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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PRRC2A-SFN (FusionGDB2 ID:69207)

Fusion Gene Summary for PRRC2A-SFN

check button Fusion gene summary
Fusion gene informationFusion gene name: PRRC2A-SFN
Fusion gene ID: 69207
HgeneTgene
Gene symbol

PRRC2A

SFN

Gene ID

7916

25996

Gene nameproline rich coiled-coil 2ARNA exonuclease 2
SynonymsBAT2|D6S51|D6S51E|G2CGI-114|REX2|RFN|SFN
Cytomap

6p21.33

11q23.2

Type of geneprotein-codingprotein-coding
Descriptionprotein PRRC2AHLA-B-associated transcript 2large proline-rich protein BAT2proline-rich and coiled-coil-containing protein 2Aprotein G2oligoribonuclease, mitochondrialREX2, RNA exonuclease 2 homologRNA exonuclease 2 homologsmall fragment nuclease
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000376007, ENST00000376033, 
ENST00000383455, ENST00000383464, 
ENST00000414956, ENST00000416335, 
ENST00000422962, ENST00000428775, 
ENST00000430737, ENST00000432252, 
ENST00000435971, ENST00000439762, 
ENST00000454306, ENST00000458561, 
ENST00000466607, ENST00000468994, 
ENST00000469577, ENST00000470109, 
ENST00000473169, ENST00000484613, 
ENST00000485195, ENST00000547056, 
ENST00000547457, ENST00000547669, 
ENST00000548373, ENST00000549037, 
ENST00000549383, ENST00000549768, 
ENST00000550109, ENST00000550609, 
ENST00000550674, ENST00000551341, 
ENST00000551794, 		ENST00000339276, 
Fusion gene scores* DoF score11 X 11 X 7=8473 X 2 X 2=12
# samples 123
** MAII scorelog2(12/847*10)=-2.81932756372368
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PRRC2A [Title/Abstract] AND SFN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRRC2A(31599597)-SFN(27189704), # samples:1
Anticipated loss of major functional domain due to fusion event.PRRC2A-SFN seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PRRC2A-SFN seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PRRC2A-SFN 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
TgeneSFN

GO:0006139

nucleobase-containing compound metabolic process

10851236


check buttonFusion gene breakpoints across PRRC2A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

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
ChimerDB4HNSCTCGA-CN-6998-01APRRC2Achr6

31599597

-SFNchr1

27189704

+


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Fusion Gene ORF analysis for PRRC2A-SFN

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000376007ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
Frame-shiftENST00000376033ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000383455ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000383464ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000414956ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000416335ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000422962ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000428775ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000430737ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000432252ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000435971ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000439762ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000454306ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000458561ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000466607ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000468994ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000469577ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000470109ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000473169ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000484613ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000485195ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000547056ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000547457ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000547669ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000548373ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000549037ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000549383ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000549768ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000550109ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000550609ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000550674ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000551341ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+
intron-3CDSENST00000551794ENST00000339276PRRC2Achr6

31599597

-SFNchr1

27189704

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for PRRC2A-SFN


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for PRRC2A-SFN


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/:31599597/:27189704)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for PRRC2A-SFN


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for PRRC2A-SFN


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for PRRC2A-SFN


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for PRRC2A-SFN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource