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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:CDKL3-NF2 (FusionGDB2 ID:HG51265TG4771)

Fusion Gene Summary for CDKL3-NF2

check button Fusion gene summary
Fusion gene informationFusion gene name: CDKL3-NF2
Fusion gene ID: hg51265tg4771
HgeneTgene
Gene symbol

CDKL3

NF2

Gene ID

51265

4771

Gene namecyclin dependent kinase like 3neurofibromin 2
SynonymsNKIAMREACN|BANF|SCH
Cytomap('CDKL3')('NF2')

5q31.1

22q12.2

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase-like 3serine-threonine protein kinase NKIAMREmerlinmoesin-ezrin-radixin likemoesin-ezrin-radixin-like proteinmoesin-ezrin-radizin-like proteinneurofibromin 2 (bilateral acoustic neuroma)schwannomerlinschwannomin
Modification date2020031320200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000265334, ENST00000435211, 
ENST00000435240, ENST00000521118, 
ENST00000521755, ENST00000522501, 
ENST00000523054, ENST00000523832, 
ENST00000536186, ENST00000609383, 
ENST00000609654, 
Fusion gene scores* DoF score5 X 5 X 3=7515 X 13 X 7=1365
# samples 517
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1365*10)=-3.00529429966951
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CDKL3 [Title/Abstract] AND NF2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDKL3(133621536)-NF2(30046837), # 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
TgeneNF2

GO:0008285

negative regulation of cell proliferation

12444102|20178741

TgeneNF2

GO:0022408

negative regulation of cell-cell adhesion

17210637

TgeneNF2

GO:0042532

negative regulation of tyrosine phosphorylation of STAT protein

12444102

TgeneNF2

GO:0046426

negative regulation of JAK-STAT cascade

12444102



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


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Fusion Gene ORF analysis for CDKL3-NF2

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

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 CDKL3-NF2


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 CDKL3-NF2


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/:133621536/:30046837)
- 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
..
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}.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 CDKL3-NF2


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 CDKL3-NF2


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 CDKL3-NF2


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 CDKL3-NF2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0027832Neurofibromatosis 228CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0025500Mesothelioma6CTD_human
TgeneC0345967Malignant mesothelioma5CTD_human
TgeneC0025286Meningioma2CGI;CTD_human;ORPHANET
TgeneC3551915MENINGIOMA, FAMILIAL, SUSCEPTIBILITY TO2GENOMICS_ENGLAND
TgeneC4048809SCHWANNOMATOSIS 12CTD_human;GENOMICS_ENGLAND
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0027859Acoustic Neuroma1GENOMICS_ENGLAND
TgeneC0032229Pleural Neoplasms1CTD_human
TgeneC0205834Meningiomas, Multiple1CTD_human
TgeneC0259785Malignant Meningioma1CTD_human
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneC0281784Benign Meningioma1CTD_human
TgeneC0334605Meningothelial meningioma1CTD_human
TgeneC0334606Fibrous Meningioma1CTD_human
TgeneC0334607Psammomatous Meningioma1CTD_human
TgeneC0334608Angiomatous Meningioma1CTD_human
TgeneC0334609Hemangioblastic Meningioma1CTD_human
TgeneC0334610Hemangiopericytic Meningioma1CTD_human
TgeneC0334611Transitional Meningioma1CTD_human
TgeneC0347515Spinal Meningioma1CTD_human
TgeneC0349604Intracranial Meningioma1CTD_human
TgeneC0431121Clear Cell Meningioma1CTD_human
TgeneC0457190Xanthomatous Meningioma1CTD_human
TgeneC0751303Cerebral Convexity Meningioma1CTD_human
TgeneC0751304Parasagittal Meningioma1CTD_human
TgeneC0917817Neurofibromatosis 31ORPHANET
TgeneC1136041Familial Acoustic Neuroma1CTD_human
TgeneC1136042Neuroma, Acoustic, Bilateral1CTD_human
TgeneC1136043Schwannoma, Acoustic, Bilateral1CTD_human
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC1334261Intraorbital Meningioma1CTD_human
TgeneC1334271Intraventricular Meningioma1CTD_human
TgeneC1335107Olfactory Groove Meningioma1CTD_human
TgeneC1335929Schwannomatosis1CTD_human;ORPHANET
TgeneC1384406Secretory meningioma1CTD_human
TgeneC1384408Microcystic meningioma1CTD_human
TgeneC1527197Angioblastic Meningioma1CTD_human
TgeneC1565950Posterior Fossa Meningioma1CTD_human
TgeneC1565951Sphenoid Wing Meningioma1CTD_human
TgeneC2931480Neurofibromatosis, Type 3, mixed central and peripheral1ORPHANET
TgeneC3163622Papillary Meningioma1CTD_human