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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PPP2R4-PAX5

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PPP2R4-PAX5
FusionPDB ID: 68056
FusionGDB2.0 ID: 68056
HgeneTgene
Gene symbol

PPP2R4

PAX5

Gene ID

5524

5079

Gene nameprotein phosphatase 2 phosphatase activatorpaired box 5
SynonymsPP2A|PPP2R4|PR53ALL3|BSAP
Cytomap

9q34.11

9p13.2

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein phosphatase 2A activatorPP2A phosphatase activatorPP2A subunit B' isoform PR53phosphotyrosyl phosphatase activatorprotein phosphatase 2 regulatory subunit 4protein phosphatase 2A activator, regulatory subunit 4protein phosphpaired box protein Pax-5B-cell lineage specific activatorpaired box homeotic gene 5paired domain gene 5transcription factor PAX 5
Modification date2020032920200313
UniProtAcc.

Q02548

Ensembl transtripts involved in fusion geneENST idsENST00000337738, ENST00000347048, 
ENST00000348141, ENST00000355007, 
ENST00000357197, ENST00000358994, 
ENST00000393370, ENST00000414510, 
ENST00000419582, ENST00000423100, 
ENST00000432124, ENST00000432651, 
ENST00000434095, ENST00000435132, 
ENST00000435305, ENST00000436883, 
ENST00000452489, ENST00000524946, 
ENST00000377847, ENST00000377852, 
ENST00000377853, ENST00000414447, 
ENST00000446742, ENST00000520154, 
ENST00000520281, ENST00000522003, 
ENST00000523145, ENST00000523241, 
ENST00000358127, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 9 X 8=7208 X 7 X 6=336
# samples 129
** MAII scorelog2(12/720*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/336*10)=-1.90046432644909
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 PAX5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PPP2R4(131911224)-PAX5(37034103), # samples:1
Anticipated loss of major functional domain due to fusion event.PPP2R4-PAX5 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-PAX5 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.
PPP2R4-PAX5 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PPP2R4-PAX5 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PPP2R4-PAX5 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
PPP2R4-PAX5 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
PPP2R4-PAX5 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePPP2R4

GO:0032515

negative regulation of phosphoprotein phosphatase activity

16916641

HgenePPP2R4

GO:0032516

positive regulation of phosphoprotein phosphatase activity

16916641

HgenePPP2R4

GO:0035307

positive regulation of protein dephosphorylation

16916641

HgenePPP2R4

GO:0035308

negative regulation of protein dephosphorylation

16916641

HgenePPP2R4

GO:0043065

positive regulation of apoptotic process

17333320

HgenePPP2R4

GO:0043666

regulation of phosphoprotein phosphatase activity

16916641


check buttonFusion 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.
all structure

check buttonFusion gene breakpoints across PAX5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4SARCTCGA-IE-A3OV-01APPP2R4chr9

131911224

-PAX5chr9

37034103

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000393370PPP2R4chr9131911224-ENST00000358127PAX5chr937034103-11273273728123987391
ENST00000348141PPP2R4chr9131911224-ENST00000358127PAX5chr937034103-11273273728123987391
ENST00000347048PPP2R4chr9131911224-ENST00000358127PAX5chr937034103-10525198920643239391
ENST00000355007PPP2R4chr9131911224-ENST00000358127PAX5chr937034103-11051251525903765391

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000393370ENST00000358127PPP2R4chr9131911224-PAX5chr937034103-0.0103074050.9896926
ENST00000348141ENST00000358127PPP2R4chr9131911224-PAX5chr937034103-0.0102180790.989782
ENST00000347048ENST00000358127PPP2R4chr9131911224-PAX5chr937034103-0.01096650.98903346
ENST00000355007ENST00000358127PPP2R4chr9131911224-PAX5chr937034103-0.0104614410.98953855

