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Center for Computational Systems Medicine
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Kinase Fusion Gene Summary

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Kinase Fusion Gene Sample Information

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Kinase Fusion ORF Analysis

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Kinase Fusion Amino Acid Sequences

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Multiple Sequence Alignment of All Fusion Protein Isoforms

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Kinase Fusion Protein Functional Features

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Kinase Fusion Protein Structures

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Comparison of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

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pLDDT Scores and Difference Analysis of pLDDT Scores Between the Active Sites (Best) and Non-Active Sites.

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Ramachandran Plot of Kinase Fusion Protein Structure

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Potential Active Site Information

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Virtual Screening Results

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Kinase-Substrate Information

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Related Drugs with This Kinase Fusion Protein

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Related Disease with This Kinase Fusion Protein

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Clinical Trials of the Found Drugs/Small Molecules

Kinase Fusion Gene:CDKL5_DGCR8

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: CDKL5_DGCR8
KinaseFusionDB ID: KFG1227
FusionGDB2.0 ID: KFG1227
HgeneTgene
Gene symbol

CDKL5

DGCR8

Gene ID

6792

54487

Gene namecyclin dependent kinase like 5DGCR8 microprocessor complex subunit
SynonymsCFAP247|DEE2|EIEE2|ISSX|STK9C22orf12|DGCRK6|Gy1|pasha
Cytomap

Xp22.13

22q11.21

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase-like 5cyclin dependent kinase 5 transcriptserine/threonine kinase 9serine/threonine-protein kinase 9microprocessor complex subunit DGCR8DiGeorge syndrome critical region 8DiGeorge syndrome critical region gene 8
Modification date2024041520240411
UniProtAcc

O76039

Q8WYQ5

Ensembl transtripts involved in fusion geneENST idsENST00000379996, ENST00000379989, 
ENST00000463994, 		ENST00000351989, 
ENST00000383024, ENST00000407755, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: CDKL5 [Title/Abstract] AND DGCR8 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CDKL5(18443815)-DGCR8(20093699), # samples:1
check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCDKL5

GO:0046777

protein autophosphorylation

16935860

HgeneCDKL5

GO:0050804

modulation of chemical synaptic transmission

22922712

HgeneCDKL5

GO:0099175

regulation of postsynapse organization

22922712

TgeneDGCR8

GO:0006974

DNA damage response

34188037

TgeneDGCR8

GO:0031053

primary miRNA processing

15531877|15574589

TgeneDGCR8

GO:0031053

primary miRNA processing

15574589|24449907|24910438

TgeneDGCR8

GO:2000633

positive regulation of pre-miRNA processing

15574589|32926445


check buttonKinase Fusion gene breakpoints across CDKL5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonKinase Fusion gene breakpoints across DGCR8 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.


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Kinase Fusion Gene Sample Information

check buttonKinase Fusion gene information.
check button Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE)
* 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.
SourceSampleHgeneHchrHbpTgeneTchrTbp
ChiTaRS5.0BI547806CDKL5chrX

18443815

DGCR8chr22

20093699



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Kinase Fusion ORF Analysis


check buttonKinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)		Seq length
(amino acids)

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Kinase Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq

Multiple Sequence Alignment of All Fusion Protein Isoforms



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Kinase Fusion Protein Functional Features


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/:18443815/:20093699)
- 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
CDKL5

