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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:GNL3L-GABRB3 (FusionGDB2 ID:HG54552TG2562)

Fusion Gene Summary for GNL3L-GABRB3

check button Fusion gene summary
Fusion gene informationFusion gene name: GNL3L-GABRB3
Fusion gene ID: hg54552tg2562
HgeneTgene
Gene symbol

GNL3L

GABRB3

Gene ID

54552

2562

Gene nameG protein nucleolar 3 likegamma-aminobutyric acid type A receptor subunit beta3
SynonymsGNL3BECA5|EIEE43
Cytomap('GNL3L')('GABRB3')

Xp11.22

15q12

Type of geneprotein-codingprotein-coding
Descriptionguanine nucleotide-binding protein-like 3-like proteinG protein nucleolar 3Bguanine nucleotide binding protein-like 3 (nucleolar)-likenovel GTPasegamma-aminobutyric acid receptor subunit beta-3GABA-alpha receptor beta-2 subunitGABAA receptor beta-3 subunitgamma-aminobutyric acid (GABA) A receptor, beta 3gamma-aminobutyric acid A receptor beta 3gamma-aminobutyric acid type A receptor beta3 subu
Modification date2020031320200320
UniProtAcc

Q9NVN8

P28472

Ensembl transtripts involved in fusion geneENST00000489691, ENST00000336470, 
ENST00000360845, 
Fusion gene scores* DoF score5 X 6 X 4=1206 X 5 X 3=90
# samples 76
** MAII scorelog2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GNL3L [Title/Abstract] AND GABRB3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGNL3L(54559018)-GABRB3(26828561), # samples:2
Anticipated loss of major functional domain due to fusion event.GNL3L-GABRB3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
GNL3L-GABRB3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* 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
HgeneGNL3L

GO:0031647

regulation of protein stability

19487455

HgeneGNL3L

GO:0032091

negative regulation of protein binding

19487455

HgeneGNL3L

GO:1904816

positive regulation of protein localization to chromosome, telomeric region

19487455

TgeneGABRB3

GO:0071420

cellular response to histamine

18281286

TgeneGABRB3

GO:1902476

chloride transmembrane transport

9039914

TgeneGABRB3

GO:1904862

inhibitory synapse assembly

25489750



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
ChimerDB4SARCTCGA-UE-A6QU-01AGNL3LchrX

54559018

-GABRB3chr15

26828561

-
ChimerDB4SARCTCGA-UE-A6QU-01AGNL3LchrX

54559018

+GABRB3chr15

26828561

-


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Fusion Gene ORF analysis for GNL3L-GABRB3

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
3UTR-3CDSENST00000489691ENST00000299267GNL3LchrX

54559018

+GABRB3chr15

26828561

-
3UTR-3CDSENST00000489691ENST00000311550GNL3LchrX

54559018

+GABRB3chr15

26828561

-
3UTR-3CDSENST00000489691ENST00000400188GNL3LchrX

54559018

+GABRB3chr15

26828561

-
3UTR-3CDSENST00000489691ENST00000541819GNL3LchrX

54559018

+GABRB3chr15

26828561

-
3UTR-3CDSENST00000489691ENST00000545868GNL3LchrX

54559018

+GABRB3chr15

26828561

-
3UTR-intronENST00000489691ENST00000557641GNL3LchrX

54559018

+GABRB3chr15

26828561

-
5CDS-intronENST00000336470ENST00000557641GNL3LchrX

54559018

+GABRB3chr15

26828561

-
5CDS-intronENST00000360845ENST00000557641GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000336470ENST00000299267GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000336470ENST00000311550GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000336470ENST00000400188GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000336470ENST00000541819GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000336470ENST00000545868GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000360845ENST00000299267GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000360845ENST00000311550GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000360845ENST00000400188GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000360845ENST00000541819GNL3LchrX

54559018

+GABRB3chr15

26828561

-
Frame-shiftENST00000360845ENST00000545868GNL3LchrX

54559018

+GABRB3chr15

26828561

-

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 GNL3L-GABRB3


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 GNL3L-GABRB3


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/:54559018/:26828561)
- 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
GNL3L

