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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:LDLR-ANGPTL4 (FusionGDB2 ID:HG3949TG51129)

Fusion Gene Summary for LDLR-ANGPTL4

check button Fusion gene summary
Fusion gene informationFusion gene name: LDLR-ANGPTL4
Fusion gene ID: hg3949tg51129
HgeneTgene
Gene symbol

LDLR

ANGPTL4

Gene ID

3949

51129

Gene namelow density lipoprotein receptorangiopoietin like 4
SynonymsFH|FHC|FHCL1|LDLCQ2ARP4|FIAF|HARP|HFARP|NL2|PGAR|TGQTL|UNQ171|pp1158
Cytomap('LDLR')('ANGPTL4')

19p13.2

19p13.2

Type of geneprotein-codingprotein-coding
Descriptionlow-density lipoprotein receptorLDL receptorlow-density lipoprotein receptor class A domain-containing protein 3angiopoietin-related protein 4PPARG angiopoietin related proteinfasting-induced adipose factorhepatic angiopoietin-related proteinhepatic fibrinogen/angiopoietin-related proteinperoxisome proliferator-activated receptor (PPAR) gamma induced angiopoie
Modification date2020032220200322
UniProtAcc

P01130

.
Ensembl transtripts involved in fusion geneENST00000455727, ENST00000535915, 
ENST00000545707, ENST00000557933, 
ENST00000558013, ENST00000558518, 
ENST00000560628, 
Fusion gene scores* DoF score23 X 17 X 15=58654 X 4 X 3=48
# samples 336
** MAII scorelog2(33/5865*10)=-4.15159317867005
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/48*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LDLR [Title/Abstract] AND ANGPTL4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLDLR(11200291)-ANGPTL4(8429090), # 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
TgeneANGPTL4

GO:0043066

negative regulation of apoptotic process

10698685

TgeneANGPTL4

GO:0043335

protein unfolding

29899144

TgeneANGPTL4

GO:0051005

negative regulation of lipoprotein lipase activity

19542565|29899144



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
ChimerDB4UCSTCGA-N9-A4Q8-01ALDLRchr19

11200291

+ANGPTL4chr19

8429090

+


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Fusion Gene ORF analysis for LDLR-ANGPTL4

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-5UTRENST00000455727ENST00000301455LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000455727ENST00000393962LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000455727ENST00000541807LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000535915ENST00000301455LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000535915ENST00000393962LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000535915ENST00000541807LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000545707ENST00000301455LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000545707ENST00000393962LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000545707ENST00000541807LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000557933ENST00000301455LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000557933ENST00000393962LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000557933ENST00000541807LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000558013ENST00000301455LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000558013ENST00000393962LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000558013ENST00000541807LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000558518ENST00000301455LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000558518ENST00000393962LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
5CDS-5UTRENST00000558518ENST00000541807LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
intron-5UTRENST00000560628ENST00000301455LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
intron-5UTRENST00000560628ENST00000393962LDLRchr19

11200291

+ANGPTL4chr19

8429090

+
intron-5UTRENST00000560628ENST00000541807LDLRchr19

11200291

+ANGPTL4chr19

8429090

+

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 LDLR-ANGPTL4


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 LDLR-ANGPTL4


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/:11200291/:8429090)
- 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
LDLR

P01130

.
FUNCTION: Binds LDL, the major cholesterol-carrying lipoprotein of plasma, and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. {ECO:0000269|PubMed:3005267, ECO:0000269|PubMed:6091915}.; FUNCTION: (Microbial infection) Acts as a receptor for hepatitis C virus in hepatocytes, but not through a direct interaction with viral proteins. {ECO:0000269|PubMed:10535997, ECO:0000269|PubMed:12615904}.; FUNCTION: (Microbial infection) Acts as a receptor for Vesicular stomatitis virus. {ECO:0000269|PubMed:23589850}.; FUNCTION: (Microbial infection) In case of HIV-1 infection, may function as a receptor for extracellular Tat in neurons, mediating its internalization in uninfected cells. {ECO:0000269|PubMed:11100124}.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 LDLR-ANGPTL4


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 LDLR-ANGPTL4


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 LDLR-ANGPTL4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneLDLRP01130DB00707Porfimer sodiumOther/unknownSmall moleculeApproved|Investigational

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Related Diseases for LDLR-ANGPTL4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLDLRC0745103Hyperlipoproteinemia Type IIa61CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneLDLRC0020445Hypercholesterolemia, Familial9CTD_human;GENOMICS_ENGLAND
HgeneLDLRC1704417Hyperlipoproteinemia Type IIb7CTD_human
HgeneLDLRC0020443Hypercholesterolemia6CTD_human;GENOMICS_ENGLAND
HgeneLDLRC0004153Atherosclerosis5CTD_human
HgeneLDLRC1563937Atherogenesis5CTD_human
HgeneLDLRC0400966Non-alcoholic Fatty Liver Disease3CTD_human
HgeneLDLRC3241937Nonalcoholic Steatohepatitis3CTD_human
HgeneLDLRC0010054Coronary Arteriosclerosis2CTD_human
HgeneLDLRC0020473Hyperlipidemia2CTD_human
HgeneLDLRC1706412Lipidemias2CTD_human
HgeneLDLRC1956346Coronary Artery Disease2CTD_human
HgeneLDLRC0010068Coronary heart disease1CTD_human
HgeneLDLRC0015695Fatty Liver1CTD_human
HgeneLDLRC0020507Hyperplasia1CTD_human
HgeneLDLRC0028754Obesity1CTD_human
HgeneLDLRC0034362Q Fever1CTD_human
HgeneLDLRC0085762Alcohol abuse1PSYGENET
HgeneLDLRC0242339Dyslipidemias1CTD_human
HgeneLDLRC0519066Acute Q fever1CTD_human
HgeneLDLRC0598784Dyslipoproteinemias1CTD_human
HgeneLDLRC1443892Chronic Q Fever1CTD_human
HgeneLDLRC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
HgeneLDLRC1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
HgeneLDLRC2711227Steatohepatitis1CTD_human
HgeneLDLRC2973787Coxiella burnetii Infection1CTD_human
HgeneLDLRC4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007097Carcinoma1CTD_human
TgeneC0010054Coronary Arteriosclerosis1CTD_human
TgeneC0015695Fatty Liver1CTD_human
TgeneC0020557Hypertriglyceridemia1CTD_human
TgeneC0024232Lymphatic Metastasis1CTD_human
TgeneC0027626Neoplasm Invasiveness1CTD_human
TgeneC0027627Neoplasm Metastasis1CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC0242339Dyslipidemias1CTD_human
TgeneC0598784Dyslipoproteinemias1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1956346Coronary Artery Disease1CTD_human
TgeneC2711227Steatohepatitis1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human