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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:TSC2-SYNGR3 (FusionGDB2 ID:93827)

Fusion Gene Summary for TSC2-SYNGR3

check button Fusion gene summary
Fusion gene informationFusion gene name: TSC2-SYNGR3
Fusion gene ID: 93827
HgeneTgene
Gene symbol

TSC2

SYNGR3

Gene ID

7249

9143

Gene nameTSC complex subunit 2synaptogyrin 3
SynonymsLAM|PPP1R160|TSC4-
Cytomap

16p13.3

16p13.3

Type of geneprotein-codingprotein-coding
Descriptiontuberinprotein phosphatase 1, regulatory subunit 160tuberous sclerosis 2 proteinsynaptogyrin-3
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000219476, ENST00000382538, 
ENST00000401874, ENST00000353929, 
ENST00000439673, ENST00000350773, 
ENST00000568454, ENST00000568366, 
ENST00000248121, ENST00000562045, 
Fusion gene scores* DoF score10 X 12 X 6=7201 X 1 X 1=1
# samples 121
** MAII scorelog2(12/720*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(1/1*10)=3.32192809488736
Context

PubMed: TSC2 [Title/Abstract] AND SYNGR3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTSC2(2120613)-SYNGR3(2041974), # 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 buttonFusion gene breakpoints across TSC2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SYNGR3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4KIRPTCGA-GL-7966TSC2chr16

2120613

+SYNGR3chr16

2041974

+


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Fusion Gene ORF analysis for TSC2-SYNGR3

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
intron-3CDSENST00000219476ENST00000248121TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-5UTRENST00000219476ENST00000562045TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-3CDSENST00000382538ENST00000248121TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-5UTRENST00000382538ENST00000562045TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-3CDSENST00000401874ENST00000248121TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-5UTRENST00000401874ENST00000562045TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-3CDSENST00000353929ENST00000248121TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-5UTRENST00000353929ENST00000562045TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-3CDSENST00000439673ENST00000248121TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-5UTRENST00000439673ENST00000562045TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-3CDSENST00000350773ENST00000248121TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-5UTRENST00000350773ENST00000562045TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-3CDSENST00000568454ENST00000248121TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-5UTRENST00000568454ENST00000562045TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-3CDSENST00000568366ENST00000248121TSC2chr16

2120613

+SYNGR3chr16

2041974

+
intron-5UTRENST00000568366ENST00000562045TSC2chr16

2120613

+SYNGR3chr16

2041974

+

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 TSC2-SYNGR3


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for TSC2-SYNGR3


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 TSC2-SYNGR3


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 TSC2-SYNGR3


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 TSC2-SYNGR3


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 TSC2-SYNGR3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTSC2C1860707TUBEROUS SCLEROSIS 2 (disorder)21CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTSC2C0041341Tuberous Sclerosis14CLINGEN;CTD_human;GENOMICS_ENGLAND
HgeneTSC2C1854465TUBEROUS SCLEROSIS 1 (disorder)6CLINGEN
HgeneTSC2C0751674Lymphangioleiomyomatosis5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneTSC2C0265319Fibrous skin tumor of tuberous sclerosis4CTD_human
HgeneTSC2C0022665Kidney Neoplasm3CTD_human
HgeneTSC2C0740457Malignant neoplasm of kidney3CTD_human
HgeneTSC2C1846385FOCAL CORTICAL DYSPLASIA OF TAYLOR3CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTSC2C0022333Jacksonian Seizure2CTD_human
HgeneTSC2C0036572Seizures2CTD_human
HgeneTSC2C0149958Complex partial seizures2CTD_human
HgeneTSC2C0234533Generalized seizures2CTD_human
HgeneTSC2C0234535Clonic Seizures2CTD_human
HgeneTSC2C0270824Visual seizure2CTD_human
HgeneTSC2C0270844Tonic Seizures2CTD_human
HgeneTSC2C0270846Epileptic drop attack2CTD_human
HgeneTSC2C0422850Seizures, Somatosensory2CTD_human
HgeneTSC2C0422852Seizures, Auditory2CTD_human
HgeneTSC2C0422853Olfactory seizure2CTD_human
HgeneTSC2C0422854Gustatory seizure2CTD_human
HgeneTSC2C0422855Vertiginous seizure2CTD_human
HgeneTSC2C0494475Tonic - clonic seizures2CTD_human
HgeneTSC2C0751056Non-epileptic convulsion2CTD_human
HgeneTSC2C0751110Single Seizure2CTD_human
HgeneTSC2C0751123Atonic Absence Seizures2CTD_human
HgeneTSC2C0751494Convulsive Seizures2CTD_human
HgeneTSC2C0751495Seizures, Focal2CTD_human
HgeneTSC2C0751496Seizures, Sensory2CTD_human
HgeneTSC2C1838327Polycystic kidneys, severe infantile with tuberous sclerosis2ORPHANET
HgeneTSC2C3495874Nonepileptic Seizures2CTD_human
HgeneTSC2C4048158Convulsions2CTD_human
HgeneTSC2C4316903Absence Seizures2CTD_human
HgeneTSC2C4317109Epileptic Seizures2CTD_human
HgeneTSC2C4317123Myoclonic Seizures2CTD_human
HgeneTSC2C4505436Generalized Absence Seizures2CTD_human
HgeneTSC2C0004352Autistic Disorder1CTD_human
HgeneTSC2C0006111Brain Diseases1CTD_human
HgeneTSC2C0007137Squamous cell carcinoma1CTD_human
HgeneTSC2C0014544Epilepsy1CTD_human
HgeneTSC2C0021368Inflammation1CTD_human
HgeneTSC2C0023267Fibroid Tumor1CTD_human
HgeneTSC2C0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneTSC2C0026640Mouth Neoplasms1CTD_human
HgeneTSC2C0026998Acute Myeloid Leukemia, M11CTD_human
HgeneTSC2C0027746Nerve Degeneration1CTD_human
HgeneTSC2C0030297Pancreatic Neoplasm1CTD_human
HgeneTSC2C0032927Precancerous Conditions1CTD_human
HgeneTSC2C0037769West Syndrome1CTD_human
HgeneTSC2C0042133Uterine Fibroids1CTD_human
HgeneTSC2C0085584Encephalopathies1CTD_human
HgeneTSC2C0086237Epilepsy, Cryptogenic1CTD_human
HgeneTSC2C0153381Malignant neoplasm of mouth1CTD_human
HgeneTSC2C0236018Aura1CTD_human
HgeneTSC2C0279607Adult Hepatocellular Carcinoma1ORPHANET
HgeneTSC2C0282313Condition, Preneoplastic1CTD_human
HgeneTSC2C0346647Malignant neoplasm of pancreas1CTD_human
HgeneTSC2C0393698Cryptogenic Infantile Spasms1CTD_human
HgeneTSC2C0393699Symptomatic Infantile Spasms1CTD_human
HgeneTSC2C0546878Nodding spasm1CTD_human
HgeneTSC2C0553558Jackknife Seizures1CTD_human
HgeneTSC2C0684276Hypsarrhythmia1CTD_human
HgeneTSC2C0751111Awakening Epilepsy1CTD_human
HgeneTSC2C1527306spasmus nutans1CTD_human
HgeneTSC2C1527366Salaam Seizures1CTD_human
HgeneTSC2C1846386Focal Cortical Dysplasia of Taylor, Type IIa1CTD_human
HgeneTSC2C1846389Focal Cortical Dysplasia of Taylor, Type IIb1CTD_human
HgeneTSC2C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human