to fusion event.	PHF20-RPN2 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. PHF20-RPN2 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	PHF20	GO:0043981	histone H4-K5 acetylation	20018852
Hgene	PHF20	GO:0043982	histone H4-K8 acetylation	20018852
Hgene	PHF20	GO:0043984	histone H4-K16 acetylation	20018852

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:34528969/chr20:35812583)
- 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 PHF20 (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 RPN2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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)

ENST00000374012

PHF20

chr20

34528969

ENST00000237530

RPN2

chr20

35812583

5212

3025

123

4907

1594

ENST00000374012

PHF20

chr20

34528969

ENST00000373622

RPN2

chr20

35812583

5164

3025

123

4859

1578

ENST00000374012

PHF20

chr20

34528969

ENST00000237530

RPN2

chr20

35812582

5212

3025

123

4907

1594

ENST00000374012

PHF20

chr20

34528969

ENST00000373622

RPN2

chr20

35812582

5164

3025

123

4859

1578

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
ENST00000374012	ENST00000237530	PHF20	chr20	34528969	+	RPN2	chr20	35812583	+	0.000503938	0.9994961
ENST00000374012	ENST00000373622	PHF20	chr20	34528969	+	RPN2	chr20	35812583	+	0.000510163	0.9994898
ENST00000374012	ENST00000237530	PHF20	chr20	34528969	+	RPN2	chr20	35812582	+	0.000503938	0.9994961
ENST00000374012	ENST00000373622	PHF20	chr20	34528969	+	RPN2	chr20	35812582	+	0.000510163	0.9994898

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

Top

Fusion Protein Breakpoint Sequences for PHF20-RPN2

+/-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
PHF20	chr20	34528969	RPN2	chr20	35812582	3025	967	VTHRMDSIEKELDGSSTVFLLALTII
PHF20	chr20	34528969	RPN2	chr20	35812583	3025	967	VTHRMDSIEKELDGSSTVFLLALTII

Top

Potential FusionNeoAntigen Information of PHF20-RPN2 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.