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Fusion Amino Acid Sequences


check button 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

>68056_68056_1_PPP2R4-PAX5_PPP2R4_chr9_131911224_ENST00000347048_PAX5_chr9_37034103_ENST00000358127_length(amino acids)=391AA_BP=
MDLEKNYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKV
ATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQQPPNQPVPASSHSIVSTGSVTQVSSVSTDSAGSSYS
ISGILGITSPSADTNKRKRDEGIQESPVPNGHSLPGRDFLRKQMRGDLFTQQQLEVLDRVFERQHYSDIFTTTEPIKPEQTTEYSAMASL
AGGLDDMKANLASPTPADIGSSVPGPQSYPIVTGRDLASTTLPGYPPHVPPAGQGSYSAPTLTGMVPGSEFSGSPYSHPQYSSYNDSWRF

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

>68056_68056_2_PPP2R4-PAX5_PPP2R4_chr9_131911224_ENST00000348141_PAX5_chr9_37034103_ENST00000358127_length(amino acids)=391AA_BP=
MDLEKNYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKV
ATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQQPPNQPVPASSHSIVSTGSVTQVSSVSTDSAGSSYS
ISGILGITSPSADTNKRKRDEGIQESPVPNGHSLPGRDFLRKQMRGDLFTQQQLEVLDRVFERQHYSDIFTTTEPIKPEQTTEYSAMASL
AGGLDDMKANLASPTPADIGSSVPGPQSYPIVTGRDLASTTLPGYPPHVPPAGQGSYSAPTLTGMVPGSEFSGSPYSHPQYSSYNDSWRF

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

>68056_68056_3_PPP2R4-PAX5_PPP2R4_chr9_131911224_ENST00000355007_PAX5_chr9_37034103_ENST00000358127_length(amino acids)=391AA_BP=
MDLEKNYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKV
ATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQQPPNQPVPASSHSIVSTGSVTQVSSVSTDSAGSSYS
ISGILGITSPSADTNKRKRDEGIQESPVPNGHSLPGRDFLRKQMRGDLFTQQQLEVLDRVFERQHYSDIFTTTEPIKPEQTTEYSAMASL
AGGLDDMKANLASPTPADIGSSVPGPQSYPIVTGRDLASTTLPGYPPHVPPAGQGSYSAPTLTGMVPGSEFSGSPYSHPQYSSYNDSWRF

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

>68056_68056_4_PPP2R4-PAX5_PPP2R4_chr9_131911224_ENST00000393370_PAX5_chr9_37034103_ENST00000358127_length(amino acids)=391AA_BP=
MDLEKNYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKV
ATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQQPPNQPVPASSHSIVSTGSVTQVSSVSTDSAGSSYS
ISGILGITSPSADTNKRKRDEGIQESPVPNGHSLPGRDFLRKQMRGDLFTQQQLEVLDRVFERQHYSDIFTTTEPIKPEQTTEYSAMASL
AGGLDDMKANLASPTPADIGSSVPGPQSYPIVTGRDLASTTLPGYPPHVPPAGQGSYSAPTLTGMVPGSEFSGSPYSHPQYSSYNDSWRF

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

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr9:131911224/chr9:37034103)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.PAX5

