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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:PPP2R4-PRRX2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PPP2R4-PRRX2
	FusionPDB ID: 68058
	FusionGDB2.0 ID: 68058
		Hgene	Tgene
	Gene symbol	PPP2R4	PRRX2
	Gene ID	5524	51450
	Gene name	protein phosphatase 2 phosphatase activator	paired related homeobox 2
	Synonyms	PP2A\|PPP2R4\|PR53	PMX2\|PRX2
	Cytomap	9q34.11	9q34.11
	Type of gene	protein-coding	protein-coding
	Description	serine/threonine-protein phosphatase 2A activatorPP2A phosphatase activatorPP2A subunit B' isoform PR53phosphotyrosyl phosphatase activatorprotein phosphatase 2 regulatory subunit 4protein phosphatase 2A activator, regulatory subunit 4protein phosph	paired mesoderm homeobox protein 2PRX-2paired-like homeodomain protein PRX2paired-related homeobox protein 2testicular tissue protein Li 148testicular tissue protein Li 160
	Modification date	20200329	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000337738, ENST00000348141, ENST00000355007, ENST00000357197, ENST00000358994, ENST00000393370, ENST00000452489, ENST00000347048, ENST00000414510, ENST00000419582, ENST00000423100, ENST00000432124, ENST00000432651, ENST00000434095, ENST00000435132, ENST00000435305, ENST00000436883, ENST00000524946,	ENST00000372469,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	10 X 9 X 8=720	5 X 4 X 6=120
	# samples	12	7
	** MAII score	log2(12/720*10)=-2.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/120*10)=-0.777607578663552 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PPP2R4 [Title/Abstract] AND PRRX2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PPP2R4(131898874)-PRRX2(132481509), # samples:1 PRRX2(132428405)-PPP2R4(131882791), # samples:1 PRRX2(132428405)-PPP2R4(131882792), # samples:1
Anticipated loss of major functional domain due to fusion event.	PPP2R4-PRRX2 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. PPP2R4-PRRX2 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. PRRX2-PPP2R4 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. PRRX2-PPP2R4 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	PPP2R4	GO:0032515	negative regulation of phosphoprotein phosphatase activity	16916641
Hgene	PPP2R4	GO:0032516	positive regulation of phosphoprotein phosphatase activity	16916641
Hgene	PPP2R4	GO:0035307	positive regulation of protein dephosphorylation	16916641
Hgene	PPP2R4	GO:0035308	negative regulation of protein dephosphorylation	16916641
Hgene	PPP2R4	GO:0043065	positive regulation of apoptotic process	17333320
Hgene	PPP2R4	GO:0043666	regulation of phosphoprotein phosphatase activity	16916641

Fusion gene breakpoints across PPP2R4 (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 PRRX2 (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 Gene Sample Information

Fusion gene information from FusionGDB2.0.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	ESCA	TCGA-2H-A9GR	PPP2R4	chr9	131898874	+	PRRX2	chr9	132481509	+

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Fusion ORF Analysis

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)
ENST00000358994	PPP2R4	chr9	131898874	+	ENST00000372469	PRRX2	chr9	132481509	+	1644	897	8	1399	463
ENST00000393370	PPP2R4	chr9	131898874	+	ENST00000372469	PRRX2	chr9	132481509	+	1715	968	169	1470	433
ENST00000337738	PPP2R4	chr9	131898874	+	ENST00000372469	PRRX2	chr9	132481509	+	1804	1057	153	1559	468
ENST00000348141	PPP2R4	chr9	131898874	+	ENST00000372469	PRRX2	chr9	132481509	+	1715	968	151	1470	439
ENST00000452489	PPP2R4	chr9	131898874	+	ENST00000372469	PRRX2	chr9	132481509	+	1750	1003	99	1505	468
ENST00000357197	PPP2R4	chr9	131898874	+	ENST00000372469	PRRX2	chr9	132481509	+	1537	790	78	1292	404
ENST00000355007	PPP2R4	chr9	131898874	+	ENST00000372469	PRRX2	chr9	132481509	+	1493	746	73	1248	391

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
ENST00000358994	ENST00000372469	PPP2R4	chr9	131898874	+	PRRX2	chr9	132481509	+	0.016912274	0.9830877
ENST00000393370	ENST00000372469	PPP2R4	chr9	131898874	+	PRRX2	chr9	132481509	+	0.013333802	0.98666614
ENST00000337738	ENST00000372469	PPP2R4	chr9	131898874	+	PRRX2	chr9	132481509	+	0.008633498	0.99136645
ENST00000348141	ENST00000372469	PPP2R4	chr9	131898874	+	PRRX2	chr9	132481509	+	0.013839127	0.9861609
ENST00000452489	ENST00000372469	PPP2R4	chr9	131898874	+	PRRX2	chr9	132481509	+	0.009482493	0.99051756
ENST00000357197	ENST00000372469	PPP2R4	chr9	131898874	+	PRRX2	chr9	132481509	+	0.02192586	0.9780741
ENST00000355007	ENST00000372469	PPP2R4	chr9	131898874	+	PRRX2	chr9	132481509	+	0.017804958	0.9821951

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>68058_68058_1_PPP2R4-PRRX2_PPP2R4_chr9_131898874_ENST00000337738_PRRX2_chr9_132481509_ENST00000372469_length(amino acids)=468AA_BP=1
MSSGSSEPLVEPGRGRVGARVKGERGLQASGSAPGRSKMAEGERQPPPDSSEEAPPATQNFIIPKKEIHTVPDMGKWKRSQAYADYIGFI
LTLNEGVKGKKLTFEYRVSEMWNEVHEEKEQAAKQSVSCDECIPLPRAGHCAPSEAIEKLVALLNTLDRWIDETPPVDQPSRFGNKAYRT
WYAKLDEEAENLVATVVPTHLAAAVPEVAVYLKESVGNSTRIDYGTGHEAAFAAFLCCLCKIGVLRVDDQIAIVFKVFNRYLEVMRKLQK
TYRMEPAGSQGVWGLDDFQFLPFIWGSSQLIGECPSPGRGSAAKRKKKQRRNRTTFNSSQLQALERVFERTHYPDAFVREELARRVNLSE
ARVQVWFQNRRAKFRRNERAMLASRSASLLKSYSQEAAIEQPVAPRPTALSPDYLSWTASSPYSTVPPYSPGSSGPATPGVNMANSIASL

--------------------------------------------------------------

>68058_68058_2_PPP2R4-PRRX2_PPP2R4_chr9_131898874_ENST00000348141_PRRX2_chr9_132481509_ENST00000372469_length(amino acids)=439AA_BP=1
MSSGSSEPLVEPGRGRVGARVKGERGLQASGSAPGRSKMAEGERQPPPDSSEEAPPATQNFIIPKKEIHTVPDMGKWKRSQVPFGTVAYA
DYIGFILTLNEGVKGKKLTFEYRVSEAIEKLVALLNTLDRWIDETPPVDQPSRFGNKAYRTWYAKLDEEAENLVATVVPTHLAAAVPEVA
VYLKESVGNSTRIDYGTGHEAAFAAFLCCLCKIGVLRVDDQIAIVFKVFNRYLEVMRKLQKTYRMEPAGSQGVWGLDDFQFLPFIWGSSQ
LIGECPSPGRGSAAKRKKKQRRNRTTFNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLASRSASL

--------------------------------------------------------------

>68058_68058_3_PPP2R4-PRRX2_PPP2R4_chr9_131898874_ENST00000355007_PRRX2_chr9_132481509_ENST00000372469_length(amino acids)=391AA_BP=1
MSSGSSEPLVEPGRGRVGARVKGERGLQASGSAPGRSKMAEGERQPPPDSSEEAPPATQNFIIPKKEIHTVPDMGKWKRSQAYADYIGFI
LTLNEGVKGKKLTFEYRVSEEAENLVATVVPTHLAAAVPEVAVYLKESVGNSTRIDYGTGHEAAFAAFLCCLCKIGVLRVDDQIAIVFKV
FNRYLEVMRKLQKTYRMEPAGSQGVWGLDDFQFLPFIWGSSQLIGECPSPGRGSAAKRKKKQRRNRTTFNSSQLQALERVFERTHYPDAF
VREELARRVNLSEARVQVWFQNRRAKFRRNERAMLASRSASLLKSYSQEAAIEQPVAPRPTALSPDYLSWTASSPYSTVPPYSPGSSGPA

--------------------------------------------------------------

>68058_68058_4_PPP2R4-PRRX2_PPP2R4_chr9_131898874_ENST00000357197_PRRX2_chr9_132481509_ENST00000372469_length(amino acids)=404AA_BP=1
MSSGSSEPLVEPGRGRVGARVKGERGLQASGSAPGRSKMAEGERQPPPDSSEEAPPATQNFIIPKKEIHTVPDMGKWKRSQAIEKLVALL
NTLDRWIDETPPVDQPSRFGNKAYRTWYAKLDEEAENLVATVVPTHLAAAVPEVAVYLKESVGNSTRIDYGTGHEAAFAAFLCCLCKIGV
LRVDDQIAIVFKVFNRYLEVMRKLQKTYRMEPAGSQGVWGLDDFQFLPFIWGSSQLIGECPSPGRGSAAKRKKKQRRNRTTFNSSQLQAL
ERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLASRSASLLKSYSQEAAIEQPVAPRPTALSPDYLSWTASSPYS