PHF20-RPN2_34528969_35812582.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)
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B50:02	KELDGSSTV	0.9988	0.7133	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B13:02	KELDGSSTV	0.9967	0.687	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B45:01	KELDGSSTV	0.9963	0.919	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B13:01	KELDGSSTV	0.9856	0.9912	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B35:08	ELDGSSTVF	0.8545	0.8936	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:02	ELDGSSTVF	0.8449	0.9458	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:03	KELDGSSTV	0.8302	0.974	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B47:01	KELDGSSTV	0.8115	0.8581	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B41:01	KELDGSSTV	0.6149	0.9831	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B50:01	KELDGSSTV	0.5989	0.726	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:13	KELDGSSTV	0.591	0.971	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B35:02	ELDGSSTVF	0.3243	0.9645	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B35:04	ELDGSSTVF	0.3243	0.9645	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:03	KELDGSSTVF	0.9987	0.9596	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B13:01	KELDGSSTVF	0.9961	0.9191	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:03	KELDGSSTVF	0.9821	0.8956	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:13	KELDGSSTVF	0.9564	0.7941	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B50:02	EKELDGSSTV	0.8501	0.7335	8	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B45:01	EKELDGSSTV	0.6966	0.9578	8	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B13:01	KELDGSSTVFL	0.9992	0.9487	9	20
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B47:01	KELDGSSTVFL	0.9991	0.6087	9	20
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:13	KELDGSSTVFL	0.9902	0.8967	9	20
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C04:07	ELDGSSTVF	0.9998	0.6726	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C04:10	ELDGSSTVF	0.9998	0.6249	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C05:09	ELDGSSTVF	0.9998	0.9566	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B40:06	KELDGSSTV	0.9997	0.755	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C08:15	ELDGSSTVF	0.9995	0.9837	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:10	KELDGSSTV	0.9866	0.7526	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B40:03	KELDGSSTV	0.9604	0.6301	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:21	ELDGSSTVF	0.8557	0.9324	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:09	KELDGSSTV	0.8435	0.5063	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:31	ELDGSSTVF	0.7902	0.9229	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:08	KELDGSSTV	0.6415	0.9523	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C08:04	ELDGSSTVF	0.5188	0.9005	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C08:13	ELDGSSTVF	0.5188	0.9005	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C04:06	ELDGSSTVF	0.4954	0.7348	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C04:14	ELDGSSTVF	0.434	0.5482	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C08:03	ELDGSSTVF	0.3324	0.9738	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B35:12	ELDGSSTVF	0.3243	0.9645	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C05:09	KELDGSSTVF	0.9997	0.9345	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C08:15	KELDGSSTVF	0.9985	0.9779	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:08	KELDGSSTVF	0.9888	0.9299	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:05	KELDGSSTVF	0.9341	0.9668	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:08	KELDGSSTVFL	0.9941	0.9569	9	20
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C05:01	ELDGSSTVF	0.9998	0.9566	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C04:03	ELDGSSTVF	0.9998	0.7316	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C04:01	ELDGSSTVF	0.9998	0.6726	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C08:02	ELDGSSTVF	0.9995	0.9837	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C18:01	ELDGSSTVF	0.9995	0.7515	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B40:04	KELDGSSTV	0.9987	0.8358	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:26	KELDGSSTV	0.8302	0.974	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:07	KELDGSSTV	0.8302	0.974	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:13	KELDGSSTV	0.8302	0.974	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B35:23	ELDGSSTVF	0.7665	0.9013	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B35:20	ELDGSSTVF	0.7579	0.9566	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B41:03	KELDGSSTV	0.7439	0.7112	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:08	ELDGSSTVF	0.6986	0.8628	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:11	ELDGSSTVF	0.6887	0.8609	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:13	ELDGSSTVF	0.6589	0.6871	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B50:05	KELDGSSTV	0.5989	0.726	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B50:04	KELDGSSTV	0.5989	0.726	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:02	KELDGSSTV	0.3904	0.9734	9	18
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B18:04	ELDGSSTVF	0.3889	0.8416	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C08:01	ELDGSSTVF	0.3324	0.9738	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B35:09	ELDGSSTVF	0.3243	0.9645	10	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C05:01	KELDGSSTVF	0.9997	0.9345	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C04:03	KELDGSSTVF	0.9997	0.8131	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:13	KELDGSSTVF	0.9987	0.9596	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:26	KELDGSSTVF	0.9987	0.9596	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B44:07	KELDGSSTVF	0.9987	0.9596	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-C08:02	KELDGSSTVF	0.9985	0.9779	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:53	KELDGSSTVF	0.9979	0.9406	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B40:04	KELDGSSTVF	0.9978	0.7707	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:54	KELDGSSTVF	0.9941	0.926	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B18:11	KELDGSSTVF	0.9917	0.9575	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B41:03	KELDGSSTVF	0.9478	0.5891	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B48:02	KELDGSSTVF	0.9475	0.9749	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:02	KELDGSSTVF	0.9364	0.8061	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B15:20	KELDGSSTVF	0.9246	0.9784	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B35:28	KELDGSSTVF	0.9235	0.9764	9	19
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B40:04	KELDGSSTVFL	0.9997	0.7649	9	20
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B39:02	KELDGSSTVFL	0.9928	0.9006	9	20
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	HLA-B41:03	KELDGSSTVFL	0.9563	0.6172	9	20

Top

Potential FusionNeoAntigen Information of PHF20-RPN2 in HLA II

PHF20-RPN2_34528969_35812582.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)
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	DRB1-1358	THRMDSIEKELDGSS	1	16
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	DRB1-1381	THRMDSIEKELDGSS	1	16
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	DRB1-1388	THRMDSIEKELDGSS	1	16
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	DRB1-1389	THRMDSIEKELDGSS	1	16
PHF20-RPN2	chr20	34528969	chr20	35812582	3025	DRB1-1389	VTHRMDSIEKELDGS	0	15

