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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:ABCA2-STXBP1 (FusionGDB2 ID:HG20TG6812)

Fusion Gene Summary for ABCA2-STXBP1

check button Fusion gene summary
Fusion gene informationFusion gene name: ABCA2-STXBP1
Fusion gene ID: hg20tg6812
HgeneTgene
Gene symbol

ABCA2

STXBP1

Gene ID

20

6812

Gene nameATP binding cassette subfamily A member 2syntaxin binding protein 1
SynonymsABC2MUNC18-1|N-Sec1|NSEC1|P67|RBSEC1|UNC18|unc-18A|unc18-1
Cytomap('ABCA2')('STXBP1')

9q34.3

9q34.11

Type of geneprotein-codingprotein-coding
DescriptionATP-binding cassette sub-family A member 2ATP-binding cassette 2ATP-binding cassette transporter 2ATP-binding cassette, sub-family A (ABC1), member 2ATP-binding cassette, sub-family A, member 2syntaxin-binding protein 1neuronal SEC1protein unc-18 homolog 1protein unc-18 homolog A
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000265662, ENST00000341511, 
ENST00000371605, ENST00000492260, 
Fusion gene scores* DoF score9 X 10 X 3=27013 X 13 X 7=1183
# samples 1013
** MAII scorelog2(10/270*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/1183*10)=-3.18586654531133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ABCA2 [Title/Abstract] AND STXBP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointABCA2(139922527)-STXBP1(130444685), # samples:1
Anticipated loss of major functional domain due to fusion event.ABCA2-STXBP1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ABCA2-STXBP1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ABCA2-STXBP1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism 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
HgeneABCA2

GO:0006357

regulation of transcription by RNA polymerase II

15238223

HgeneABCA2

GO:0010872

regulation of cholesterol esterification

24201375

HgeneABCA2

GO:0032384

negative regulation of intracellular cholesterol transport

21810484

HgeneABCA2

GO:0032805

positive regulation of low-density lipoprotein particle receptor catabolic process

21810484

HgeneABCA2

GO:0042986

positive regulation of amyloid precursor protein biosynthetic process

20704561

HgeneABCA2

GO:0045540

regulation of cholesterol biosynthetic process

21810484

HgeneABCA2

GO:0046512

sphingosine biosynthetic process

26510981

HgeneABCA2

GO:0071072

negative regulation of phospholipid biosynthetic process

24201375

HgeneABCA2

GO:0090155

negative regulation of sphingolipid biosynthetic process

24201375

HgeneABCA2

GO:0090156

cellular sphingolipid homeostasis

26510981

HgeneABCA2

GO:0090370

negative regulation of cholesterol efflux

21810484

HgeneABCA2

GO:0099040

ceramide translocation

24201375

HgeneABCA2

GO:1905598

negative regulation of low-density lipoprotein receptor activity

21810484

HgeneABCA2

GO:1905601

negative regulation of receptor-mediated endocytosis involved in cholesterol transport

21810484

TgeneSTXBP1

GO:0072659

protein localization to plasma membrane

17543282



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
ChimerDB4ACCTCGA-OR-A5JT-01AABCA2chr9

139922527

-STXBP1chr9

130444685

+


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Fusion Gene ORF analysis for ABCA2-STXBP1

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-intronENST00000265662ENST00000481942ABCA2chr9

139922527

-STXBP1chr9

130444685

+
5CDS-intronENST00000341511ENST00000481942ABCA2chr9

139922527

-STXBP1chr9

130444685

+
5CDS-intronENST00000371605ENST00000481942ABCA2chr9

139922527

-STXBP1chr9

130444685

+
5UTR-3CDSENST00000492260ENST00000373299ABCA2chr9

139922527

-STXBP1chr9

130444685

+
5UTR-3CDSENST00000492260ENST00000373302ABCA2chr9

139922527

-STXBP1chr9

130444685

+
5UTR-intronENST00000492260ENST00000481942ABCA2chr9

139922527

-STXBP1chr9

130444685

+
Frame-shiftENST00000265662ENST00000373299ABCA2chr9

139922527

-STXBP1chr9

130444685

+
Frame-shiftENST00000265662ENST00000373302ABCA2chr9

139922527

-STXBP1chr9

130444685

+
Frame-shiftENST00000341511ENST00000373299ABCA2chr9

139922527

-STXBP1chr9

130444685

+
Frame-shiftENST00000341511ENST00000373302ABCA2chr9

139922527

-STXBP1chr9

130444685

+
Frame-shiftENST00000371605ENST00000373299ABCA2chr9

139922527

-STXBP1chr9

130444685

+
Frame-shiftENST00000371605ENST00000373302ABCA2chr9

139922527

-STXBP1chr9

130444685

+

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 ABCA2-STXBP1


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)
ABCA2chr9139922526-STXBP1chr9130444684+4.07E-111
ABCA2chr9139922526-STXBP1chr9130444684+4.07E-111


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.
genomic feature of top 1%

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Fusion Protein Features for ABCA2-STXBP1


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/:139922527/:130444685)
- 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 ABCA2-STXBP1


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 ABCA2-STXBP1


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 ABCA2-STXBP1


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 ABCA2-STXBP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC2677326Epileptic Encephalopathy, Early Infantile, 413CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0037769West Syndrome2ORPHANET
TgeneC0751122Infantile Severe Myoclonic Epilepsy2CTD_human;ORPHANET
TgeneC1535926Neurodevelopmental Disorders2CTD_human
TgeneC2748910Rett Syndrome, Atypical2ORPHANET
TgeneC0014544Epilepsy1CTD_human
TgeneC0014550Myoclonic Epilepsy1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0086237Epilepsy, Cryptogenic1CTD_human
TgeneC0236018Aura1CTD_human
TgeneC0338478Idiopathic Myoclonic Epilepsy1CTD_human
TgeneC0338479Symptomatic Myoclonic Epilepsy1CTD_human
TgeneC0393695Early Childhood Epilepsy, Myoclonic1CTD_human
TgeneC0393702Myoclonic Astatic Epilepsy1CTD_human
TgeneC0393703Myoclonic Absence Epilepsy1CTD_human
TgeneC0393706Early infantile epileptic encephalopathy with suppression bursts1ORPHANET
TgeneC0438414Myoclonic Encephalopathy1CTD_human
TgeneC0751111Awakening Epilepsy1CTD_human
TgeneC0751120Benign Infantile Myoclonic Epilepsy1CTD_human
TgeneC0917800Epilepsy, Myoclonic, Infantile1CTD_human