Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:ATP13A3-LRRC15 (FusionGDB2 ID:HG79572TG131578)

Fusion Gene Summary for ATP13A3-LRRC15

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP13A3-LRRC15
Fusion gene ID: hg79572tg131578
HgeneTgene
Gene symbol

ATP13A3

LRRC15

Gene ID

79572

131578

Gene nameATPase 13A3leucine rich repeat containing 15
SynonymsAFURS1LIB
Cytomap('ATP13A3')('LRRC15')

3q29

3q29

Type of geneprotein-codingprotein-coding
Descriptionprobable cation-transporting ATPase 13A3ATPase family homolog up-regulated in senescence cells 1ATPase type 13A3leucine-rich repeat-containing protein 15hLibleucine-rich repeat protein induced by beta amyloidleucine-rich repeat protein induced by beta-amyloid homolog
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000256031, ENST00000439040, 
Fusion gene scores* DoF score7 X 10 X 5=3502 X 2 X 2=8
# samples 123
** MAII scorelog2(12/350*10)=-1.54432051622381
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/8*10)=1.90689059560852
Context

PubMed: ATP13A3 [Title/Abstract] AND LRRC15 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP13A3(194146071)-LRRC15(194084141), # samples:1
ATP13A3(194146070)-LRRC15(194081775), # samples:1
Anticipated loss of major functional domain due to fusion event.ATP13A3-LRRC15 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ATP13A3-LRRC15 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
ATP13A3-LRRC15 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ATP13A3-LRRC15 seems lost the major protein functional domain in Hgene 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

check buttonFusion gene breakpoints across ATP13A3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across LRRC15 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BRCATCGA-A2-A0ET-01AATP13A3chr3

194146071

-LRRC15chr3

194084141

-
ChimerDB4BRCATCGA-A2-A0ETATP13A3chr3

194146070

-LRRC15chr3

194081775

-


Top

Fusion Gene ORF analysis for ATP13A3-LRRC15

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
5CDS-5UTRENST00000256031ENST00000347624ATP13A3chr3