Top

Fusion breakpoint peptide structures of PHF20-RPN2

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
8638	SIEKELDGSSTVFL	PHF20	RPN2	chr20	34528969	chr20	35812582	3025

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PHF20-RPN2

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	8638	SIEKELDGSSTVFL	-7.15543	-7.26883
HLA-B14:02	3BVN	8638	SIEKELDGSSTVFL	-4.77435	-5.80965
HLA-B52:01	3W39	8638	SIEKELDGSSTVFL	-6.80875	-6.92215
HLA-B52:01	3W39	8638	SIEKELDGSSTVFL	-4.20386	-5.23916
HLA-A11:01	4UQ2	8638	SIEKELDGSSTVFL	-7.5194	-8.5547
HLA-A11:01	4UQ2	8638	SIEKELDGSSTVFL	-6.9601	-7.0735
HLA-A24:02	5HGA	8638	SIEKELDGSSTVFL	-7.52403	-7.63743
HLA-A24:02	5HGA	8638	SIEKELDGSSTVFL	-5.82433	-6.85963
HLA-B27:05	6PYJ	8638	SIEKELDGSSTVFL	-3.28285	-4.31815
HLA-B44:05	3DX8	8638	SIEKELDGSSTVFL	-5.91172	-6.94702
HLA-B44:05	3DX8	8638	SIEKELDGSSTVFL	-4.24346	-4.35686

Top

Vaccine Design for the FusionNeoAntigens of PHF20-RPN2

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
PHF20-RPN2	chr20	34528969	chr20	35812582	10	19	ELDGSSTVF	AGTTGGATGGTTCAAGCACTGTCTTCC
PHF20-RPN2	chr20	34528969	chr20	35812582	8	18	EKELDGSSTV	AGAAGGAGTTGGATGGTTCAAGCACTGTCT
PHF20-RPN2	chr20	34528969	chr20	35812582	9	18	KELDGSSTV	AGGAGTTGGATGGTTCAAGCACTGTCT
PHF20-RPN2	chr20	34528969	chr20	35812582	9	19	KELDGSSTVF	AGGAGTTGGATGGTTCAAGCACTGTCTTCC
PHF20-RPN2	chr20	34528969	chr20	35812582	9	20	KELDGSSTVFL	AGGAGTTGGATGGTTCAAGCACTGTCTTCCTGT

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
PHF20-RPN2	chr20	34528969	chr20	35812582	0	15	VTHRMDSIEKELDGS	TTACGCACAGGATGGACTCCATTGAGAAGGAGTTGGATGGTTCAA
PHF20-RPN2	chr20	34528969	chr20	35812582	1	16	THRMDSIEKELDGSS	CGCACAGGATGGACTCCATTGAGAAGGAGTTGGATGGTTCAAGCA

Top

Information of the samples that have these potential fusion neoantigens of PHF20-RPN2

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	PHF20-RPN2	chr20	34528969	ENST00000374012	chr20	35812582	ENST00000237530	TCGA-A8-A079

Top

Potential target of CAR-T therapy development for PHF20-RPN2

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

RPN2

chr20:34528969

chr20:35812582

ENST00000237530

541_561

632.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812582

ENST00000237530

572_592

632.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812582

ENST00000237530

597_617

632.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812582

ENST00000373622

541_561

616.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812582

ENST00000373622

572_592

616.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812582

ENST00000373622

597_617

616.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812583

ENST00000237530

541_561

632.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812583

ENST00000237530

572_592

632.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812583

ENST00000237530

597_617

632.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812583

ENST00000373622

541_561

616.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812583

ENST00000373622

572_592

616.0

Transmembrane

Helical

Tgene

RPN2

chr20:34528969

chr20:35812583

ENST00000373622

597_617

616.0

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

Top

Related Drugs to PHF20-RPN2

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to PHF20-RPN2

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)