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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:BNC2-C9orf92 (FusionGDB2 ID:HG54796TG100129385)

Fusion Gene Summary for BNC2-C9orf92

check button Fusion gene summary
Fusion gene informationFusion gene name: BNC2-C9orf92
Fusion gene ID: hg54796tg100129385
HgeneTgene
Gene symbol

BNC2

C9orf92

Gene ID

54796

100129385

Gene namebasonuclin 2chromosome 9 open reading frame 92
SynonymsBSN2|LUTOEm:AL513424.1
Cytomap('BNC2')('C9orf92')

9p22.3-p22.2

9p22.3

Type of geneprotein-codingprotein-coding
Descriptionzinc finger protein basonuclin-2putative uncharacterized protein C9orf92
Modification date2020031320200320
UniProtAcc

Q6ZN30

A6NGG3

Ensembl transtripts involved in fusion geneENST00000380666, ENST00000380667, 
ENST00000380672, ENST00000545497, 
ENST00000471301, 
Fusion gene scores* DoF score12 X 16 X 6=11524 X 4 X 7=112
# samples 168
** MAII scorelog2(16/1152*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/112*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BNC2 [Title/Abstract] AND C9orf92 [Title/Abstract] AND fusion [Title/Abstract]

Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus (pmid: 30487138)
Most frequent breakpointBNC2(16552528)-C9orf92(16215897), # samples:2
BNC2(16435553)-C9orf92(16215897), # samples:2
BNC2(16727795)-C9orf92(16215897), # samples:2
BNC2(16870644)-C9orf92(16215897), # samples:2
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
ChimerDB4GBMTCGA-14-0871-01ABNC2chr9

16435553

-C9orf92chr9

16215897

-
ChimerDB4GBMTCGA-28-2509-01ABNC2chr9

16552528

-C9orf92chr9

16215897

-
ChimerDB4KIRCTCGA-CZ-5460-01ABNC2chr9

16435553

-C9orf92chr9

16215897

-
ChimerDB4LIHCTCGA-DD-AAD5BNC2chr9

16400418

-C9orf92chr9

16215897

-
ChimerDB4SARCTCGA-WK-A8XY-01ABNC2chr9

16727795

-C9orf92chr9

16215897

-
ChimerDB4SARCTCGA-WK-A8XY-01ABNC2chr9

16870644

-C9orf92chr9

16215897

-
ChimerDB4SKCMTCGA-DA-A1I4-06ABNC2chr9

16832242

-C9orf92chr9

16215897

-
ChimerDB4SKCMTCGA-DA-A1I4-06ABNC2chr9

16870644

-C9orf92chr9

16215897

-
ChimerDB4SKCMTCGA-DA-A1I4-06ABNC2chr9

16870644

-C9orf92chr9

16245787

-
ChimerDB4SKCMTCGA-ER-A197-06ABNC2chr9

16727795

-C9orf92chr9

16215897

-
ChimerDB4SKCMTCGA-GN-A26D-06ABNC2chr9

16552528

-C9orf92chr9

16215897

-


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Fusion Gene ORF analysis for BNC2-C9orf92

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-5UTRENST00000380666ENST00000380683BNC2chr9

16435553

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380666ENST00000380683BNC2chr9

16552528

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380666ENST00000380683BNC2chr9

16727795

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380666ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380666ENST00000380685BNC2chr9

16435553

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380666ENST00000380685BNC2chr9

16552528

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380666ENST00000380685BNC2chr9

16727795

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380666ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380667ENST00000380683BNC2chr9

16435553

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380667ENST00000380683BNC2chr9

16552528

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380667ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380667ENST00000380685BNC2chr9

16435553

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380667ENST00000380685BNC2chr9

16552528

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380667ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380672ENST00000380683BNC2chr9

16435553

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380672ENST00000380683BNC2chr9

16552528

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380672ENST00000380683BNC2chr9

16727795

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380672ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380672ENST00000380685BNC2chr9

16435553

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380672ENST00000380685BNC2chr9

16552528

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380672ENST00000380685BNC2chr9

16727795

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000380672ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000545497ENST00000380683BNC2chr9

