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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:AP1S3-GIGYF2 (FusionGDB2 ID:HG130340TG26058)

Fusion Gene Summary for AP1S3-GIGYF2

check button Fusion gene summary
Fusion gene informationFusion gene name: AP1S3-GIGYF2
Fusion gene ID: hg130340tg26058
HgeneTgene
Gene symbol

AP1S3

GIGYF2

Gene ID

130340

26058

Gene nameadaptor related protein complex 1 subunit sigma 3GRB10 interacting GYF protein 2
SynonymsPSORS15GYF2|PARK11|PERQ2|PERQ3|TNRC15
Cytomap('AP1S3')('GIGYF2')

2q36.1

2q37.1

Type of geneprotein-codingprotein-coding
DescriptionAP-1 complex subunit sigma-3adapter-related protein complex 1 subunit sigma-1Cadaptor protein complex AP-1 sigma-1C subunitadaptor related protein complex 1 sigma 3 subunitadaptor-related protein complex 1 subunit sigma-1Cclathrin assembly protein coGRB10-interacting GYF protein 2PERQ amino acid rich, with GYF domain 3PERQ amino acid-rich with GYF domain-containing protein 2Parkinson disease (autosomal recessive, early onset) 11trinucleotide repeat-containing gene 15 protein
Modification date2020031320200313
UniProtAcc

Q96PC3

.
Ensembl transtripts involved in fusion geneENST00000396653, ENST00000396654, 
ENST00000409375, ENST00000423110, 
ENST00000443700, ENST00000446015, 
Fusion gene scores* DoF score6 X 6 X 3=10817 X 18 X 6=1836
# samples 619
** MAII scorelog2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1836*10)=-3.27249473508286
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AP1S3 [Title/Abstract] AND GIGYF2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAP1S3(224702165)-GIGYF2(233671201), # samples:1
Anticipated loss of major functional domain due to fusion event.AP1S3-GIGYF2 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneGIGYF2

GO:0016441

posttranscriptional gene silencing

27157137

TgeneGIGYF2

GO:0061157

mRNA destabilization

27157137



check button Fusion gene information
* 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
ChimerDB4Non-CancerERR188311AP1S3chr2

224702165

-GIGYF2chr2

233671201

+


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Fusion Gene ORF analysis for AP1S3-GIGYF2

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
5CDS-intronENST00000396653ENST00000452341AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000396653ENST00000482666AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000396654ENST00000452341AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000396654ENST00000482666AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000409375ENST00000452341AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000409375ENST00000482666AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000423110ENST00000452341AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000423110ENST00000482666AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000443700ENST00000452341AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000443700ENST00000482666AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000446015ENST00000452341AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
5CDS-intronENST00000446015ENST00000482666AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396653ENST00000373563AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396653ENST00000373566AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396653ENST00000409196AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396653ENST00000409451AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396653ENST00000409480AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396653ENST00000409547AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396654ENST00000373563AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396654ENST00000373566AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396654ENST00000409196AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396654ENST00000409451AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396654ENST00000409480AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000396654ENST00000409547AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000409375ENST00000373563AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000409375ENST00000373566AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000409375ENST00000409196AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000409375ENST00000409451AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000409375ENST00000409480AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000409375ENST00000409547AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000423110ENST00000373563AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000423110ENST00000373566AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000423110ENST00000409196AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000423110ENST00000409451AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000423110ENST00000409480AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000423110ENST00000409547AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000443700ENST00000373563AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000443700ENST00000373566AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000443700ENST00000409196AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000443700ENST00000409451AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000443700ENST00000409480AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000443700ENST00000409547AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000446015ENST00000373563AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000446015ENST00000373566AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000446015ENST00000409196AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000446015ENST00000409451AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000446015ENST00000409480AP1S3chr2

224702165

-GIGYF2chr2

233671201

+
Frame-shiftENST00000446015ENST00000409547AP1S3chr2

224702165

-GIGYF2chr2

233671201

+

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 AP1S3-GIGYF2


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)
AP1S3chr2224702164-GIGYF2chr2233671200+2.77E-081
AP1S3chr2224702164-GIGYF2chr2233671200+2.77E-081


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.
genomic feature of top 1%

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Fusion Protein Features for AP1S3-GIGYF2


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/:224702165/:233671201)
- 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
AP1S3

Q96PC3

.
FUNCTION: Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. Involved in TLR3 trafficking (PubMed:24791904). {ECO:0000269|PubMed:24791904}.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 AP1S3-GIGYF2


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 AP1S3-GIGYF2


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 AP1S3-GIGYF2


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 AP1S3-GIGYF2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAP1S3C4015235PSORIASIS 15, PUSTULAR, SUSCEPTIBILITY TO2GENOMICS_ENGLAND;UNIPROT
HgeneAP1S3C0030246Pustulosis of Palms and Soles1CTD_human;ORPHANET
HgeneAP1S3C0343055Generalized pustular psoriasis1ORPHANET
HgeneAP1S3C0392439Acrodermatitis continua of Hallopeau1ORPHANET
TgeneC4083045PARKINSON DISEASE 11, AUTOSOMAL DOMINANT, SUSCEPTIBILITY TO5CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1535926Neurodevelopmental Disorders1CTD_human