--------------------------------------------------------------

>68058_68058_5_PPP2R4-PRRX2_PPP2R4_chr9_131898874_ENST00000358994_PRRX2_chr9_132481509_ENST00000372469_length(amino acids)=463AA_BP=1
MWRRKEEVTVQLSLPCPHMSSKLLEPAGAHLSSGSSEPLVEPGRGRVGARVKGERGLQASGSAPGRSKMAEGERQPPPDSSEEAPPATQN
FIIPKKEIHTVPDMGKWKRSQAYADYIGFILTLNEGVKGKKLTFEYRVSEAIEKLVALLNTLDRWIDETPPVDQPSRFGNKAYRTWYAKL
DEEAENLVATVVPTHLAAAVPEVAVYLKESVGNSTRIDYGTGHEAAFAAFLCCLCKIGVLRVDDQIAIVFKVFNRYLEVMRKLQKTYRME
PAGSQGVWGLDDFQFLPFIWGSSQLIGECPSPGRGSAAKRKKKQRRNRTTFNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQV
WFQNRRAKFRRNERAMLASRSASLLKSYSQEAAIEQPVAPRPTALSPDYLSWTASSPYSTVPPYSPGSSGPATPGVNMANSIASLRLKAK

--------------------------------------------------------------

>68058_68058_6_PPP2R4-PRRX2_PPP2R4_chr9_131898874_ENST00000393370_PRRX2_chr9_132481509_ENST00000372469_length(amino acids)=433AA_BP=1
MSSGSSEPLVEPGRGRVGARVKGERGLQASGSAPGRSKMAEGERQPPPDSSEEAPPATQNFIIPKKEIHTVPDMGKWKRSQAYADYIGFI
LTLNEGVKGKKLTFEYRVSEAIEKLVALLNTLDRWIDETPPVDQPSRFGNKAYRTWYAKLDEEAENLVATVVPTHLAAAVPEVAVYLKES
VGNSTRIDYGTGHEAAFAAFLCCLCKIGVLRVDDQIAIVFKVFNRYLEVMRKLQKTYRMEPAGSQGVWGLDDFQFLPFIWGSSQLIGECP
SPGRGSAAKRKKKQRRNRTTFNSSQLQALERVFERTHYPDAFVREELARRVNLSEARVQVWFQNRRAKFRRNERAMLASRSASLLKSYSQ

--------------------------------------------------------------

>68058_68058_7_PPP2R4-PRRX2_PPP2R4_chr9_131898874_ENST00000452489_PRRX2_chr9_132481509_ENST00000372469_length(amino acids)=468AA_BP=1
MSSGSSEPLVEPGRGRVGARVKGERGLQASGSAPGRSKMAEGERQPPPDSSEEAPPATQNFIIPKKEIHTVPDMGKWKRSQAYADYIGFI
LTLNEGVKGKKLTFEYRVSEMWNEVHEEKEQAAKQSVSCDECIPLPRAGHCAPSEAIEKLVALLNTLDRWIDETPPVDQPSRFGNKAYRT
WYAKLDEEAENLVATVVPTHLAAAVPEVAVYLKESVGNSTRIDYGTGHEAAFAAFLCCLCKIGVLRVDDQIAIVFKVFNRYLEVMRKLQK
TYRMEPAGSQGVWGLDDFQFLPFIWGSSQLIGECPSPGRGSAAKRKKKQRRNRTTFNSSQLQALERVFERTHYPDAFVREELARRVNLSE
ARVQVWFQNRRAKFRRNERAMLASRSASLLKSYSQEAAIEQPVAPRPTALSPDYLSWTASSPYSTVPPYSPGSSGPATPGVNMANSIASL

--------------------------------------------------------------

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr9:131898874/chr9:132481509)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	.
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.	FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000337738

183_189

263.3333333333333

359.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000337738

240_242

263.3333333333333

359.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000355007

183_189

186.33333333333334

282.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000357197

183_189

199.33333333333334

295.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000358994

183_189

228.33333333333334

324.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000393370

183_189

228.33333333333334

324.0

Nucleotide binding

Note=ATP

Tgene

PRRX2

chr9:131898874

chr9:132481509

ENST00000372469

104_163

86.33333333333333

254.0

DNA binding

Homeobox

Tgene

PRRX2

chr9:131898874

chr9:132481509

ENST00000372469

230_243

86.33333333333333

254.0

Motif

OAR

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000337738

342_343

263.3333333333333

359.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000355007

240_242

186.33333333333334

282.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000355007

342_343

186.33333333333334

282.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000357197

240_242

199.33333333333334

295.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000357197

342_343

199.33333333333334

295.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000358994

240_242

228.33333333333334

324.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000358994

342_343

228.33333333333334

324.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000393370

240_242

228.33333333333334

324.0

Nucleotide binding

Note=ATP

Hgene

PPP2R4

chr9:131898874

chr9:132481509

ENST00000393370

342_343

228.33333333333334

324.0

Nucleotide binding

Note=ATP

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
PPP2R4
PRRX2

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to PPP2R4-PRRX2

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 PPP2R4-PRRX2

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