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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:BEST1-LCN2 (FusionGDB2 ID:HG7439TG3934)

Fusion Gene Summary for BEST1-LCN2

check button Fusion gene summary
Fusion gene informationFusion gene name: BEST1-LCN2
Fusion gene ID: hg7439tg3934
HgeneTgene
Gene symbol

BEST1

LCN2

Gene ID

7439

3934

Gene namebestrophin 1lipocalin 2
SynonymsARB|BEST|BMD|Best1V1Delta2|RP50|TU15B|VMD224p3|MSFI|NGAL|p25
Cytomap('BEST1')('LCN2')

11q12.3

9q34.11

Type of geneprotein-codingprotein-coding
Descriptionbestrophin-1Best diseasevitelliform macular dystrophy protein 2neutrophil gelatinase-associated lipocalin25 kDa alpha-2-microglobulin-related subunit of MMP-9migration-stimulating factor inhibitoroncogene 24p3siderocalin LCN2
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000449131, ENST00000301774, 
ENST00000378042, ENST00000378043, 
ENST00000435278, ENST00000526988, 
ENST00000534553, 
Fusion gene scores* DoF score10 X 12 X 8=96011 X 10 X 5=550
# samples 1212
** MAII scorelog2(12/960*10)=-3
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/550*10)=-2.1963972128035
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BEST1 [Title/Abstract] AND LCN2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBEST1(61732869)-LCN2(130911741), # 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
HgeneBEST1

GO:0006821

chloride transport

17003041

HgeneBEST1

GO:0030321

transepithelial chloride transport

17003041

TgeneLCN2

GO:0042742

defense response to bacterium

27780864

TgeneLCN2

GO:0097577

sequestering of iron ion

27780864



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
ChimerDB4READTCGA-AG-A011BEST1chr11

61732869

+LCN2chr9

130911741

+


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Fusion Gene ORF analysis for BEST1-LCN2

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
3UTR-3UTRENST00000449131ENST00000470902BEST1chr11

61732869

+LCN2chr9

130911741

+
3UTR-5UTRENST00000449131ENST00000277480BEST1chr11

61732869

+LCN2chr9

130911741

+
3UTR-5UTRENST00000449131ENST00000373013BEST1chr11

61732869

+LCN2chr9

130911741

+
3UTR-5UTRENST00000449131ENST00000540948BEST1chr11

61732869

+LCN2chr9

130911741

+
3UTR-intronENST00000449131ENST00000372998BEST1chr11

61732869

+LCN2chr9

130911741

+
3UTR-intronENST00000449131ENST00000373017BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-3UTRENST00000301774ENST00000470902BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-3UTRENST00000378042ENST00000470902BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-3UTRENST00000378043ENST00000470902BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-3UTRENST00000435278ENST00000470902BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-3UTRENST00000526988ENST00000470902BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-3UTRENST00000534553ENST00000470902BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000301774ENST00000277480BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000301774ENST00000373013BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000301774ENST00000540948BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000378042ENST00000277480BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000378042ENST00000373013BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000378042ENST00000540948BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000378043ENST00000277480BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000378043ENST00000373013BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000378043ENST00000540948BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000435278ENST00000277480BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000435278ENST00000373013BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000435278ENST00000540948BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000526988ENST00000277480BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000526988ENST00000373013BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000526988ENST00000540948BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000534553ENST00000277480BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000534553ENST00000373013BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-5UTRENST00000534553ENST00000540948BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000301774ENST00000372998BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000301774ENST00000373017BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000378042ENST00000372998BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000378042ENST00000373017BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000378043ENST00000372998BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000378043ENST00000373017BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000435278ENST00000372998BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000435278ENST00000373017BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000526988ENST00000372998BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000526988ENST00000373017BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000534553ENST00000372998BEST1chr11

61732869

+LCN2chr9

130911741

+
intron-intronENST00000534553ENST00000373017BEST1chr11

61732869

+LCN2chr9

130911741

+

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 BEST1-LCN2


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 BEST1-LCN2


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/:61732869/:130911741)
- 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

- 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 BEST1-LCN2


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 BEST1-LCN2


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 BEST1-LCN2


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 BEST1-LCN2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBEST1C0339510Vitelliform Macular Dystrophy20CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneBEST1C3888198BESTROPHINOPATHY, AUTOSOMAL RECESSIVE6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneBEST1C3888099Autosomal dominant vitreoretinochoroidopathy3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneBEST1C2750789RETINITIS PIGMENTOSA, CONCENTRIC (disorder)2CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneBEST1C0015397Disorder of eye1GENOMICS_ENGLAND
HgeneBEST1C0026010Microphthalmos1ORPHANET
HgeneBEST1C0155359Scleral staphyloma1GENOMICS_ENGLAND
HgeneBEST1C1842914Adult-Onset Vitelliform Macular Dystrophy1CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneBEST1C2674009Microcornea, Rod-Cone Dystrophy, Cataract, And Posterior Staphyloma1CTD_human;ORPHANET
HgeneBEST1C2745945Juvenile-Onset Vitelliform Macular Dystrophy1CTD_human;ORPHANET
TgeneC0022660Kidney Failure, Acute5CTD_human
TgeneC1565662Acute Kidney Insufficiency5CTD_human
TgeneC2609414Acute kidney injury5CTD_human
TgeneC0022658Kidney Diseases4CTD_human
TgeneC0019193Hepatitis, Toxic2CTD_human
TgeneC0023893Liver Cirrhosis, Experimental2CTD_human
TgeneC0860207Drug-Induced Liver Disease2CTD_human
TgeneC1262760Hepatitis, Drug-Induced2CTD_human
TgeneC3658290Drug-Induced Acute Liver Injury2CTD_human
TgeneC4277682Chemical and Drug Induced Liver Injury2CTD_human
TgeneC4279912Chemically-Induced Liver Toxicity2CTD_human
TgeneC0002875Cooley's anemia1CTD_human
TgeneC0003873Rheumatoid Arthritis1CTD_human
TgeneC0005283beta Thalassemia1CTD_human
TgeneC0006663Calcinosis1CTD_human
TgeneC0006826Malignant Neoplasms1CTD_human
TgeneC0007570Celiac Disease1CTD_human
TgeneC0011616Contact Dermatitis1CTD_human
TgeneC0013221Drug toxicity1CTD_human
TgeneC0018824Heart valve disease1CTD_human
TgeneC0019025Hemoglobin F Disease1CTD_human
TgeneC0019188Hepatitis, Animal1CTD_human
TgeneC0021368Inflammation1CTD_human
TgeneC0027627Neoplasm Metastasis1CTD_human
TgeneC0027651Neoplasms1CTD_human
TgeneC0035222Respiratory Distress Syndrome, Adult1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0041755Adverse reaction to drug1CTD_human
TgeneC0085578Thalassemia Minor1CTD_human
TgeneC0086692Benign Neoplasm1CTD_human
TgeneC0162351Contact hypersensitivity1CTD_human
TgeneC0263628Tumoral calcinosis1CTD_human
TgeneC0271979Thalassemia Intermedia1CTD_human
TgeneC0403447Chronic Kidney Insufficiency1CTD_human
TgeneC0521174Microcalcification1CTD_human
TgeneC1561643Chronic Kidney Diseases1CTD_human