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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:CTNNB1-KLK3 (FusionGDB2 ID:20323)

Fusion Gene Summary for CTNNB1-KLK3

check button Fusion gene summary
Fusion gene informationFusion gene name: CTNNB1-KLK3
Fusion gene ID: 20323
HgeneTgene
Gene symbol

CTNNB1

KLK3

Gene ID

1499

3818

Gene namecatenin beta 1kallikrein B1
SynonymsCTNNB|EVR7|MRD19|NEDSDV|armadilloKLK3|PKK|PKKD|PPK
Cytomap

3p22.1

4q35.2

Type of geneprotein-codingprotein-coding
Descriptioncatenin beta-1catenin (cadherin-associated protein), beta 1, 88kDaplasma kallikreinkallikrein B, plasma (Fletcher factor) 1kininogeninplasma prekallikrein
Modification date2020032720200320
UniProtAcc

P35222

P07288

Ensembl transtripts involved in fusion geneENST00000349496, ENST00000396183, 
ENST00000396185, ENST00000405570, 
ENST00000453024, ENST00000471014, 
ENST00000326003, ENST00000360617, 
ENST00000595952, ENST00000593997, 
ENST00000597483, 
Fusion gene scores* DoF score19 X 14 X 13=345830 X 32 X 3=2880
# samples 2137
** MAII scorelog2(21/3458*10)=-4.04147663597616
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(37/2880*10)=-2.96047163581336
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CTNNB1 [Title/Abstract] AND KLK3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTNNB1(41281528)-KLK3(51363498), # 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
HgeneCTNNB1

GO:0000209

protein polyubiquitination

29374064

HgeneCTNNB1

GO:0008285

negative regulation of cell proliferation

12970740

HgeneCTNNB1

GO:0030997

regulation of centriole-centriole cohesion

18086858

HgeneCTNNB1

GO:0032355

response to estradiol

15304487

HgeneCTNNB1

GO:0033234

negative regulation of protein sumoylation

22155184

HgeneCTNNB1

GO:0043065

positive regulation of apoptotic process

12651860|12970740

HgeneCTNNB1

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

29374064

HgeneCTNNB1

GO:0043525

positive regulation of neuron apoptotic process

19591802

HgeneCTNNB1

GO:0045893

positive regulation of transcription, DNA-templated

12970740|18787224

HgeneCTNNB1

GO:0045944

positive regulation of transcription by RNA polymerase II

9065402|11751639|12651860|14660579|18193033

HgeneCTNNB1

GO:0060070

canonical Wnt signaling pathway

10644691|12937339|19187541

HgeneCTNNB1

GO:0071681

cellular response to indole-3-methanol

10868478

HgeneCTNNB1

GO:0090279

regulation of calcium ion import

19996314

HgeneCTNNB1

GO:1904798

positive regulation of core promoter binding

22723415

HgeneCTNNB1

GO:2000008

regulation of protein localization to cell surface

19996314

TgeneKLK3

GO:0031639

plasminogen activation

89876

TgeneKLK3

GO:0051919

positive regulation of fibrinolysis

89876


check buttonFusion gene breakpoints across CTNNB1 (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 KLK3 (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
ChimerDB4PRADTCGA-HC-7232CTNNB1chr3

41281528

+KLK3chr19

51363498

+


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Fusion Gene ORF analysis for CTNNB1-KLK3

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-3UTRENST00000349496ENST00000326003CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-3UTRENST00000349496ENST00000360617CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-3UTRENST00000349496ENST00000595952CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-3UTRENST00000396183ENST00000326003CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-3UTRENST00000396183ENST00000360617CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-3UTRENST00000396183ENST00000595952CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-3UTRENST00000396185ENST00000326003CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-3UTRENST00000396185ENST00000360617CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-3UTRENST00000396185ENST00000595952CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-intronENST00000349496ENST00000593997CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-intronENST00000349496ENST00000597483CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-intronENST00000396183ENST00000593997CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-intronENST00000396183ENST00000597483CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-intronENST00000396185ENST00000593997CTNNB1chr3

41281528

+KLK3chr19

51363498

+
3UTR-intronENST00000396185ENST00000597483CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000405570ENST00000326003CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000405570ENST00000360617CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000405570ENST00000595952CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000453024ENST00000326003CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000453024ENST00000360617CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000453024ENST00000595952CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000471014ENST00000326003CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000471014ENST00000360617CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-3UTRENST00000471014ENST00000595952CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-intronENST00000405570ENST00000593997CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-intronENST00000405570ENST00000597483CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-intronENST00000453024ENST00000593997CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-intronENST00000453024ENST00000597483CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-intronENST00000471014ENST00000593997CTNNB1chr3

41281528

+KLK3chr19

51363498

+
intron-intronENST00000471014ENST00000597483CTNNB1chr3

41281528

+KLK3chr19

51363498

+

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 CTNNB1-KLK3


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 CTNNB1-KLK3


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/:41281528/:51363498)
- 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
CTNNB1

P35222

KLK3

P07288

FUNCTION: Key downstream component of the canonical Wnt signaling pathway (PubMed:17524503, PubMed:18077326, PubMed:18086858, PubMed:18957423, PubMed:21262353, PubMed:22155184, PubMed:22647378, PubMed:22699938). In the absence of Wnt, forms a complex with AXIN1, AXIN2, APC, CSNK1A1 and GSK3B that promotes phosphorylation on N-terminal Ser and Thr residues and ubiquitination of CTNNB1 via BTRC and its subsequent degradation by the proteasome (PubMed:17524503, PubMed:18077326, PubMed:18086858, PubMed:18957423, PubMed:21262353, PubMed:22155184, PubMed:22647378, PubMed:22699938). In the presence of Wnt ligand, CTNNB1 is not ubiquitinated and accumulates in the nucleus, where it acts as a coactivator for transcription factors of the TCF/LEF family, leading to activate Wnt responsive genes (PubMed:17524503, PubMed:18077326, PubMed:18086858, PubMed:18957423, PubMed:21262353, PubMed:22155184, PubMed:22647378, PubMed:22699938). Involved in the regulation of cell adhesion, as component of an E-cadherin:catenin adhesion complex (By similarity). Acts as a negative regulator of centrosome cohesion (PubMed:18086858). Involved in the CDK2/PTPN6/CTNNB1/CEACAM1 pathway of insulin internalization (PubMed:21262353). Blocks anoikis of malignant kidney and intestinal epithelial cells and promotes their anchorage-independent growth by down-regulating DAPK2 (PubMed:18957423). Disrupts PML function and PML-NB formation by inhibiting RANBP2-mediated sumoylation of PML (PubMed:22155184). Promotes neurogenesis by maintaining sympathetic neuroblasts within the cell cycle (By similarity). Involved in chondrocyte differentiation via interaction with SOX9: SOX9-binding competes with the binding sites of TCF/LEF within CTNNB1, thereby inhibiting the Wnt signaling (By similarity). {ECO:0000250|UniProtKB:Q02248, ECO:0000269|PubMed:17524503, ECO:0000269|PubMed:18077326, ECO:0000269|PubMed:18086858, ECO:0000269|PubMed:18957423, ECO:0000269|PubMed:21262353, ECO:0000269|PubMed:22155184, ECO:0000269|PubMed:22647378, ECO:0000269|PubMed:22699938}.FUNCTION: Hydrolyzes semenogelin-1 thus leading to the liquefaction of the seminal coagulum.

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 CTNNB1-KLK3


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 CTNNB1-KLK3


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 CTNNB1-KLK3


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 CTNNB1-KLK3


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