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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:AGAP3-RELN (FusionGDB2 ID:HG116988TG5649)

Fusion Gene Summary for AGAP3-RELN

check button Fusion gene summary
Fusion gene informationFusion gene name: AGAP3-RELN
Fusion gene ID: hg116988tg5649
HgeneTgene
Gene symbol

AGAP3

RELN

Gene ID

116988

5649

Gene nameArfGAP with GTPase domain, ankyrin repeat and PH domain 3reelin
SynonymsAGAP-3|CENTG3|CRAG|MRIP-1|cnt-g3ETL7|LIS2|PRO1598|RL
Cytomap('AGAP3')('RELN')

7q36.1

7q22.1

Type of geneprotein-codingprotein-coding
Descriptionarf-GAP with GTPase, ANK repeat and PH domain-containing protein 3CRAM-associated GTPaseCRMP (collapsin response mediator protein) associatedMR1-interacting proteincentaurin-gamma-3reelin
Modification date2020031320200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000397238, ENST00000473312, 
ENST00000479901, ENST00000335367, 
ENST00000463381, ENST00000476375, 
Fusion gene scores* DoF score15 X 6 X 10=90011 X 11 X 6=726
# samples 1411
** MAII scorelog2(14/900*10)=-2.68449817427207
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/726*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AGAP3 [Title/Abstract] AND RELN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAGAP3(150784159)-RELN(103191743), # samples:4
Anticipated loss of major functional domain due to fusion event.AGAP3-RELN seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AGAP3-RELN seems lost the major protein functional domain in Tgene 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


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
ChimerDB4LUSCTCGA-68-8250-01AAGAP3chr7

150784159

-RELNchr7

103191743

-
ChimerDB4LUSCTCGA-68-8250-01AAGAP3chr7

150784159

+RELNchr7

103191743

-
ChimerDB4LUSCTCGA-68-8250AGAP3chr7

150784159

+RELNchr7

103191743

-


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Fusion Gene ORF analysis for AGAP3-RELN

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-intronENST00000397238ENST00000473945AGAP3chr7

150784159

+RELNchr7

103191743

-
5CDS-intronENST00000473312ENST00000473945AGAP3chr7

150784159

+RELNchr7

103191743

-
5CDS-intronENST00000479901ENST00000473945AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000397238ENST00000343529AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000397238ENST00000424685AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000397238ENST00000428762AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000473312ENST00000343529AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000473312ENST00000424685AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000473312ENST00000428762AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000479901ENST00000343529AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000479901ENST00000424685AGAP3chr7

150784159

+RELNchr7

103191743

-
Frame-shiftENST00000479901ENST00000428762AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000335367ENST00000343529AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000335367ENST00000424685AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000335367ENST00000428762AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000463381ENST00000343529AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000463381ENST00000424685AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000463381ENST00000428762AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000476375ENST00000343529AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000476375ENST00000424685AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-3CDSENST00000476375ENST00000428762AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-intronENST00000335367ENST00000473945AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-intronENST00000463381ENST00000473945AGAP3chr7

150784159

+RELNchr7

103191743

-
intron-intronENST00000476375ENST00000473945AGAP3chr7

150784159

+RELNchr7

103191743

-

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 AGAP3-RELN


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 AGAP3-RELN


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/:150784159/:103191743)
- 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 AGAP3-RELN


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 AGAP3-RELN


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 AGAP3-RELN


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 AGAP3-RELN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0005586Bipolar Disorder8CTD_human;PSYGENET
TgeneC0011570Mental Depression4PSYGENET
TgeneC0011581Depressive disorder4CTD_human;PSYGENET
TgeneC0036341Schizophrenia4CTD_human
TgeneC0004352Autistic Disorder3CTD_human
TgeneC0005587Depression, Bipolar3CTD_human
TgeneC0024713Manic Disorder3CTD_human
TgeneC0041696Unipolar Depression3CTD_human;PSYGENET
TgeneC0338831Manic3CTD_human
TgeneC1269683Major Depressive Disorder3CTD_human;PSYGENET
TgeneC0796089LISSENCEPHALY SYNDROME, NORMAN-ROBERTS TYPE2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC1510586Autism Spectrum Disorders2CTD_human
TgeneC0002395Alzheimer's Disease1CTD_human
TgeneC0011265Presenile dementia1CTD_human
TgeneC0011573Endogenous depression1CTD_human
TgeneC0011574Involutional Depression1CTD_human
TgeneC0017181Gastrointestinal Hemorrhage1GENOMICS_ENGLAND
TgeneC0019569Hirschsprung Disease1GENOMICS_ENGLAND
TgeneC0019829Hodgkin Disease1GENOMICS_ENGLAND
TgeneC0020179Huntington Disease1GENOMICS_ENGLAND
TgeneC0025193Melancholia1CTD_human
TgeneC0086133Depressive Syndrome1CTD_human
TgeneC0276496Familial Alzheimer Disease (FAD)1CTD_human
TgeneC0282126Depression, Neurotic1CTD_human
TgeneC0494463Alzheimer Disease, Late Onset1CTD_human
TgeneC0525045Mood Disorders1PSYGENET
TgeneC0546126Acute Confusional Senile Dementia1CTD_human
TgeneC0750900Alzheimer's Disease, Focal Onset1CTD_human
TgeneC0750901Alzheimer Disease, Early Onset1CTD_human
TgeneC1571983Involutional paraphrenia1CTD_human
TgeneC1571984Psychosis, Involutional1CTD_human
TgeneC1838062Autosomal Dominant Lateral Temporal Lobe Epilepsy1ORPHANET
TgeneC4225327EPILEPSY, FAMILIAL TEMPORAL LOBE, 71CTD_human;GENOMICS_ENGLAND;UNIPROT