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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:KNTC1-FBXL12 (FusionGDB2 ID:43343)

Fusion Gene Summary for KNTC1-FBXL12

check button Fusion gene summary
Fusion gene informationFusion gene name: KNTC1-FBXL12
Fusion gene ID: 43343
HgeneTgene
Gene symbol

KNTC1

FBXL12

Gene ID

9735

54850

Gene namekinetochore associated 1F-box and leucine rich repeat protein 12
SynonymsRODFbl12
Cytomap

12q24.31

19p13.2

Type of geneprotein-codingprotein-coding
Descriptionkinetochore-associated protein 1Rough Deal homolog, centromere/kinetochore proteinF-box/LRR-repeat protein 12F-box protein FBL12
Modification date2020031320200313
UniProtAcc

P50748

Q9NXK8

Ensembl transtripts involved in fusion geneENST00000333479, ENST00000436959, 
ENST00000450485, ENST00000534995, 
ENST00000537348, ENST00000545065, 
ENST00000247977, ENST00000585379, 
ENST00000586469, ENST00000586651, 
ENST00000588922, ENST00000589626, 
ENST00000591009, ENST00000592067, 
ENST00000586073, 
Fusion gene scores* DoF score10 X 9 X 7=6305 X 7 X 4=140
# samples 1010
** MAII scorelog2(10/630*10)=-2.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/140*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KNTC1 [Title/Abstract] AND FBXL12 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKNTC1(123065217)-FBXL12(9922393), # 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
HgeneKNTC1

GO:0007093

mitotic cell cycle checkpoint

11146660


check buttonFusion gene breakpoints across KNTC1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across FBXL12 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4OVTCGA-24-1474KNTC1chr12

123065217

+FBXL12chr19

9922393

-


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Fusion Gene ORF analysis for KNTC1-FBXL12

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-3UTRENST00000333479ENST00000247977KNTC1chr12

123065217

+FBXL12chr19

9922393

-
5CDS-3UTRENST00000333479ENST00000585379KNTC1chr12

123065217

+FBXL12chr19

9922393

-
5CDS-3UTRENST00000333479ENST00000586469KNTC1chr12

123065217

+FBXL12chr19

9922393

-
5CDS-3UTRENST00000333479ENST00000586651KNTC1chr12

123065217

+FBXL12chr19

9922393

-
5CDS-3UTRENST00000333479ENST00000588922KNTC1chr12

123065217

+FBXL12chr19

9922393

-
5CDS-3UTRENST00000333479ENST00000589626KNTC1chr12

123065217

+FBXL12chr19

9922393

-
5CDS-3UTRENST00000333479ENST00000591009KNTC1chr12

123065217

+FBXL12chr19

9922393

-
5CDS-3UTRENST00000333479ENST00000592067KNTC1chr12

123065217

+FBXL12chr19

9922393

-
5CDS-intronENST00000333479ENST00000586073KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000436959ENST00000247977KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000436959ENST00000585379KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000436959ENST00000586469KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000436959ENST00000586651KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000436959ENST00000588922KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000436959ENST00000589626KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000436959ENST00000591009KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000436959ENST00000592067KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000450485ENST00000247977KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000450485ENST00000585379KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000450485ENST00000586469KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000450485ENST00000586651KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000450485ENST00000588922KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000450485ENST00000589626KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000450485ENST00000591009KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000450485ENST00000592067KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000534995ENST00000247977KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000534995ENST00000585379KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000534995ENST00000586469KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000534995ENST00000586651KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000534995ENST00000588922KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000534995ENST00000589626KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000534995ENST00000591009KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000534995ENST00000592067KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000537348ENST00000247977KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000537348ENST00000585379KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000537348ENST00000586469KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000537348ENST00000586651KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000537348ENST00000588922KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000537348ENST00000589626KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000537348ENST00000591009KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000537348ENST00000592067KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000545065ENST00000247977KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000545065ENST00000585379KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000545065ENST00000586469KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000545065ENST00000586651KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000545065ENST00000588922KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000545065ENST00000589626KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000545065ENST00000591009KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-3UTRENST00000545065ENST00000592067KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-intronENST00000436959ENST00000586073KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-intronENST00000450485ENST00000586073KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-intronENST00000534995ENST00000586073KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-intronENST00000537348ENST00000586073KNTC1chr12

123065217

+FBXL12chr19

9922393

-
intron-intronENST00000545065ENST00000586073KNTC1chr12

123065217

+FBXL12chr19

9922393

-

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 KNTC1-FBXL12


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for KNTC1-FBXL12


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/:123065217/:9922393)
- 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
KNTC1

P50748

FBXL12

Q9NXK8

FUNCTION: Essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis. Required for the assembly of the dynein-dynactin and MAD1-MAD2 complexes onto kinetochores (PubMed:11146660, PubMed:11590237, PubMed:15824131). Its function related to the spindle assembly machinery is proposed to depend on its association in the mitotic RZZ complex. {ECO:0000269|PubMed:11146660, ECO:0000269|PubMed:11590237, ECO:0000269|PubMed:15824131, ECO:0000305}.FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. Mediates the polyubiquitination and proteasomal degradation of CAMK1 leading to disruption of cyclin D1/CDK4 complex assembly which results in G1 cell cycle arrest in lung epithelia. {ECO:0000269|PubMed:23707388}.

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 KNTC1-FBXL12


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 KNTC1-FBXL12


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 KNTC1-FBXL12


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 KNTC1-FBXL12


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