O76039

DGCR8

Q8WYQ5

FUNCTION: Mediates phosphorylation of MECP2 (PubMed:15917271, PubMed:16935860). May regulate ciliogenesis (PubMed:29420175). {ECO:0000269|PubMed:15917271, ECO:0000269|PubMed:16935860, ECO:0000269|PubMed:29420175}.FUNCTION: Component of the microprocessor complex that acts as a RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, DGCR8 function as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11 bp away form the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs (PubMed:26027739, PubMed:26748718). The heme-bound DGCR8 dimer binds pri-miRNAs as a cooperative trimer (of dimers) and is active in triggering pri-miRNA cleavage, whereas the heme-free DGCR8 monomer binds pri-miRNAs as a dimer and is much less active. Both double-stranded and single-stranded regions of a pri-miRNA are required for its binding (PubMed:15531877, PubMed:15574589, PubMed:15589161, PubMed:16751099, PubMed:16906129, PubMed:16963499, PubMed:17159994). Specifically recognizes and binds N6-methyladenosine (m6A)-containing pri-miRNAs, a modification required for pri-miRNAs processing (PubMed:25799998). Involved in the silencing of embryonic stem cell self-renewal (By similarity). {ECO:0000250|UniProtKB:Q9EQM6, ECO:0000269|PubMed:15531877, ECO:0000269|PubMed:15574589, ECO:0000269|PubMed:15589161, ECO:0000269|PubMed:16751099, ECO:0000269|PubMed:16906129, ECO:0000269|PubMed:16963499, ECO:0000269|PubMed:17159994, ECO:0000269|PubMed:25799998, ECO:0000269|PubMed:26027739, ECO:0000269|PubMed:26748718}.

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.

check button - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


check button - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


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Kinase-Substrate Information of CDKL5_DGCR8


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
CDKL5O76039humanTNRC18O15417S660RDPERPEsAkAFGRE
CDKL5O76039humanMPLKIPQ8TAP9S40GGGPrPPsPrDGyGs
CDKL5O76039humanLRRC4CQ9HCJ2S631PLLIRMNsKDNVQET
CDKL5O76039humanMAPRE2Q15555S223stPsRPssAkRASSS
CDKL5O76039humanPPP1R26Q5T8A7T606GGHVRPStPKKMQEVPPP1R26_N
CDKL5O76039humanELOAQ14241S285EENRRPPsGDNAREK
CDKL5O76039humanHNRNPFP52597T215GPyDrPGtArryIGI
CDKL5O76039humanZC3H14Q6PJT7T734LkWIRPQtsE_____
CDKL5O76039humanRPL13P26373S52RIAPRPAsGPIRPIVRibosomal_L13e
CDKL5O76039humanCEP131Q9UPN4S35PVSRRPGsAATTkPI
CDKL5O76039humanPHF23Q9BUL5S400RLGGPPKsGEP____
CDKL5O76039humanZKSCAN8Q15776S141DILGRPVsARVHGHR
CDKL5O76039humanYLPM1P49750S1089GLVrPGssREKVPGG
CDKL5O76039humanVIRMAQ69YN4S1759LPPLRPLsSTGYRPs
CDKL5O76039humanCDKL5O76039Y171NNANytEyVATRWYRPkinase
CDKL5O76039humanYLPM1P49750S1088rGLVrPGssREKVPG
CDKL5O76039humanRBMXP38159S261DyPsrGysDrDGyGR
CDKL5O76039humanZNF592Q92610S1100NHLKRPVsGVGDAPG
CDKL5O76039humanMAP1SQ66K74S900DrAsRPLsARsEPsE
CDKL5O76039humanCDKL5O76039T169EGNNANytEyVATRWPkinase
CDKL5O76039humanMAP1AP78559S900GtIsPtssLEEDKGF
CDKL5O76039humanDLG5Q8TDM6S1115QKRRRPKsAPSFRPK
CDKL5O76039humanSMTNP53814S139LYSGRPNsGSREDSK
CDKL5O76039humanCLSPNQ9HAW4S1246FEAIRPGsAQQVKTG
CDKL5O76039humanTCOF1Q13428S801PAAARAPsAKGtISATreacle
CDKL5O76039humanEP400Q96L91S729sPVNRPssAtNkALs


check button Biological Network Integration of This Kinase and Substrates
(GeneMANIA website)