Q9NVN8

GABRB3

P28472

FUNCTION: Stabilizes TERF1 telomeric association by preventing TERF1 recruitment by PML. Stabilizes TERF1 protein by preventing its ubiquitination and hence proteasomal degradation. Does so by interfering with TERF1-binding to FBXO4 E3 ubiquitin-protein ligase. Required for cell proliferation. By stabilizing TRF1 protein during mitosis, promotes metaphase-to-anaphase transition. Stabilizes MDM2 protein by preventing its ubiquitination, and hence proteasomal degradation. By acting on MDM2, may affect TP53 activity. Required for normal processing of ribosomal pre-rRNA. Binds GTP. {ECO:0000269|PubMed:16251348, ECO:0000269|PubMed:17034816, ECO:0000269|PubMed:19487455, ECO:0000269|PubMed:21132010}.FUNCTION: Ligand-gated chloride channel which is a component of the heteropentameric receptor for GABA, the major inhibitory neurotransmitter in the brain (PubMed:18514161, PubMed:22303015, PubMed:26950270, PubMed:22243422, PubMed:24909990). Plays an important role in the formation of functional inhibitory GABAergic synapses in addition to mediating synaptic inhibition as a GABA-gated ion channel (PubMed:25489750). The gamma2 subunit is necessary but not sufficient for a rapid formation of active synaptic contacts and the synaptogenic effect of this subunit is influenced by the type of alpha and beta subunits present in the receptor pentamer (By similarity). The alpha1/beta3/gamma2 receptor exhibits synaptogenic activity (PubMed:25489750). The alpha2/beta3/gamma2 receptor shows very little or no synaptogenic activity (By similarity). Functions also as histamine receptor and mediates cellular responses to histamine (PubMed:18281286). Plays an important role in somatosensation and in the production of antinociception (By similarity). {ECO:0000250|UniProtKB:P63080, ECO:0000269|PubMed:18281286, ECO:0000269|PubMed:18514161, ECO:0000269|PubMed:22243422, ECO:0000269|PubMed:22303015, ECO:0000269|PubMed:24909990, ECO:0000269|PubMed:25489750, ECO:0000269|PubMed:26950270}.

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 GNL3L-GABRB3


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 GNL3L-GABRB3


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 GNL3L-GABRB3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneGABRB3P28472DB00898EthanolSmall moleculeApproved
TgeneGABRB3P28472DB06716FospropofolPotentiatorSmall moleculeApproved|Illicit|Investigational
TgeneGABRB3P28472DB00602IvermectinAgonistSmall moleculeApproved|Investigational|Vet_approved
TgeneGABRB3P28472DB00818PropofolPotentiatorSmall moleculeApproved|Investigational|Vet_approved
TgeneGABRB3P28472DB00592PiperazineAgonistSmall moleculeApproved|Vet_approved
TgeneGABRB3P28472DB00431LindaneSmall moleculeApproved|Withdrawn

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Related Diseases for GNL3L-GABRB3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC4310712EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 436CTD_human;UNIPROT
TgeneC0011570Mental Depression5PSYGENET
TgeneC0011581Depressive disorder5PSYGENET
TgeneC0001973Alcoholic Intoxication, Chronic4PSYGENET
TgeneC2677087EPILEPSY, CHILDHOOD ABSENCE, SUSCEPTIBILITY TO, 53GENOMICS_ENGLAND;UNIPROT
TgeneC0004352Autistic Disorder2CTD_human
TgeneC0005586Bipolar Disorder2PSYGENET
TgeneC0014544Epilepsy2CTD_human
TgeneC0036341Schizophrenia2PSYGENET
TgeneC0086237Epilepsy, Cryptogenic2CTD_human
TgeneC0236018Aura2CTD_human
TgeneC0238111Lennox-Gastaut syndrome2ORPHANET
TgeneC0751111Awakening Epilepsy2CTD_human
TgeneC0001890Akinetic Petit Mal1CTD_human
TgeneC0014553Absence Epilepsy1CTD_human
TgeneC0021603Sleep Initiation and Maintenance Disorders1CTD_human
TgeneC0033139Primary Insomnia1CTD_human
TgeneC0162635Angelman Syndrome1CTD_human
TgeneC0270541Rebound Insomnia1CTD_human
TgeneC0349255Nonorganic Insomnia1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0393759Transient Insomnia1CTD_human
TgeneC0541798Early Awakening1CTD_human
TgeneC0751124Epilepsy, Absence, Atypical1CTD_human
TgeneC0751249Chronic Insomnia1CTD_human
TgeneC0751250Psychophysiological Insomnia1CTD_human
TgeneC0751251Secondary Insomnia1CTD_human
TgeneC0751252Sleep Initiation Dysfunction1CTD_human
TgeneC0917801Sleeplessness1CTD_human
TgeneC1510586Autism Spectrum Disorders1CTD_human
TgeneC1535926Neurodevelopmental Disorders1CTD_human
TgeneC1838604EPILEPSY, CHILDHOOD ABSENCE, 11ORPHANET
TgeneC3711376Isodicentric Chromosome 15 Syndrome1CTD_human
TgeneC4281785Childhood Absence Epilepsy1CTD_human
TgeneC4317339Juvenile Absence Epilepsy1CTD_human
TgeneC4552765Epilepsy, Minor1CTD_human
TgeneC4553705Absence Seizure Disorder1CTD_human