Q02548

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: Transcription factor that plays an essential role in commitment of lymphoid progenitors to the B-lymphocyte lineage (PubMed:10811620, PubMed:27181361). Fulfills a dual role by repressing B-lineage inappropriate genes and simultaneously activating B-lineage-specific genes (PubMed:10811620, PubMed:27181361). In turn, regulates cell adhesion and migration, induces V(H)-to-D(H)J(H) recombination, facilitates pre-B-cell receptor signaling and promotes development to the mature B-cell stage (PubMed:32612238). Repression of the cohesin-release factor WAPL causes global changes of the chromosomal architecture in pro-B cells to facilitate the generation of a diverse antibody repertoire (PubMed:32612238). {ECO:0000269|PubMed:10811620, ECO:0000269|PubMed:27181361, ECO:0000269|PubMed:32612238}.; FUNCTION: (Microbial infection) Plays an essential role in the maintenance of Epstein-Barr virus genome copy number within the host cell by promoting EBNA1/oriP-dependent binding and transcription (PubMed:31941781). Participates also in the inhibition of lytic EBV reactivation by modulating viral BZLF1 activity (PubMed:23678172). {ECO:0000269|PubMed:23678172, ECO:0000269|PubMed:31941781}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePPP2R4chr9:131911224chr9:37034103ENST00000337738-1111183_189852.3333333333334359.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000337738-1111240_242852.3333333333334359.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000337738-1111342_343852.3333333333334359.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000355007-99183_189776.0282.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000355007-99240_242776.0282.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000355007-99342_343776.0282.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000357197-99183_189788.6666666666666295.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000357197-99240_242788.6666666666666295.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000357197-99342_343788.6666666666666295.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000358994-1111183_189817.3333333333334324.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000358994-1111240_242817.3333333333334324.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000358994-1111342_343817.3333333333334324.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000393370-1010183_189818.0324.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000393370-1010240_242818.0324.0Nucleotide bindingNote=ATP
HgenePPP2R4chr9:131911224chr9:37034103ENST00000393370-1010342_343818.0324.0Nucleotide bindingNote=ATP
TgenePAX5chr9:131911224chr9:37034103ENST00000358127-11016_14215.333333333333334392.0DNA bindingPaired
TgenePAX5chr9:131911224chr9:37034103ENST000003778470816_1420.0329.0DNA bindingPaired
TgenePAX5chr9:131911224chr9:37034103ENST000003778520916_1420358.0DNA bindingPaired
TgenePAX5chr9:131911224chr9:37034103ENST000003778530916_1420363.0DNA bindingPaired
TgenePAX5chr9:131911224chr9:37034103ENST000004144470916_1420.0349.0DNA bindingPaired
TgenePAX5chr9:131911224chr9:37034103ENST000004467420816_1420.0292.0DNA bindingPaired
TgenePAX5chr9:131911224chr9:37034103ENST000005202810816_1420.0320.0DNA bindingPaired
TgenePAX5chr9:131911224chr9:37034103ENST00000358127-11019_7515.333333333333334392.0RegionPAI subdomain
TgenePAX5chr9:131911224chr9:37034103ENST00000358127-11094_14215.333333333333334392.0RegionRED subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000003778470819_750.0329.0RegionPAI subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000003778470894_1420.0329.0RegionRED subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000003778520919_750358.0RegionPAI subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000003778520994_1420358.0RegionRED subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000003778530919_750363.0RegionPAI subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000003778530994_1420363.0RegionRED subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000004144470919_750.0349.0RegionPAI subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000004144470994_1420.0349.0RegionRED subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000004467420819_750.0292.0RegionPAI subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000004467420894_1420.0292.0RegionRED subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000005202810819_750.0320.0RegionPAI subdomain
TgenePAX5chr9:131911224chr9:37034103ENST000005202810894_1420.0320.0RegionRED subdomain

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Protein-Protein Interaction


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)
GenePPI interactors
PAX5TLE4, DAXX, RUNX1, MYB, ID3, EP300, TBP, RB1, MAPK1, KAT2B, CDKN1B, UBE3A, RAD52, HMGB3, HOXC8, MAPK9, NFYC, FBLN1, GRHL2, DTX2, CSNK2A1, UBE2I, CCNC, BCAS2, C1orf109, GNG13, ZMYM5, SEC14L4, RNF144B, OSGIN1, CIB3, SAE1, STAC, TLK2, HMBOX1, NGLY1, NEIL2, LONRF1, LDLRAP1, LARP4, UBXN7, ACOT12, CKS1B, KLHL38, HGS, CXorf38, KRTAP10-8, PNMA5, KRTAP9-3, UBXN2B, CDK3, BKRF1, HIST1H3A, PAX8, KLHL14,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PPP2R4
PAX5all structure


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to PPP2R4-PAX5


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

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Related Diseases to PPP2R4-PAX5


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgenePAX5C0006413Burkitt Lymphoma4ORPHANET
TgenePAX5C1292769Precursor B-cell lymphoblastic leukemia4ORPHANET
TgenePAX5C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma2CTD_human
TgenePAX5C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma2CGI;CTD_human;UNIPROT
TgenePAX5C0023452Childhood Acute Lymphoblastic Leukemia1CTD_human
TgenePAX5C0023453L2 Acute Lymphoblastic Leukemia1CTD_human
TgenePAX5C1535926Neurodevelopmental Disorders1CTD_human