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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:CDKL5-SUV39H1 (FusionGDB2 ID:HG6792TG6839)

Fusion Gene Summary for CDKL5-SUV39H1

check button Fusion gene summary
Fusion gene informationFusion gene name: CDKL5-SUV39H1
Fusion gene ID: hg6792tg6839
HgeneTgene
Gene symbol

CDKL5

SUV39H1

Gene ID

6792

6839

Gene namecyclin dependent kinase like 5suppressor of variegation 3-9 homolog 1
SynonymsCFAP247|EIEE2|ISSX|STK9H3-K9-HMTase 1|KMT1A|MG44|SUV39H
Cytomap('CDKL5')('SUV39H1')

Xp22.13

Xp11.23

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase-like 5cyclin dependent kinase 5 transcriptserine/threonine kinase 9serine/threonine-protein kinase 9histone-lysine N-methyltransferase SUV39H1Su(var)3-9 homolog 1histone H3-K9 methyltransferase 1histone-lysine N-methyltransferase, H3 lysine-9 specific 1lysine N-methyltransferase 1Aposition-effect variegation 3-9 homolog
Modification date2020031520200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000379996, ENST00000379989, 
ENST00000463994, 
Fusion gene scores* DoF score7 X 6 X 3=1263 X 3 X 2=18
# samples 83
** MAII scorelog2(8/126*10)=-0.655351828612554
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CDKL5 [Title/Abstract] AND SUV39H1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDKL5(18443815)-SUV39H1(48564656), # samples:2
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
HgeneCDKL5

GO:0046777

protein autophosphorylation

16935860

HgeneCDKL5

GO:0099175

regulation of postsynapse organization

22922712

TgeneSUV39H1

GO:0000183

chromatin silencing at rDNA

18485871

TgeneSUV39H1

GO:0006974

cellular response to DNA damage stimulus

23509280

TgeneSUV39H1

GO:0071456

cellular response to hypoxia

21402781



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-CG-4437-01ACDKL5chrX

18443815

+SUV39H1chrX

48564656

+


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Fusion Gene ORF analysis for CDKL5-SUV39H1

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-3CDSENST00000379996ENST00000337852CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
5UTR-3CDSENST00000379996ENST00000376687CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
5UTR-3CDSENST00000379996ENST00000453214CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
5UTR-3UTRENST00000379996ENST00000482260CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
intron-3CDSENST00000379989ENST00000337852CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
intron-3CDSENST00000379989ENST00000376687CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
intron-3CDSENST00000379989ENST00000453214CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
intron-3CDSENST00000463994ENST00000337852CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
intron-3CDSENST00000463994ENST00000376687CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
intron-3CDSENST00000463994ENST00000453214CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
intron-3UTRENST00000379989ENST00000482260CDKL5chrX

18443815

+SUV39H1chrX

48564656

+
intron-3UTRENST00000463994ENST00000482260CDKL5chrX

18443815

+SUV39H1chrX

48564656

+

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 CDKL5-SUV39H1


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)
CDKL5chrX18443815+SUV39H1chrX48564655+1.08E-081
CDKL5chrX18443815+SUV39H1chrX48564655+1.08E-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 CDKL5-SUV39H1


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/:48564656)
- 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 CDKL5-SUV39H1


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 CDKL5-SUV39H1


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 CDKL5-SUV39H1


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 CDKL5-SUV39H1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCDKL5C1839333EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 223CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCDKL5C0037769West Syndrome2ORPHANET
HgeneCDKL5C0014544Epilepsy1CTD_human
HgeneCDKL5C0022333Jacksonian Seizure1CTD_human
HgeneCDKL5C0035372Rett Syndrome1CTD_human
HgeneCDKL5C0036572Seizures1CTD_human
HgeneCDKL5C0086237Epilepsy, Cryptogenic1CTD_human
HgeneCDKL5C0149958Complex partial seizures1CTD_human
HgeneCDKL5C0162635Angelman Syndrome1CTD_human;GENOMICS_ENGLAND
HgeneCDKL5C0234533Generalized seizures1CTD_human
HgeneCDKL5C0234535Clonic Seizures1CTD_human
HgeneCDKL5C0236018Aura1CTD_human
HgeneCDKL5C0270824Visual seizure1CTD_human
HgeneCDKL5C0270844Tonic Seizures1CTD_human
HgeneCDKL5C0270846Epileptic drop attack1CTD_human
HgeneCDKL5C0393706Early infantile epileptic encephalopathy with suppression bursts1ORPHANET
HgeneCDKL5C0422850Seizures, Somatosensory1CTD_human
HgeneCDKL5C0422852Seizures, Auditory1CTD_human
HgeneCDKL5C0422853Olfactory seizure1CTD_human
HgeneCDKL5C0422854Gustatory seizure1CTD_human
HgeneCDKL5C0422855Vertiginous seizure1CTD_human
HgeneCDKL5C0494475Tonic - clonic seizures1CTD_human
HgeneCDKL5C0751056Non-epileptic convulsion1CTD_human
HgeneCDKL5C0751110Single Seizure1CTD_human
HgeneCDKL5C0751111Awakening Epilepsy1CTD_human
HgeneCDKL5C0751123Atonic Absence Seizures1CTD_human
HgeneCDKL5C0751494Convulsive Seizures1CTD_human
HgeneCDKL5C0751495Seizures, Focal1CTD_human
HgeneCDKL5C0751496Seizures, Sensory1CTD_human
HgeneCDKL5C1535926Neurodevelopmental Disorders1CTD_human
HgeneCDKL5C2748910Rett Syndrome, Atypical1ORPHANET
HgeneCDKL5C3495874Nonepileptic Seizures1CTD_human
HgeneCDKL5C4048158Convulsions1CTD_human
HgeneCDKL5C4316903Absence Seizures1CTD_human
HgeneCDKL5C4317109Epileptic Seizures1CTD_human
HgeneCDKL5C4317123Myoclonic Seizures1CTD_human
HgeneCDKL5C4505436Generalized Absence Seizures1CTD_human
TgeneC0007621Neoplastic Cell Transformation1CTD_human
TgeneC0333704Chromosome Breaks1CTD_human
TgeneC0376628Chromosome Breakage1CTD_human