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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:APOL1-LYPD3 (FusionGDB2 ID:HG8542TG27076)

Fusion Gene Summary for APOL1-LYPD3

check button Fusion gene summary
Fusion gene informationFusion gene name: APOL1-LYPD3
Fusion gene ID: hg8542tg27076
HgeneTgene
Gene symbol

APOL1

LYPD3

Gene ID

8542

27076

Gene nameapolipoprotein L1LY6/PLAUR domain containing 3
SynonymsAPO-L|APOL|APOL-I|FSGS4C4.4A
Cytomap('APOL1')('LYPD3')

22q12.3

19q13.31

Type of geneprotein-codingprotein-coding
Descriptionapolipoprotein L1apolipoprotein L 1apolipoprotein L1-B3ly6/PLAUR domain-containing protein 32310061G07RikGPI-anchored metastasis-associated protein C4.4A homologGPI-anchored metastasis-associated protein homologMIG-C4matrigel-induced gene C4 protein
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000319136, ENST00000347595, 
ENST00000397279, ENST00000422706, 
ENST00000426053, ENST00000397278, 
ENST00000440669, 
Fusion gene scores* DoF score3 X 3 X 1=91 X 1 X 1=1
# samples 31
** MAII scorelog2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(1/1*10)=3.32192809488736
Context

PubMed: APOL1 [Title/Abstract] AND LYPD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPOL1(36661664)-LYPD3(43965849), # samples:1
Anticipated loss of major functional domain due to fusion event.APOL1-LYPD3 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.
APOL1-LYPD3 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.
APOL1-LYPD3 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneAPOL1

GO:0045087

innate immune response

17192540

HgeneAPOL1

GO:0051838

cytolysis by host of symbiont cells

12621437|17192540

HgeneAPOL1

GO:1902476

chloride transmembrane transport

16020735


check buttonFusion gene breakpoints across APOL1 (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 LYPD3 (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


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Fusion Gene ORF analysis for APOL1-LYPD3

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

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
ENST00000397278ENST00000244333APOL1chr2236661664+LYPD3chr1943965849+0.0027048590.9972951

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Fusion Genomic Features for APOL1-LYPD3


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

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Fusion Protein Features for APOL1-LYPD3


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/chr22:36661664/chr19:43965849)
- 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
TgeneLYPD3chr22:36661664chr19:43965849ENST0000024433305140_2220347.0DomainNote=UPAR/Ly6 2
TgeneLYPD3chr22:36661664chr19:43965849ENST000002443330533_1260347.0DomainNote=UPAR/Ly6 1

