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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:C12orf66-NXF3 (FusionGDB2 ID:HG144577TG56000)

Fusion Gene Summary for C12orf66-NXF3

check button Fusion gene summary
Fusion gene informationFusion gene name: C12orf66-NXF3
Fusion gene ID: hg144577tg56000
HgeneTgene
Gene symbol

C12orf66

NXF3

Gene ID

144577

56000

Gene namechromosome 12 open reading frame 66nuclear RNA export factor 3
Synonyms--
Cytomap('C12orf66')('NXF3')

12q14.2

Xq22.1

Type of geneprotein-codingprotein-coding
DescriptionKICSTOR complex protein C12orf66UPF0536 protein C12orf66nuclear RNA export factor 3TAP-like protein 3TAPL-3
Modification date2020031320200313
UniProtAcc

Q96MD2

.
Ensembl transtripts involved in fusion geneENST00000311915, ENST00000398055, 
ENST00000544871, ENST00000540673, 
Fusion gene scores* DoF score4 X 2 X 2=164 X 2 X 2=16
# samples 34
** MAII scorelog2(3/16*10)=0.906890595608518
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(4/16*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: C12orf66 [Title/Abstract] AND NXF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC12orf66(64609458)-NXF3(102339811), # samples:3
Anticipated loss of major functional domain due to fusion event.C12orf66-NXF3 seems lost the major protein functional domain in Hgene 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
TgeneNXF3

GO:0006406

mRNA export from nucleus

11545741



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
ChimerDB4SARCTCGA-HB-A3YV-01AC12orf66chr12

64609458

-NXF3chrX

102339811

-
ChimerDB4SARCTCGA-X9-A971-01AC12orf66chr12

64609458

-NXF3chrX

102339811

-


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Fusion Gene ORF analysis for C12orf66-NXF3

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-5UTRENST00000311915ENST00000425644C12orf66chr12

64609458

-NXF3chrX

102339811

-
5CDS-5UTRENST00000398055ENST00000425644C12orf66chr12

64609458

-NXF3chrX

102339811

-
5CDS-5UTRENST00000544871ENST00000425644C12orf66chr12

64609458

-NXF3chrX

102339811

-
5CDS-intronENST00000311915ENST00000425463C12orf66chr12

64609458

-NXF3chrX

102339811

-
5CDS-intronENST00000398055ENST00000425463C12orf66chr12

64609458

-NXF3chrX

102339811

-
5CDS-intronENST00000544871ENST00000425463C12orf66chr12

64609458

-NXF3chrX

102339811

-
Frame-shiftENST00000311915ENST00000395065C12orf66chr12

64609458

-NXF3chrX

102339811

-
Frame-shiftENST00000398055ENST00000395065C12orf66chr12

64609458

-NXF3chrX

102339811

-
Frame-shiftENST00000544871ENST00000395065C12orf66chr12

64609458

-NXF3chrX

102339811

-
intron-3CDSENST00000540673ENST00000395065C12orf66chr12

64609458

-NXF3chrX

102339811

-
intron-5UTRENST00000540673ENST00000425644C12orf66chr12

64609458

-NXF3chrX

102339811

-
intron-intronENST00000540673ENST00000425463C12orf66chr12

64609458

-NXF3chrX

102339811

-

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 C12orf66-NXF3


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)


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Fusion Protein Features for C12orf66-NXF3


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/:64609458/:102339811)
- 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
C12orf66

Q96MD2

.
FUNCTION: As part of the KICSTOR complex functions in the amino acid-sensing branch of the TORC1 signaling pathway. Recruits, in an amino acid-independent manner, the GATOR1 complex to the lysosomal membranes and allows its interaction with GATOR2 and the RAG GTPases. Functions upstream of the RAG GTPases and is required to negatively regulate mTORC1 signaling in absence of amino acids. In absence of the KICSTOR complex mTORC1 is constitutively localized to the lysosome and activated. The KICSTOR complex is also probably involved in the regulation of mTORC1 by glucose. {ECO:0000269|PubMed:28199306}.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 C12orf66-NXF3


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 C12orf66-NXF3


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 C12orf66-NXF3


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 C12orf66-NXF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneC12orf66C0032460Polycystic Ovary Syndrome1CTD_human
HgeneC12orf66C1136382Sclerocystic Ovaries1CTD_human