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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:NUP50-C10orf11 (FusionGDB2 ID:HG10762TG83938)

Fusion Gene Summary for NUP50-C10orf11

check button Fusion gene summary
Fusion gene informationFusion gene name: NUP50-C10orf11
Fusion gene ID: hg10762tg83938
HgeneTgene
Gene symbol

NUP50

C10orf11

Gene ID

10762

83938

Gene namenucleoporin 50leucine rich melanocyte differentiation associated
SynonymsNPAP60|NPAP60LC10orf11|CDA017
Cytomap('NUP50')('C10orf11')

22q13.31

10q22.2-q22.3

Type of geneprotein-codingprotein-coding
Descriptionnuclear pore complex protein Nup5050 kDa nucleoporinnuclear pore-associated protein 60Lnucleoporin 50kDnucleoporin 50kDanucleoporin Nup50leucine-rich melanocyte differentiation-associated proteinleucine-rich repeat-containing protein C10orf11
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000486184, ENST00000347635, 
ENST00000396096, ENST00000407019, 
ENST00000425733, 
Fusion gene scores* DoF score8 X 7 X 3=16832 X 23 X 8=5888
# samples 943
** MAII scorelog2(9/168*10)=-0.900464326449086
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(43/5888*10)=-3.77536910646755
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NUP50 [Title/Abstract] AND C10orf11 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNUP50(45567564)-C10orf11(77795765), # samples:1
NUP50(45567564)-C10orf11(77795766), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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


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
ChimerDB4STADTCGA-BR-A4IY-01ANUP50chr22

45567564

+C10orf11chr10

77795766

+
ChimerDB4STADTCGA-BR-A4IYNUP50chr22

45567564

+C10orf11chr10

77795765

+


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Fusion Gene ORF analysis for NUP50-C10orf11

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
3UTR-3UTRENST00000486184ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795766

+
3UTR-3UTRENST00000486184ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795765

+
3UTR-3UTRENST00000486184ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795766

+
3UTR-3UTRENST00000486184ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795765

+
3UTR-intronENST00000486184ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795766

+
3UTR-intronENST00000486184ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-3UTRENST00000347635ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-3UTRENST00000347635ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-3UTRENST00000347635ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-3UTRENST00000347635ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-3UTRENST00000396096ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-3UTRENST00000396096ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-3UTRENST00000396096ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-3UTRENST00000396096ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-3UTRENST00000407019ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-3UTRENST00000407019ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-3UTRENST00000407019ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-3UTRENST00000407019ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-intronENST00000347635ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-intronENST00000347635ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-intronENST00000396096ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-intronENST00000396096ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795765

+
5CDS-intronENST00000407019ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795766

+
5CDS-intronENST00000407019ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795765

+
5UTR-3UTRENST00000425733ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795766

+
5UTR-3UTRENST00000425733ENST00000372499NUP50chr22

45567564

+C10orf11chr10

77795765

+
5UTR-3UTRENST00000425733ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795766

+
5UTR-3UTRENST00000425733ENST00000593699NUP50chr22

45567564

+C10orf11chr10

77795765

+
5UTR-intronENST00000425733ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795766

+
5UTR-intronENST00000425733ENST00000496424NUP50chr22

45567564

+C10orf11chr10

77795765

+

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 NUP50-C10orf11


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)
NUP50chr2245567564+C10orf11chr1077795765+0.0083389530.9916611
NUP50chr2245567564+C10orf11chr1077795765+0.0083389530.9916611
NUP50chr2245567564+C10orf11chr1077795765+0.0083389530.9916611
NUP50chr2245567564+C10orf11chr1077795765+0.0083389530.9916611


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 NUP50-C10orf11


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/:45567564/:77795765)
- 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 NUP50-C10orf11


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 NUP50-C10orf11


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 NUP50-C10orf11


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 NUP50-C10orf11


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