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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:LPIN1-TBC1D7 (FusionGDB2 ID:49533)

Fusion Gene Summary for LPIN1-TBC1D7

check button Fusion gene summary
Fusion gene informationFusion gene name: LPIN1-TBC1D7
Fusion gene ID: 49533
HgeneTgene
Gene symbol

LPIN1

TBC1D7

Gene ID

23175

51256

Gene namelipin 1TBC1 domain family member 7
SynonymsPAP1MGCPH|PIG51|TBC7
Cytomap

2p25.1

6p24.1

Type of geneprotein-codingprotein-coding
Descriptionphosphatidate phosphatase LPIN1TBC1 domain family member 7TS complex subunit 3cell migration-inducing protein 23
Modification date2020031320200313
UniProtAcc

Q14693

.
Ensembl transtripts involved in fusion geneENST00000256720, ENST00000396098, 
ENST00000396099, ENST00000425416, 
ENST00000449576, ENST00000396097, 
ENST00000404113, ENST00000464517, 
ENST00000607532, ENST00000343141, 
ENST00000379307, ENST00000607658, 
ENST00000356436, ENST00000379300, 
Fusion gene scores* DoF score5 X 5 X 5=1254 X 3 X 3=36
# samples 54
** MAII scorelog2(5/125*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LPIN1 [Title/Abstract] AND TBC1D7 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLPIN1(11905859)-TBC1D7(13325406), # samples:1
Anticipated loss of major functional domain due to fusion event.LPIN1-TBC1D7 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
LPIN1-TBC1D7 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
LPIN1-TBC1D7 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
TgeneTBC1D7

GO:0031398

positive regulation of protein ubiquitination

17658474

TgeneTBC1D7

GO:0043547

positive regulation of GTPase activity

17646400


check buttonFusion gene breakpoints across LPIN1 (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 TBC1D7 (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
ChimerDB4BLCATCGA-HQ-A2OE-01ALPIN1chr2

11905859

+TBC1D7chr6

13325406

-


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Fusion Gene ORF analysis for LPIN1-TBC1D7

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-5UTRENST00000256720ENST00000607532LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-5UTRENST00000396098ENST00000607532LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-5UTRENST00000396099ENST00000607532LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-5UTRENST00000425416ENST00000607532LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-5UTRENST00000449576ENST00000607532LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000256720ENST00000343141LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000256720ENST00000379307LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000256720ENST00000607658LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000396098ENST00000343141LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000396098ENST00000379307LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000396098ENST00000607658LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000396099ENST00000343141LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000396099ENST00000379307LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000396099ENST00000607658LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000425416ENST00000343141LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000425416ENST00000379307LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000425416ENST00000607658LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000449576ENST00000343141LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000449576ENST00000379307LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
5CDS-intronENST00000449576ENST00000607658LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000256720ENST00000356436LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000256720ENST00000379300LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000396098ENST00000356436LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000396098ENST00000379300LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000396099ENST00000356436LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000396099ENST00000379300LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000425416ENST00000356436LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000425416ENST00000379300LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000449576ENST00000356436LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
Frame-shiftENST00000449576ENST00000379300LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-3CDSENST00000396097ENST00000356436LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-3CDSENST00000396097ENST00000379300LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-3CDSENST00000404113ENST00000356436LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-3CDSENST00000404113ENST00000379300LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-3CDSENST00000464517ENST00000356436LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-3CDSENST00000464517ENST00000379300LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-5UTRENST00000396097ENST00000607532LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-5UTRENST00000404113ENST00000607532LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-5UTRENST00000464517ENST00000607532LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000396097ENST00000343141LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000396097ENST00000379307LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000396097ENST00000607658LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000404113ENST00000343141LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000404113ENST00000379307LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000404113ENST00000607658LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000464517ENST00000343141LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000464517ENST00000379307LPIN1chr2

11905859

+TBC1D7chr6

13325406

-
intron-intronENST00000464517ENST00000607658LPIN1chr2

11905859

+TBC1D7chr6

13325406

-

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 LPIN1-TBC1D7


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 LPIN1-TBC1D7


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/:11905859/:13325406)
- 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
LPIN1

Q14693

.
FUNCTION: Acts as a magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis and therefore controls the metabolism of fatty acids at different levels (PubMed:20231281). Acts also as nuclear transcriptional coactivator for PPARGC1A/PPARA regulatory pathway to modulate lipid metabolism gene expression. Is involved in adipocyte differentiation. Isoform 1 is recruited at the mitochondrion outer membrane and is involved in mitochondrial fission by converting phosphatidic acid to diacylglycerol (By similarity). {ECO:0000250|UniProtKB:Q91ZP3, ECO:0000269|PubMed:20231281}.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 LPIN1-TBC1D7


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 LPIN1-TBC1D7


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 LPIN1-TBC1D7


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 LPIN1-TBC1D7


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource