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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:ARFIP1-LRBA (FusionGDB2 ID:HG27236TG987)

Fusion Gene Summary for ARFIP1-LRBA

check button Fusion gene summary
Fusion gene informationFusion gene name: ARFIP1-LRBA
Fusion gene ID: hg27236tg987
HgeneTgene
Gene symbol

ARFIP1

LRBA

Gene ID

27236

987

Gene nameADP ribosylation factor interacting protein 1LPS responsive beige-like anchor protein
SynonymsHSU52521BGL|CDC4L|CVID8|LAB300|LBA
Cytomap('ARFIP1')('LRBA')

4q31.3

4q31.3

Type of geneprotein-codingprotein-coding
Descriptionarfaptin-1lipopolysaccharide-responsive and beige-like anchor proteinCDC4-like proteinLPS-responsive vesicle trafficking, beach and anchor containingvesicle trafficking, beach and anchor containing
Modification date2020031320200320
UniProtAcc

P53367

.
Ensembl transtripts involved in fusion geneENST00000353617, ENST00000356064, 
ENST00000405727, ENST00000429148, 
ENST00000451320, ENST00000511289, 
Fusion gene scores* DoF score11 X 7 X 7=53925 X 25 X 10=6250
# samples 1127
** MAII scorelog2(11/539*10)=-2.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(27/6250*10)=-4.53282487738598
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARFIP1 [Title/Abstract] AND LRBA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARFIP1(153701378)-LRBA(151604869), # 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
HgeneARFIP1

GO:0006886

intracellular protein transport

12606037

HgeneARFIP1

GO:0050708

regulation of protein secretion

12606037



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
ChimerDB4Non-Cancer43NARFIP1chr4

153701378

+LRBAchr4

151604869

-


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Fusion Gene ORF analysis for ARFIP1-LRBA

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
5UTR-3CDSENST00000353617ENST00000510413ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-3CDSENST00000353617ENST00000535741ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-3CDSENST00000356064ENST00000510413ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-3CDSENST00000356064ENST00000535741ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-intronENST00000353617ENST00000357115ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-intronENST00000353617ENST00000503716ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-intronENST00000353617ENST00000507224ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-intronENST00000356064ENST00000357115ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-intronENST00000356064ENST00000503716ARFIP1chr4

153701378

+LRBAchr4

151604869

-
5UTR-intronENST00000356064ENST00000507224ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-3CDSENST00000405727ENST00000510413ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-3CDSENST00000405727ENST00000535741ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-3CDSENST00000429148ENST00000510413ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-3CDSENST00000429148ENST00000535741ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-3CDSENST00000451320ENST00000510413ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-3CDSENST00000451320ENST00000535741ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-3CDSENST00000511289ENST00000510413ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-3CDSENST00000511289ENST00000535741ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000405727ENST00000357115ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000405727ENST00000503716ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000405727ENST00000507224ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000429148ENST00000357115ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000429148ENST00000503716ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000429148ENST00000507224ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000451320ENST00000357115ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000451320ENST00000503716ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000451320ENST00000507224ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000511289ENST00000357115ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000511289ENST00000503716ARFIP1chr4

153701378

+LRBAchr4

151604869

-
intron-intronENST00000511289ENST00000507224ARFIP1chr4

153701378

+LRBAchr4

151604869

-

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 ARFIP1-LRBA


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 ARFIP1-LRBA


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/:153701378/:151604869)
- 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
ARFIP1

P53367

.
FUNCTION: Plays a role in controlling biogenesis of secretory granules at the trans-Golgi network (PubMed:22981988). Mechanisitically, binds ARF-GTP at the neck of a growing secretory granule precursor and forms a protective scaffold (PubMed:9038142, PubMed:22981988). Once the granule precursor has been completely loaded, active PRKD1 phosphorylates ARFIP1 and releases it from ARFs (PubMed:22981988). In turn, ARFs induce fission (PubMed:22981988). Through this mechanism, ensures proper secretory granule formation at the Golgi of pancreatic beta cells (PubMed:22981988). {ECO:0000269|PubMed:22981988, ECO:0000269|PubMed:9038142}.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 ARFIP1-LRBA


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 ARFIP1-LRBA


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 ARFIP1-LRBA


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 ARFIP1-LRBA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3553512IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT