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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:CCNYL2-TSC2 (FusionGDB2 ID:HG414194TG7249)

Fusion Gene Summary for CCNYL2-TSC2

check button Fusion gene summary
Fusion gene informationFusion gene name: CCNYL2-TSC2
Fusion gene ID: hg414194tg7249
HgeneTgene
Gene symbol

CCNYL2

TSC2

Gene ID

414194

7249

Gene nameTSC complex subunit 2
SynonymsLAM|PPP1R160|TSC4
Cytomap('CCNYL2')('TSC2')

16p13.3

Type of geneprotein-coding
Descriptiontuberinprotein phosphatase 1, regulatory subunit 160tuberous sclerosis 2 protein
Modification date20200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000483242, 
Fusion gene scores* DoF score1 X 1 X 1=16 X 9 X 4=216
# samples 18
** MAII scorelog2(1/1*10)=3.32192809488736log2(8/216*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CCNYL2 [Title/Abstract] AND TSC2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCCNYL2(42916211)-TSC2(2108748), # 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


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
ChimerDB4TGCTTCGA-2G-AAG5-01ACCNYL2chr10

42916211

-TSC2chr16

2108748

+


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Fusion Gene ORF analysis for CCNYL2-TSC2

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-3CDSENST00000483242ENST00000219476CCNYL2chr10

42916211

-TSC2chr16

2108748

+
5UTR-3CDSENST00000483242ENST00000350773CCNYL2chr10

42916211

-TSC2chr16

2108748

+
5UTR-3CDSENST00000483242ENST00000353929CCNYL2chr10

42916211

-TSC2chr16

2108748

+
5UTR-3CDSENST00000483242ENST00000382538CCNYL2chr10

42916211

-TSC2chr16

2108748

+
5UTR-3CDSENST00000483242ENST00000401874CCNYL2chr10

42916211

-TSC2chr16

2108748

+
5UTR-3CDSENST00000483242ENST00000439673CCNYL2chr10

42916211

-TSC2chr16

2108748

+
5UTR-3CDSENST00000483242ENST00000568454CCNYL2chr10

42916211

-TSC2chr16

2108748

+
5UTR-intronENST00000483242ENST00000568366CCNYL2chr10

42916211

-TSC2chr16

2108748

+

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 CCNYL2-TSC2


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)
CCNYL2chr1042916210-TSC2chr162108747+0.88142490.11857514
CCNYL2chr1042916210-TSC2chr162108747+0.88142490.11857514


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 CCNYL2-TSC2


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/:42916211/:2108748)
- 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 CCNYL2-TSC2


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 CCNYL2-TSC2


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 CCNYL2-TSC2


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 CCNYL2-TSC2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1860707TUBEROUS SCLEROSIS 2 (disorder)21CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0041341Tuberous Sclerosis14CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneC1854465TUBEROUS SCLEROSIS 1 (disorder)6CLINGEN
TgeneC0751674Lymphangioleiomyomatosis5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0265319Fibrous skin tumor of tuberous sclerosis4CTD_human
TgeneC0022665Kidney Neoplasm3CTD_human
TgeneC0740457Malignant neoplasm of kidney3CTD_human
TgeneC1846385FOCAL CORTICAL DYSPLASIA OF TAYLOR3CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0022333Jacksonian Seizure2CTD_human
TgeneC0036572Seizures2CTD_human
TgeneC0149958Complex partial seizures2CTD_human
TgeneC0234533Generalized seizures2CTD_human
TgeneC0234535Clonic Seizures2CTD_human
TgeneC0270824Visual seizure2CTD_human
TgeneC0270844Tonic Seizures2CTD_human
TgeneC0270846Epileptic drop attack2CTD_human
TgeneC0422850Seizures, Somatosensory2CTD_human
TgeneC0422852Seizures, Auditory2CTD_human
TgeneC0422853Olfactory seizure2CTD_human
TgeneC0422854Gustatory seizure2CTD_human
TgeneC0422855Vertiginous seizure2CTD_human
TgeneC0494475Tonic - clonic seizures2CTD_human
TgeneC0751056Non-epileptic convulsion2CTD_human
TgeneC0751110Single Seizure2CTD_human
TgeneC0751123Atonic Absence Seizures2CTD_human
TgeneC0751494Convulsive Seizures2CTD_human
TgeneC0751495Seizures, Focal2CTD_human
TgeneC0751496Seizures, Sensory2CTD_human
TgeneC1838327Polycystic kidneys, severe infantile with tuberous sclerosis2ORPHANET
TgeneC3495874Nonepileptic Seizures2CTD_human
TgeneC4048158Convulsions2CTD_human
TgeneC4316903Absence Seizures2CTD_human
TgeneC4317109Epileptic Seizures2CTD_human
TgeneC4317123Myoclonic Seizures2CTD_human
TgeneC4505436Generalized Absence Seizures2CTD_human
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0006111Brain Diseases1CTD_human
TgeneC0007137Squamous cell carcinoma1CTD_human
TgeneC0014544Epilepsy1CTD_human
TgeneC0021368Inflammation1CTD_human
TgeneC0023267Fibroid Tumor1CTD_human
TgeneC0023467Leukemia, Myelocytic, Acute1CTD_human
TgeneC0026640Mouth Neoplasms1CTD_human
TgeneC0026998Acute Myeloid Leukemia, M11CTD_human
TgeneC0027746Nerve Degeneration1CTD_human
TgeneC0030297Pancreatic Neoplasm1CTD_human
TgeneC0032927Precancerous Conditions1CTD_human
TgeneC0037769West Syndrome1CTD_human
TgeneC0042133Uterine Fibroids1CTD_human
TgeneC0085584Encephalopathies1CTD_human
TgeneC0086237Epilepsy, Cryptogenic1CTD_human
TgeneC0153381Malignant neoplasm of mouth1CTD_human
TgeneC0236018Aura1CTD_human
TgeneC0279607Adult Hepatocellular Carcinoma1ORPHANET
TgeneC0282313Condition, Preneoplastic1CTD_human
TgeneC0346647Malignant neoplasm of pancreas1CTD_human
TgeneC0393698Cryptogenic Infantile Spasms1CTD_human
TgeneC0393699Symptomatic Infantile Spasms1CTD_human
TgeneC0546878Nodding spasm1CTD_human
TgeneC0553558Jackknife Seizures1CTD_human
TgeneC0684276Hypsarrhythmia1CTD_human
TgeneC0751111Awakening Epilepsy1CTD_human
TgeneC1527306spasmus nutans1CTD_human
TgeneC1527366Salaam Seizures1CTD_human
TgeneC1846386Focal Cortical Dysplasia of Taylor, Type IIa1CTD_human
TgeneC1846389Focal Cortical Dysplasia of Taylor, Type IIb1CTD_human
TgeneC1879321Acute Myeloid Leukemia (AML-M2)1CTD_human