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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-CHEK1 (FusionGDB2 ID:20315)

Fusion Gene Summary for CTNNB1-CHEK1

check button Fusion gene summary
Fusion gene informationFusion gene name: CTNNB1-CHEK1
Fusion gene ID: 20315
HgeneTgene
Gene symbol

CTNNB1

CHEK1

Gene ID

1499

1111

Gene namecatenin beta 1checkpoint kinase 1
SynonymsCTNNB|EVR7|MRD19|NEDSDV|armadilloCHK1
Cytomap

3p22.1

11q24.2

Type of geneprotein-codingprotein-coding
Descriptioncatenin beta-1catenin (cadherin-associated protein), beta 1, 88kDaserine/threonine-protein kinase Chk1CHK1 checkpoint homologCheckpoint, S. pombe, homolog of, 1Chk1-Scell cycle checkpoint kinase
Modification date2020032720200313
UniProtAcc

P35222

O14757

Ensembl transtripts involved in fusion geneENST00000349496, ENST00000396183, 
ENST00000396185, ENST00000453024, 
ENST00000405570, ENST00000471014, 
ENST00000532449, ENST00000278916, 
ENST00000427383, ENST00000428830, 
ENST00000438015, ENST00000524737, 
ENST00000534070, ENST00000544373, 
Fusion gene scores* DoF score19 X 14 X 13=34583 X 3 X 3=27
# samples 213
** MAII scorelog2(21/3458*10)=-4.04147663597616
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CTNNB1 [Title/Abstract] AND CHEK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTNNB1(41241161)-CHEK1(125496643), # 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

TgeneCHEK1

GO:0000077

DNA damage checkpoint

16963448

TgeneCHEK1

GO:0006915

apoptotic process

23028632

TgeneCHEK1

GO:0006975

DNA damage induced protein phosphorylation

16963448

TgeneCHEK1

GO:0010569

regulation of double-strand break repair via homologous recombination

15665856

TgeneCHEK1

GO:0018107

peptidyl-threonine phosphorylation

15665856

TgeneCHEK1

GO:0045787

positive regulation of cell cycle

26296656

TgeneCHEK1

GO:0045839

negative regulation of mitotic nuclear division

15311285

TgeneCHEK1

GO:0046602

regulation of mitotic centrosome separation

15311285


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 CHEK1 (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
ChimerDB4ESCATCGA-L5-A4OWCTNNB1chr3

41241161

+CHEK1chr11

125496643

+


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Fusion Gene ORF analysis for CTNNB1-CHEK1

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
5UTR-3UTRENST00000349496ENST00000532449CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-3UTRENST00000396183ENST00000532449CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-3UTRENST00000396185ENST00000532449CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-3UTRENST00000453024ENST00000532449CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000349496ENST00000278916CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000349496ENST00000427383CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000349496ENST00000428830CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000349496ENST00000438015CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000349496ENST00000524737CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000349496ENST00000534070CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000349496ENST00000544373CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396183ENST00000278916CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396183ENST00000427383CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396183ENST00000428830CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396183ENST00000438015CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396183ENST00000524737CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396183ENST00000534070CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396183ENST00000544373CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396185ENST00000278916CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396185ENST00000427383CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396185ENST00000428830CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396185ENST00000438015CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396185ENST00000524737CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396185ENST00000534070CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000396185ENST00000544373CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000453024ENST00000278916CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000453024ENST00000427383CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000453024ENST00000428830CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000453024ENST00000438015CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000453024ENST00000524737CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000453024ENST00000534070CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
5UTR-5UTRENST00000453024ENST00000544373CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-3UTRENST00000405570ENST00000532449CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-3UTRENST00000471014ENST00000532449CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000405570ENST00000278916CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000405570ENST00000427383CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000405570ENST00000428830CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000405570ENST00000438015CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000405570ENST00000524737CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000405570ENST00000534070CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000405570ENST00000544373CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000471014ENST00000278916CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000471014ENST00000427383CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000471014ENST00000428830CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000471014ENST00000438015CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000471014ENST00000524737CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000471014ENST00000534070CTNNB1chr3

41241161

+CHEK1chr11

125496643

+
intron-5UTRENST00000471014ENST00000544373CTNNB1chr3

41241161

+CHEK1chr11

125496643

+

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-CHEK1


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)
CTNNB1chr341241161+CHEK1chr11125496642+3.66E-060.9999963
CTNNB1chr341241161+CHEK1chr11125496642+3.66E-060.9999963

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.
genomic feature of top 1%

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Fusion Protein Features for CTNNB1-CHEK1


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/:41241161/:125496643)
- 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

CHEK1

O14757

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: Serine/threonine-protein kinase which is required for checkpoint-mediated cell cycle arrest and activation of DNA repair in response to the presence of DNA damage or unreplicated DNA (PubMed:11535615, PubMed:12446774, PubMed:12399544, PubMed:14559997, PubMed:14988723, PubMed:15311285, PubMed:15665856, PubMed:15650047). May also negatively regulate cell cycle progression during unperturbed cell cycles (PubMed:11535615, PubMed:12446774, PubMed:12399544, PubMed:14559997, PubMed:14988723, PubMed:15311285, PubMed:15665856, PubMed:15650047). This regulation is achieved by a number of mechanisms that together help to preserve the integrity of the genome (PubMed:11535615, PubMed:12446774, PubMed:12399544, PubMed:14559997, PubMed:14988723, PubMed:15311285, PubMed:15665856, PubMed:15650047). Recognizes the substrate consensus sequence [R-X-X-S/T] (PubMed:11535615, PubMed:12446774, PubMed:12399544, PubMed:14559997, PubMed:14988723, PubMed:15311285, PubMed:15665856, PubMed:15650047). Binds to and phosphorylates CDC25A, CDC25B and CDC25C (PubMed:9278511, PubMed:12676583, PubMed:14681206, PubMed:12676925, PubMed:12759351, PubMed:19734889, PubMed:14559997). Phosphorylation of CDC25A at 'Ser-178' and 'Thr-507' and phosphorylation of CDC25C at 'Ser-216' creates binding sites for 14-3-3 proteins which inhibit CDC25A and CDC25C (PubMed:9278511). Phosphorylation of CDC25A at 'Ser-76', 'Ser-124', 'Ser-178', 'Ser-279' and 'Ser-293' promotes proteolysis of CDC25A (PubMed:9278511, PubMed:12676583, PubMed:14681206, PubMed:12676925, PubMed:12759351, PubMed:19734889). Phosphorylation of CDC25A at 'Ser-76' primes the protein for subsequent phosphorylation at 'Ser-79', 'Ser-82' and 'Ser-88' by NEK11, which is required for polyubiquitination and degradation of CDCD25A (PubMed:9278511, PubMed:19734889, PubMed:20090422). Inhibition of CDC25 leads to increased inhibitory tyrosine phosphorylation of CDK-cyclin complexes and blocks cell cycle progression (PubMed:9278511). Also phosphorylates NEK6 (PubMed:18728393). Binds to and phosphorylates RAD51 at 'Thr-309', which promotes the release of RAD51 from BRCA2 and enhances the association of RAD51 with chromatin, thereby promoting DNA repair by homologous recombination (PubMed:15665856). Phosphorylates multiple sites within the C-terminus of TP53, which promotes activation of TP53 by acetylation and promotes cell cycle arrest and suppression of cellular proliferation (PubMed:10673501, PubMed:15659650, PubMed:16511572). Also promotes repair of DNA cross-links through phosphorylation of FANCE (PubMed:17296736). Binds to and phosphorylates TLK1 at 'Ser-743', which prevents the TLK1-dependent phosphorylation of the chromatin assembly factor ASF1A (PubMed:12660173, PubMed:12955071). This may enhance chromatin assembly both in the presence or absence of DNA damage (PubMed:12660173, PubMed:12955071). May also play a role in replication fork maintenance through regulation of PCNA (PubMed:18451105). May regulate the transcription of genes that regulate cell-cycle progression through the phosphorylation of histones (By similarity). Phosphorylates histone H3.1 (to form H3T11ph), which leads to epigenetic inhibition of a subset of genes (By similarity). May also phosphorylate RB1 to promote its interaction with the E2F family of transcription factors and subsequent cell cycle arrest (PubMed:17380128). Phosphorylates SPRTN, promoting SPRTN recruitment to chromatin (PubMed:31316063). Reduces replication stress and activates the G2/M checkpoint, by phosphorylating and inactivating PABIR1/FAM122A and promoting the serine/threonine-protein phosphatase 2A-mediated dephosphorylation and stabilization of WEE1 levels and activity (PubMed:33108758). {ECO:0000250|UniProtKB:O35280, ECO:0000269|PubMed:10673501, ECO:0000269|PubMed:11535615, ECO:0000269|PubMed:12399544, ECO:0000269|PubMed:12446774, ECO:0000269|PubMed:12660173, ECO:0000269|PubMed:12676583, ECO:0000269|PubMed:12676925, ECO:0000269|PubMed:12759351, ECO:0000269|PubMed:12955071, ECO:0000269|PubMed:14559997, ECO:0000269|PubMed:14681206, ECO:0000269|PubMed:14988723, ECO:0000269|PubMed:15311285, ECO:0000269|PubMed:15650047, ECO:0000269|PubMed:15659650, ECO:0000269|PubMed:15665856, ECO:0000269|PubMed:16511572, ECO:0000269|PubMed:17296736, ECO:0000269|PubMed:17380128, ECO:0000269|PubMed:18451105, ECO:0000269|PubMed:18728393, ECO:0000269|PubMed:19734889, ECO:0000269|PubMed:20090422, ECO:0000269|PubMed:31316063, ECO:0000269|PubMed:33108758, ECO:0000269|PubMed:9278511}.; FUNCTION: [Isoform 2]: Endogenous repressor of isoform 1, interacts with, and antagonizes CHK1 to promote the S to G2/M phase transition. {ECO:0000269|PubMed:22184239}.

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-CHEK1


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-CHEK1


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-CHEK1


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-CHEK1


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