Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:ABCD3-ARHGAP29 (FusionGDB2 ID:HG5825TG9411)

Fusion Gene Summary for ABCD3-ARHGAP29

check button Fusion gene summary
Fusion gene informationFusion gene name: ABCD3-ARHGAP29
Fusion gene ID: hg5825tg9411
HgeneTgene
Gene symbol

ABCD3

ARHGAP29

Gene ID

5825

9411

Gene nameATP binding cassette subfamily D member 3Rho GTPase activating protein 29
SynonymsABC43|CBAS5|PMP70|PXMP1|ZWS2PARG1
Cytomap('ABCD3')('ARHGAP29')

1p21.3

1p22.1

Type of geneprotein-codingprotein-coding
DescriptionATP-binding cassette sub-family D member 370 kDa peroxisomal membrane proteinATP-binding cassette, sub-family D (ALD), member 3Peroxisomal membrane protein-1 (70kD)dJ824O18.1 (ATP-binding cassette, sub-family D (ALD), member 3 (PMP70, PXMP1))peroxisorho GTPase-activating protein 29PTPL1-associated RhoGAP 1 (PARG1)PTPL1-associated RhoGAP protein 1rho-type GTPase-activating protein 29
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000315713, ENST00000370214, 
ENST00000394233, ENST00000454898, 
ENST00000536817, ENST00000484213, 
Fusion gene scores* DoF score6 X 5 X 4=1203 X 3 X 3=27
# samples 63
** MAII scorelog2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ABCD3 [Title/Abstract] AND ARHGAP29 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointABCD3(94884144)-ARHGAP29(94685948), # samples:2
Anticipated loss of major functional domain due to fusion event.ABCD3-ARHGAP29 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ABCD3-ARHGAP29 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ABCD3-ARHGAP29 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
ABCD3-ARHGAP29 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
HgeneABCD3

GO:0007031

peroxisome organization

9425230



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
ChimerDB4BLCATCGA-GV-A3QH-01AABCD3chr1

94884144

-ARHGAP29chr1

94685948

-
ChimerDB4BLCATCGA-GV-A3QH-01AABCD3chr1

94884144

+ARHGAP29chr1

94685948

-


Top

Fusion Gene ORF analysis for ABCD3-ARHGAP29

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-intronENST00000315713ENST00000370217ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5CDS-intronENST00000315713ENST00000482481ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5CDS-intronENST00000370214ENST00000370217ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5CDS-intronENST00000370214ENST00000482481ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5CDS-intronENST00000394233ENST00000370217ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5CDS-intronENST00000394233ENST00000482481ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5CDS-intronENST00000454898ENST00000370217ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5CDS-intronENST00000454898ENST00000482481ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5UTR-3CDSENST00000536817ENST00000260526ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5UTR-intronENST00000536817ENST00000370217ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
5UTR-intronENST00000536817ENST00000482481ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
Frame-shiftENST00000315713ENST00000260526ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
Frame-shiftENST00000370214ENST00000260526ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
Frame-shiftENST00000394233ENST00000260526ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
Frame-shiftENST00000454898ENST00000260526ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
intron-3CDSENST00000484213ENST00000260526ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
intron-intronENST00000484213ENST00000370217ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-
intron-intronENST00000484213ENST00000482481ABCD3chr1

94884144

+ARHGAP29chr1

94685948

-

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

Top

Fusion Genomic Features for ABCD3-ARHGAP29


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)


Top

Fusion Protein Features for ABCD3-ARHGAP29


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/:94884144/:94685948)
- 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


Top

Fusion Gene Sequence for ABCD3-ARHGAP29


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.

Top

Fusion Gene PPI Analysis for ABCD3-ARHGAP29


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


Top

Related Drugs for ABCD3-ARHGAP29


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for ABCD3-ARHGAP29


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneABCD3C0009402Colorectal Carcinoma1CTD_human
HgeneABCD3C0009404Colorectal Neoplasms1CTD_human
HgeneABCD3C0043459Zellweger Syndrome1CTD_human
HgeneABCD3C0751594Zellweger-Like Syndrome1CTD_human
HgeneABCD3C3658299Zellweger Spectrum1CTD_human
HgeneABCD3C4225390BILE ACID SYNTHESIS DEFECT, CONGENITAL, 51CTD_human;GENOMICS_ENGLAND
TgeneC0008925Cleft Palate1GENOMICS_ENGLAND
TgeneC0158646Cleft palate with cleft lip1ORPHANET
TgeneC0334634Malignant lymphoma, lymphocytic, intermediate differentiation, diffuse1CTD_human
TgeneC0751958Lymphoma, Lymphocytic, Intermediate1CTD_human
TgeneC0810364Cleft Lip with or without Cleft Palate1GENOMICS_ENGLAND