16435553

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000545497ENST00000380683BNC2chr9

16552528

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000545497ENST00000380683BNC2chr9

16832242

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000545497ENST00000380685BNC2chr9

16435553

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000545497ENST00000380685BNC2chr9

16552528

-C9orf92chr9

16215897

-
5CDS-5UTRENST00000545497ENST00000380685BNC2chr9

16832242

-C9orf92chr9

16215897

-
5CDS-intronENST00000380666ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16245787

-
5CDS-intronENST00000380666ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16245787

-
5CDS-intronENST00000380667ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16245787

-
5CDS-intronENST00000380667ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16245787

-
5CDS-intronENST00000380672ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16245787

-
5CDS-intronENST00000380672ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16245787

-
intron-5UTRENST00000380666ENST00000380683BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000380666ENST00000380683BNC2chr9

16832242

-C9orf92chr9

16215897

-
intron-5UTRENST00000380666ENST00000380685BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000380666ENST00000380685BNC2chr9

16832242

-C9orf92chr9

16215897

-
intron-5UTRENST00000380667ENST00000380683BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000380667ENST00000380683BNC2chr9

16727795

-C9orf92chr9

16215897

-
intron-5UTRENST00000380667ENST00000380683BNC2chr9

16832242

-C9orf92chr9

16215897

-
intron-5UTRENST00000380667ENST00000380685BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000380667ENST00000380685BNC2chr9

16727795

-C9orf92chr9

16215897

-
intron-5UTRENST00000380667ENST00000380685BNC2chr9

16832242

-C9orf92chr9

16215897

-
intron-5UTRENST00000380672ENST00000380683BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000380672ENST00000380683BNC2chr9

16832242

-C9orf92chr9

16215897

-
intron-5UTRENST00000380672ENST00000380685BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000380672ENST00000380685BNC2chr9

16832242

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380683BNC2chr9

16435553

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380683BNC2chr9

16552528

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380683BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380683BNC2chr9

16727795

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380683BNC2chr9

16832242

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380685BNC2chr9

16435553

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380685BNC2chr9

16552528

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380685BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380685BNC2chr9

16727795

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16215897

-
intron-5UTRENST00000471301ENST00000380685BNC2chr9

16832242

-C9orf92chr9

16215897

-
intron-5UTRENST00000545497ENST00000380683BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000545497ENST00000380683BNC2chr9

16727795

-C9orf92chr9

16215897

-
intron-5UTRENST00000545497ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16215897

-
intron-5UTRENST00000545497ENST00000380685BNC2chr9

16400418

-C9orf92chr9

16215897

-
intron-5UTRENST00000545497ENST00000380685BNC2chr9

16727795

-C9orf92chr9

16215897

-
intron-5UTRENST00000545497ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16215897

-
intron-intronENST00000471301ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16245787

-
intron-intronENST00000471301ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16245787

-
intron-intronENST00000545497ENST00000380683BNC2chr9

16870644

-C9orf92chr9

16245787

-
intron-intronENST00000545497ENST00000380685BNC2chr9

16870644

-C9orf92chr9

16245787

-

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 BNC2-C9orf92


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 BNC2-C9orf92


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/:16552528/:16215897)
- 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
BNC2

Q6ZN30

C9orf92

A6NGG3

FUNCTION: Probable transcription factor specific for skin keratinocytes. May play a role in the differentiation of spermatozoa and oocytes (PubMed:14988505). May also play an important role in early urinary-tract development (PubMed:31051115). {ECO:0000269|PubMed:14988505, ECO:0000269|PubMed:31051115}.

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 BNC2-C9orf92


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 BNC2-C9orf92


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 BNC2-C9orf92


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 BNC2-C9orf92


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBNC2C0008925Cleft Palate1CTD_human
HgeneBNC2C0238506Congenital posterior urethral valves1GENOMICS_ENGLAND;ORPHANET
HgeneBNC2C0376634Craniofacial Abnormalities1CTD_human
HgeneBNC2C0919267ovarian neoplasm1CTD_human
HgeneBNC2C1140680Malignant neoplasm of ovary1CTD_human
HgeneBNC2C1837218Cleft palate, isolated1CTD_human