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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:CLK2-PPP1R12B (FusionGDB2 ID:HG1196TG4660)

Fusion Gene Summary for CLK2-PPP1R12B

check button Fusion gene summary
Fusion gene informationFusion gene name: CLK2-PPP1R12B
Fusion gene ID: hg1196tg4660
HgeneTgene
Gene symbol

CLK2

PPP1R12B

Gene ID

1196

4660

Gene nameCDC like kinase 2protein phosphatase 1 regulatory subunit 12B
Synonyms-MYPT2|PP1bp55
Cytomap('CLK2')('PPP1R12B')

1q22

1q32.1

Type of geneprotein-codingprotein-coding
Descriptiondual specificity protein kinase CLK2CLK kinaseprotein phosphatase 1 regulatory subunit 12Bmyosin phosphatase target subunit 2myosin phosphatase-targeting subunit 2protein phosphatase 1, regulatory (inhibitor) subunit 12B
Modification date2020032720200313
UniProtAcc

P49760

.
Ensembl transtripts involved in fusion geneENST00000355560, ENST00000361168, 
ENST00000368361, ENST00000497188, 
ENST00000536801, 
Fusion gene scores* DoF score5 X 6 X 5=15014 X 15 X 6=1260
# samples 616
** MAII scorelog2(6/150*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1260*10)=-2.97727992349992
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLK2 [Title/Abstract] AND PPP1R12B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLK2(155242992)-PPP1R12B(202457661), # samples:3
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
HgeneCLK2

GO:0006468

protein phosphorylation

9637771|20682768|28289210

HgeneCLK2

GO:0043484

regulation of RNA splicing

9637771



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
ChimerDB4STADTCGA-HU-8610-01ACLK2chr1

155242992

-PPP1R12Bchr1

202457661

+


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Fusion Gene ORF analysis for CLK2-PPP1R12B

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-3CDSENST00000355560ENST00000336894CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-3CDSENST00000355560ENST00000608999CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-3CDSENST00000361168ENST00000336894CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-3CDSENST00000361168ENST00000608999CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-3CDSENST00000368361ENST00000336894CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-3CDSENST00000368361ENST00000608999CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-3UTRENST00000355560ENST00000290419CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-3UTRENST00000361168ENST00000290419CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-3UTRENST00000368361ENST00000290419CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-5UTRENST00000355560ENST00000367270CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-5UTRENST00000355560ENST00000391959CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-5UTRENST00000361168ENST00000367270CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-5UTRENST00000361168ENST00000391959CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-5UTRENST00000368361ENST00000367270CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-5UTRENST00000368361ENST00000391959CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-intronENST00000355560ENST00000356764CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-intronENST00000355560ENST00000480184CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-intronENST00000361168ENST00000356764CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-intronENST00000361168ENST00000480184CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-intronENST00000368361ENST00000356764CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
5UTR-intronENST00000368361ENST00000480184CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-3CDSENST00000497188ENST00000336894CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-3CDSENST00000497188ENST00000608999CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-3CDSENST00000536801ENST00000336894CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-3CDSENST00000536801ENST00000608999CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-3UTRENST00000497188ENST00000290419CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-3UTRENST00000536801ENST00000290419CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-5UTRENST00000497188ENST00000367270CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-5UTRENST00000497188ENST00000391959CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-5UTRENST00000536801ENST00000367270CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-5UTRENST00000536801ENST00000391959CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-intronENST00000497188ENST00000356764CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-intronENST00000497188ENST00000480184CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-intronENST00000536801ENST00000356764CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+
intron-intronENST00000536801ENST00000480184CLK2chr1

155242992

-PPP1R12Bchr1

202457661

+

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 CLK2-PPP1R12B


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)
CLK2chr1155242991-PPP1R12Bchr1202457660+5.20E-081
CLK2chr1155242991-PPP1R12Bchr1202457660+5.20E-081


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 CLK2-PPP1R12B


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/:155242992/:202457661)
- 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
CLK2

P49760

.
FUNCTION: Dual specificity kinase acting on both serine/threonine and tyrosine-containing substrates. Phosphorylates serine- and arginine-rich (SR) proteins of the spliceosomal complex. May be a constituent of a network of regulatory mechanisms that enable SR proteins to control RNA splicing and can cause redistribution of SR proteins from speckles to a diffuse nucleoplasmic distribution. Acts as a suppressor of hepatic gluconeogenesis and glucose output by repressing PPARGC1A transcriptional activity on gluconeogenic genes via its phosphorylation. Phosphorylates PPP2R5B thereby stimulating the assembly of PP2A phosphatase with the PPP2R5B-AKT1 complex leading to dephosphorylation of AKT1. Phosphorylates: PTPN1, SRSF1 and SRSF3. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells. Phosphorylates PAGE4 at several serine and threonine residues and this phosphorylation attenuates the ability of PAGE4 to potentiate the transcriptional activator activity of JUN (PubMed:28289210). {ECO:0000269|PubMed:10480872, ECO:0000269|PubMed:19168442, ECO:0000269|PubMed:28289210, ECO:0000269|PubMed:8910305, ECO:0000269|PubMed:9637771}.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 CLK2-PPP1R12B


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 CLK2-PPP1R12B


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 CLK2-PPP1R12B


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCLK2P49760DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for CLK2-PPP1R12B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0027626Neoplasm Invasiveness1CTD_human
TgeneC0206692Carcinoma, Lobular1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human