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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:AP2A2-NLRC5 (FusionGDB2 ID:HG161TG84166)

Fusion Gene Summary for AP2A2-NLRC5

check button Fusion gene summary
Fusion gene informationFusion gene name: AP2A2-NLRC5
Fusion gene ID: hg161tg84166
HgeneTgene
Gene symbol

AP2A2

NLRC5

Gene ID

161

84166

Gene nameadaptor related protein complex 2 subunit alpha 2NLR family CARD domain containing 5
SynonymsADTAB|CLAPA2|HIP-9|HIP9|HYPJCLR16.1|NOD27|NOD4
Cytomap('AP2A2')('NLRC5')

11p15.5

16q13

Type of geneprotein-codingprotein-coding
DescriptionAP-2 complex subunit alpha-2100 kDa coated vesicle protein Cadapter-related protein complex 2 subunit alpha-2adaptin, alpha Badaptor related protein complex 2 alpha 2 subunitalpha-adaptin C; Huntingtin interacting protein Jalpha2-adaptinclathrin asprotein NLRC5NOD-like receptor C5caterpiller protein 16.1nucleotide-binding oligomerization domain protein 4nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5nucleotide-binding oligomerization domains 27
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000332231, ENST00000448903, 
ENST00000534328, ENST00000525891, 
Fusion gene scores* DoF score13 X 10 X 12=15603 X 3 X 2=18
# samples 223
** MAII scorelog2(22/1560*10)=-2.82597060022495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: AP2A2 [Title/Abstract] AND NLRC5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAP2A2(959505)-NLRC5(57067516), # samples:3
Anticipated loss of major functional domain due to fusion event.AP2A2-NLRC5 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AP2A2-NLRC5 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
HgeneAP2A2

GO:0072583

clathrin-dependent endocytosis

23676497

TgeneNLRC5

GO:0032088

negative regulation of NF-kappaB transcription factor activity

20434986

TgeneNLRC5

GO:0043549

regulation of kinase activity

20434986

TgeneNLRC5

GO:0045345

positive regulation of MHC class I biosynthetic process

20639463

TgeneNLRC5

GO:0045944

positive regulation of transcription by RNA polymerase II

20639463

TgeneNLRC5

GO:0060335

positive regulation of interferon-gamma-mediated signaling pathway

20061403

TgeneNLRC5

GO:0060339

negative regulation of type I interferon-mediated signaling pathway

20434986

TgeneNLRC5

GO:0060340

positive regulation of type I interferon-mediated signaling pathway

20061403



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
ChimerDB4UCECTCGA-PG-A914-01AAP2A2chr11

959505

-NLRC5chr16

57067516

+
ChimerDB4UCECTCGA-PG-A914-01AAP2A2chr11

959505

+NLRC5chr16

57067516

+
ChimerDB4UCECTCGA-PG-A914AP2A2chr11

959505

+NLRC5chr16

57067516

+


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Fusion Gene ORF analysis for AP2A2-NLRC5

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-intronENST00000332231ENST00000539144AP2A2chr11

959505

+NLRC5chr16

57067516

+
5CDS-intronENST00000332231ENST00000543141AP2A2chr11

959505

+NLRC5chr16

57067516

+
5CDS-intronENST00000448903ENST00000539144AP2A2chr11

959505

+NLRC5chr16

57067516

+
5CDS-intronENST00000448903ENST00000543141AP2A2chr11

959505

+NLRC5chr16

57067516

+
5CDS-intronENST00000534328ENST00000539144AP2A2chr11

959505

+NLRC5chr16

57067516

+
5CDS-intronENST00000534328ENST00000543141AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000332231ENST00000262510AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000332231ENST00000308149AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000332231ENST00000436936AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000448903ENST00000262510AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000448903ENST00000308149AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000448903ENST00000436936AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000534328ENST00000262510AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000534328ENST00000308149AP2A2chr11

959505

+NLRC5chr16

57067516

+
Frame-shiftENST00000534328ENST00000436936AP2A2chr11

959505

+NLRC5chr16

57067516

+
intron-3CDSENST00000525891ENST00000262510AP2A2chr11

959505

+NLRC5chr16

57067516

+
intron-3CDSENST00000525891ENST00000308149AP2A2chr11

959505

+NLRC5chr16

57067516

+
intron-3CDSENST00000525891ENST00000436936AP2A2chr11

959505

+NLRC5chr16

57067516

+
intron-intronENST00000525891ENST00000539144AP2A2chr11

959505

+NLRC5chr16

57067516

+
intron-intronENST00000525891ENST00000543141AP2A2chr11

959505

+NLRC5chr16

57067516

+

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 AP2A2-NLRC5


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)
AP2A2chr11959505+NLRC5chr1657067515+0.662958150.33704183
AP2A2chr11959505+NLRC5chr1657067515+0.662958150.33704183
AP2A2chr11959505+NLRC5chr1657067515+0.662958150.33704183
AP2A2chr11959505+NLRC5chr1657067515+0.662958150.33704183


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 AP2A2-NLRC5


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/:959505/:57067516)
- 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 AP2A2-NLRC5


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 AP2A2-NLRC5


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 AP2A2-NLRC5


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 AP2A2-NLRC5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human