check button Enriched GO biological processes of the phosphorylation target genes of the kinase
KinaseGOIDGO termP.adjust
CDKL5IDDescription0.00e+00
CDKL5GO:0072698protein localization to microtubule cytoskeleton8.83e-03
CDKL5GO:0044380protein localization to cytoskeleton8.83e-03
CDKL5GO:0098840protein transport along microtubule1.13e-02
CDKL5GO:0099118microtubule-based protein transport1.13e-02
CDKL5GO:0016358dendrite development1.13e-02
CDKL5GO:0031110regulation of microtubule polymerization or depolymerization1.13e-02
CDKL5GO:0032886regulation of microtubule-based process1.13e-02
CDKL5GO:0035372protein localization to microtubule1.13e-02
CDKL5GO:0050686negative regulation of mRNA processing1.57e-02
CDKL5GO:0043244regulation of protein-containing complex disassembly1.57e-02
CDKL5GO:0031109microtubule polymerization or depolymerization1.83e-02
CDKL5GO:0031114regulation of microtubule depolymerization1.90e-02
CDKL5GO:0070507regulation of microtubule cytoskeleton organization2.64e-02
CDKL5GO:0060999positive regulation of dendritic spine development2.76e-02
CDKL5GO:0010970transport along microtubule2.82e-02
CDKL5GO:0007019microtubule depolymerization3.21e-02
CDKL5GO:0007409axonogenesis3.91e-02
CDKL5GO:0030705cytoskeleton-dependent intracellular transport3.91e-02
CDKL5GO:0099111microtubule-based transport3.91e-02
CDKL5GO:0031124mRNA 3'-end processing3.91e-02
CDKL5GO:0060998regulation of dendritic spine development3.91e-02
CDKL5GO:0022411cellular component disassembly4.47e-02
CDKL5GO:0032984protein-containing complex disassembly4.97e-02
CDKL5GO:1901879regulation of protein depolymerization7.67e-02
CDKL5GO:0060996dendritic spine development8.94e-02
CDKL5GO:1903312negative regulation of mRNA metabolic process9.31e-02
CDKL5GO:0031123RNA 3'-end processing9.50e-02
CDKL5GO:1902414protein localization to cell junction1.02e-01
CDKL5GO:0051261protein depolymerization1.12e-01
CDKL5GO:0001578microtubule bundle formation1.27e-01
CDKL5GO:0050684regulation of mRNA processing1.30e-01
CDKL5GO:0033314mitotic DNA replication checkpoint signaling1.37e-01
CDKL5GO:0035332positive regulation of hippo signaling1.37e-01
CDKL5GO:0072205metanephric collecting duct development1.37e-01
CDKL5GO:0007018microtubule-based movement1.37e-01
CDKL5GO:1905383protein localization to presynapse1.37e-01
CDKL5GO:0031440regulation of mRNA 3'-end processing1.37e-01
CDKL5GO:0034454microtubule anchoring at centrosome1.37e-01
CDKL5GO:0051549positive regulation of keratinocyte migration1.37e-01
CDKL5GO:1990535neuron projection maintenance1.37e-01
CDKL5GO:0050770regulation of axonogenesis1.37e-01
CDKL5GO:0034333adherens junction assembly1.37e-01
CDKL5GO:0035331negative regulation of hippo signaling1.37e-01
CDKL5GO:1902902negative regulation of autophagosome assembly1.37e-01
CDKL5GO:0043967histone H4 acetylation1.37e-01
CDKL5GO:0051547regulation of keratinocyte migration1.37e-01
CDKL5GO:0072393microtubule anchoring at microtubule organizing center1.37e-01
CDKL5GO:0014029neural crest formation1.37e-01
CDKL5GO:0045176apical protein localization1.37e-01

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Related Drugs to CDKL5_DGCR8


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

check button Distribution of the number of studies mentioning CDKL5-DGCR8 and kinase inhibitors the PubMed Abstract (04-01-2024)

Fusion gene - drug pair 1Fusion gene - drug pair 2PMIDPublication dateDOIStudy title

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Related Diseases to CDKL5_DGCR8


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Related diseases from the literature mentioned this fusion gene and drug.
(PubMed, 04-01-2024)
MeSH IDMeSH term

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


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Clinical Trials of the Found Drugs/Small Molecules


check button Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024)

check button Clinical Trials from clinicaltrials.gov (06-17-2024)

Fusion GeneKinase InhibitorNCT IDStudy StatusPhasesDisease# EnrolmentDate