194146070

-LRRC15chr3

194081775

-
5CDS-5UTRENST00000256031ENST00000428839ATP13A3chr3

194146071

-LRRC15chr3

194084141

-
5CDS-5UTRENST00000256031ENST00000428839ATP13A3chr3

194146070

-LRRC15chr3

194081775

-
5CDS-5UTRENST00000439040ENST00000347624ATP13A3chr3

194146070

-LRRC15chr3

194081775

-
5CDS-5UTRENST00000439040ENST00000428839ATP13A3chr3

194146071

-LRRC15chr3

194084141

-
5CDS-5UTRENST00000439040ENST00000428839ATP13A3chr3

194146070

-LRRC15chr3

194081775

-
5CDS-intronENST00000256031ENST00000347624ATP13A3chr3

194146071

-LRRC15chr3

194084141

-
5CDS-intronENST00000256031ENST00000439944ATP13A3chr3

194146071

-LRRC15chr3

194084141

-
5CDS-intronENST00000439040ENST00000347624ATP13A3chr3

194146071

-LRRC15chr3

194084141

-
5CDS-intronENST00000439040ENST00000439944ATP13A3chr3

194146071

-LRRC15chr3

194084141

-
Frame-shiftENST00000256031ENST00000439944ATP13A3chr3

194146070

-LRRC15chr3

194081775

-
In-frameENST00000439040ENST00000439944ATP13A3chr3

194146070

-LRRC15chr3

194081775

-

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

Top

Fusion Genomic Features for ATP13A3-LRRC15


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.
genomic feature

Top

Fusion Protein Features for ATP13A3-LRRC15


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/chr3:194146071/chr3:194084141)
- 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
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-2932231_23411041227.0Compositional biasNote=Poly-Tyr
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-3033231_23411041227.0Compositional biasNote=Poly-Tyr
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-29321000_102011041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-29321074_109411041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-2932206_22611041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-2932233_25311041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-293229_4911041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-2932410_43011041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-2932449_46911041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-2932941_96111041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-2932963_98311041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-30331000_102011041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-30331074_109411041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-3033206_22611041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-3033233_25311041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-303329_4911041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-3033410_43011041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-3033449_46911041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-3033941_96111041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-3033963_98311041227.0TransmembraneHelical
TgeneLRRC15chr3:194146070chr3:194081775ENST000003476240222_530582.0DomainNote=LRRNT
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402423_4750582.0DomainNote=LRRCT
TgeneLRRC15chr3:194146070chr3:194081775ENST000004288391322_535588.0DomainNote=LRRNT
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913423_4755588.0DomainNote=LRRCT
TgeneLRRC15chr3:194146070chr3:194081775ENST000004399440222_535588.0DomainNote=LRRNT
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402423_4755588.0DomainNote=LRRCT
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402102_1230582.0RepeatNote=LRR 3
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402126_1470582.0RepeatNote=LRR 4
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402150_1710582.0RepeatNote=LRR 5
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402174_1950582.0RepeatNote=LRR 6
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402198_2190582.0RepeatNote=LRR 7
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402222_2430582.0RepeatNote=LRR 8
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402246_2670582.0RepeatNote=LRR 9
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402270_2910582.0RepeatNote=LRR 10
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402294_3150582.0RepeatNote=LRR 11
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402318_3390582.0RepeatNote=LRR 12
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402342_3630582.0RepeatNote=LRR 13
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402366_3870582.0RepeatNote=LRR 14
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402390_4110582.0RepeatNote=LRR 15
TgeneLRRC15chr3:194146070chr3:194081775ENST000003476240254_750582.0RepeatNote=LRR 1
TgeneLRRC15chr3:194146070chr3:194081775ENST000003476240278_990582.0RepeatNote=LRR 2
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913102_1235588.0RepeatNote=LRR 3
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913126_1475588.0RepeatNote=LRR 4
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913150_1715588.0RepeatNote=LRR 5
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913174_1955588.0RepeatNote=LRR 6
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913198_2195588.0RepeatNote=LRR 7
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913222_2435588.0RepeatNote=LRR 8
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913246_2675588.0RepeatNote=LRR 9
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913270_2915588.0RepeatNote=LRR 10
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913294_3155588.0RepeatNote=LRR 11
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913318_3395588.0RepeatNote=LRR 12
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913342_3635588.0RepeatNote=LRR 13
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913366_3875588.0RepeatNote=LRR 14
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913390_4115588.0RepeatNote=LRR 15
TgeneLRRC15chr3:194146070chr3:194081775ENST000004288391354_755588.0RepeatNote=LRR 1
TgeneLRRC15chr3:194146070chr3:194081775ENST000004288391378_995588.0RepeatNote=LRR 2
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402102_1235588.0RepeatNote=LRR 3
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402126_1475588.0RepeatNote=LRR 4
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402150_1715588.0RepeatNote=LRR 5
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402174_1955588.0RepeatNote=LRR 6
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402198_2195588.0RepeatNote=LRR 7
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402222_2435588.0RepeatNote=LRR 8
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402246_2675588.0RepeatNote=LRR 9
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402270_2915588.0RepeatNote=LRR 10
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402294_3155588.0RepeatNote=LRR 11
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402318_3395588.0RepeatNote=LRR 12
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402342_3635588.0RepeatNote=LRR 13
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402366_3875588.0RepeatNote=LRR 14
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402390_4115588.0RepeatNote=LRR 15
TgeneLRRC15chr3:194146070chr3:194081775ENST000004399440254_755588.0RepeatNote=LRR 1
TgeneLRRC15chr3:194146070chr3:194081775ENST000004399440278_995588.0RepeatNote=LRR 2
TgeneLRRC15chr3:194146070chr3:194081775ENST000003476240222_5380582.0Topological domainExtracellular
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402560_5810582.0Topological domainCytoplasmic
TgeneLRRC15chr3:194146070chr3:194081775ENST000004288391322_5385588.0Topological domainExtracellular
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913560_5815588.0Topological domainCytoplasmic
TgeneLRRC15chr3:194146070chr3:194081775ENST000004399440222_5385588.0Topological domainExtracellular
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402560_5815588.0Topological domainCytoplasmic
TgeneLRRC15chr3:194146070chr3:194081775ENST0000034762402539_5590582.0TransmembraneHelical
TgeneLRRC15chr3:194146070chr3:194081775ENST0000042883913539_5595588.0TransmembraneHelical
TgeneLRRC15chr3:194146070chr3:194081775ENST0000043994402539_5595588.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-29321106_112611041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000256031-29321144_116411041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-30331106_112611041227.0TransmembraneHelical
HgeneATP13A3chr3:194146070chr3:194081775ENST00000439040-30331144_116411041227.0TransmembraneHelical


Top

Fusion Gene Sequence for ATP13A3-LRRC15


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.

Top

Fusion Gene PPI Analysis for ATP13A3-LRRC15


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


Top

Related Drugs for ATP13A3-LRRC15


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for ATP13A3-LRRC15


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATP13A3C0340543Familial primary pulmonary hypertension1GENOMICS_ENGLAND
HgeneATP13A3C11509292-oxo-hept-3-ene-1,7-dioate hydratase activity1GENOMICS_ENGLAND