- 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 APOL1-LYPD3


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.
>5609_5609_1_APOL1-LYPD3_APOL1_chr22_36661664_ENST00000397278_LYPD3_chr19_43965849_ENST00000244333_length(transcript)=3361nt_BP=2450nt
TGGACTGAAGGTGGAGGGGAGCGTGTTTGCTGTGCTTGGTCATGAGCTGCTGGGAAGTTGTGACTTTCACTTTCCCTTTCGAATTCCTCG
GTATATCTTGGGGACTGGAGGACCTGTCTGGTTATTATACAGACGCATAACTGGAGGTGGGATCCACACAGCTCAGAACAGCTGGATCTT
GCTCAGTCTCTGCCAGGGGAAGATTCCTTGGAGGAGGCCCTGCAGCGACATGGAGGGAGCTGCTTTGCTGAGAGTCTCTGTCCTCTGCAT
CTGGATGAGTGCACTTTTCCTTGGTGTGGGAGTGAGGGCAGAGGAAGCTGGAGCGAGGGTGCAACAAAACGTTCCAAGTGGGACAGATAC
TGGAGATCCTCAAAGTAAGCCCCTCGGTGACTGGGCTGCTGGCACCATGGACCCAGAGAGCAGTATCTTTATTGAGGATGCCATTAAGTA
TTTCAAGGAAAAAGTGAGCACACAGAATCTGCTACTCCTGCTGACTGATAATGAGGCCTGGAACGGATTCGTGGCTGCTGCTGAACTGCC
CAGCATATCCAACTTTCTTTCCTTAGCTGGCAATACTTACCAACTCACACGAGGCATTGGGAAGGACATCCGTGCCCTCAGACGAGCCAG
AGCCAATCTTCAGTCAGTACCGCATGCCTCAGCCTCACGCCCCCGGGTCACTGAGCCAATCTCAGCTGAAAGCGGTGAACAGGTGGAGAG
GGTTAATGAACCCAGCATCCTGGAAATGAGCAGAGGAGTCAAGCTCACGGATGTGGCCCCTGTAAGCTTCTTTCTTGTGCTGGATGTAGT
CTACCTCGTGTACGAATCAAAGCACTTACATGAGGGGGCAAAGTCAGAGACAGCTGAGGAGCTGAAGAAGGTGGCTCAGGAGCTGGAGGA
GAAGCTAAACATTCTCAACAATAATTATAAGATTCTGCAGGCGGACCAAGAACTGTGACCACAGGGCAGGGCAGCCACCAGGAGAGATAT
GCCTGGCAGGGGCCAGGACAAAATGCAAACTTTTTTTTTTTTCTGAGACAGAGTCTTGCTCTGTCGCCAAGTTGGAGTGCAATGGTGCGA
TCTCAGCTCACTGCAAGCTCTGCCTCCCGTGTTCAAGCGATTCTCCTGCCTTGGCCTCCCAAGTAGCTGGGACTACAGGCGCCTACCACC
ATGCCCAGCTAATTTTTGTATTTTTAATAGAGATGGGGTTTCACCATGTTGGCCAGGATGGTCTCGATCTCCTGACCTCTTGATCTGCCC
ACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCATCGCTTTTGACCCAAATGCAAACATTTTATTAGGGGGATAAAGAGGGTG
AGGTAAAGTTTATGGAACTGAGTGTTAGGGACTTTGGCATTTCCATAGCTGAGCACAGCAGGGGAGGGGTTAATGCAGATGGCAGTGCAG
CAAGGAGAAGGCAGGAACATTGGAGCCTGCAATAAGGGAAAAATGGGAACTGGAGAGTGTGGGGAATGGGAAGAAGCAGTTTACTTTAGA
CTAAAGAATATATTGGGGGGCCGGGTGTAGTGGCTCATGCCTGTAATCCGAGCACTTTGGGAGGCCAAGGCGGGCGGATCACGAGGTCAG
GAGATCGAGACCATCCTGGCTAACACAGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCATGGTGGCGGGCGCCTGTAG
TTCCAGCTAACTGGGCGGCTGAGGCAGGAGAATGGCGTGAACCTGGGAGGTGGAGCTTGCAGTGAGCCGAGATATCGCCACTGCACTCCA
GCCTGGGTGACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAAAGAATATATTGACGGAAGAATAGAGAGGAGGCTTGAAGGAACCAG
CAATGAGAAGGCCAGGAAAAGAAAGAGCTGAAAATGGAGAAAGCCCAAGAGTTAGAACAGTTGGATACAGGAGAAGAAACAGCGGCTCCA
CTACAGACCCAGCCCCAGGTTCAATGTCCTCCGAAGAATGAAGTCTTTCCCTGGTGATGGTCCCCTGCCCTGTCTTTCCAGCATCCACTC
TCCCTTGTCCTCCTGGGGGCATATCTCAGTCAGGCAGCGGCTTCCTGATGATGGTCATTGGGGTGGTTGTCATGTGATGGGTCCCCTCCA
GGTTACTAAAGGGTGCATGTCCCCTGCTTGAACACTGAAGGGCAGGTGGTGGGCCATGGCCATGGTCCCCAGCTGAGGAGCAGGTGTCCC
TGAGAACCCAAACTTCCCAGAGAGTATGTGAGAACCAACCAATGAAAACAGTCCCATCGCTCTTACCCGGTAAGTAAACAGTCAGAAAAT
TAGCATGAAAGCAGTTTAGCATTGGGAGGAAGCTCAGATCTCTAGAGCTGTCTTGTCGCCGCCCAGGATTGACCTGTGTGTAAGTCCCAA
TAAACTCACCTACTCATCAACCCCTCGAATCCCACCCCTTGTCCGGCTGCCCCCTCCAGAGCCCACGACTGTGGCCTCAACCACATCTGT
CACCACTTCTACCTCGGCCCCAGTGAGACCCACATCCACCACCAAACCCATGCCAGCGCCAACCAGTCAGACTCCGAGACAGGGAGTAGA
ACACGAGGCCTCCCGGGATGAGGAGCCCAGGTTGACTGGAGGCGCCGCTGGCCACCAGGACCGCAGCAATTCAGGGCAGTATCCTGCAAA
AGGGGGGCCCCAGCAGCCCCATAATAAAGGCTGTGTGGCTCCCACAGCTGGATTGGCAGCCCTTCTGTTGGCCGTGGCTGCTGGTGTCCT
ACTGTGAGCTTCTCCACCTGGAAATTTCCCTCTCACCTACTTCTCTGGCCCTGGGTACCCCTCTTCTCATCACTTCCTGTTCCCACCACT
GGACTGGGCTGGCCCAGCCCCTGTTTTTCCAACATTCCCCAGTATCCCCAGCTTCTGCTGCGCTGGTTTGCGGCTTTGGGAAATAAAATA
CCGTTGTATATATTCTGCCAGGGGTGTTCTAGCTTTTTGAGGACAGCTCCTGTATCCTTCTCATCCTTGTCTCTCCGCTTGTCCTCTTGT
GATGTTAGGACAGAGTGAGAGAAGTCAGCTGTCACGGGGAAGGTGAGAGAGAGGATGCTAAGCTTCCTACTCACTTTCTCCTAGCCAGCC
TGGACTTTGGAGCGTGGGGTGGGTGGGACAATGGCTCCCCACTCTAAGCACTGCCTCCCCTACTCCCCGCATCTTTGGGGAATCGGTTCC
CCATATGTCTTCCTTACTAGACTGTGAGCTCCTCGAGGGCAGGGACCGTGCCTTATGTCTGTGTGTGATCAGTTTCTGGCACATAAATGC

>5609_5609_1_APOL1-LYPD3_APOL1_chr22_36661664_ENST00000397278_LYPD3_chr19_43965849_ENST00000244333_length(amino acids)=317AA_BP=
MKVEGSVFAVLGHELLGSCDFHFPFRIPRYILGTGGPVWLLYRRITGGGIHTAQNSWILLSLCQGKIPWRRPCSDMEGAALLRVSVLCIW
MSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPS
ISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVY

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Fusion Gene PPI Analysis for APOL1-LYPD3


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 APOL1-LYPD3


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 APOL1-LYPD3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAPOL1C1868672NEPHROTIC SYNDROME, STEROID-RESISTANT, AUTOSOMAL RECESSIVE2ORPHANET
HgeneAPOL1C2675525FOCAL SEGMENTAL GLOMERULOSCLEROSIS 4, SUSCEPTIBILITY TO2GENOMICS_ENGLAND;UNIPROT
HgeneAPOL1C0041227Trypanosomiasis1GENOMICS_ENGLAND