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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:RAPGEF6-GRIN2A (FusionGDB2 ID:72261)

Fusion Gene Summary for RAPGEF6-GRIN2A

check button Fusion gene summary
Fusion gene informationFusion gene name: RAPGEF6-GRIN2A
Fusion gene ID: 72261
HgeneTgene
Gene symbol

RAPGEF6

GRIN2A

Gene ID

51735

2903

Gene nameRap guanine nucleotide exchange factor 6glutamate ionotropic receptor NMDA type subunit 2A
SynonymsKIA001LB|PDZ-GEF2|PDZGEF2|RA-GEF-2|RAGEF2EPND|FESD|GluN2A|LKS|NMDAR2A|NR2A
Cytomap

5q31.1

16p13.2

Type of geneprotein-codingprotein-coding
Descriptionrap guanine nucleotide exchange factor 6PDZ domain containing guanine nucleotide exchange factor (GEF) 2PDZ domain-containing guanine nucleotide exchange factor 2PDZ domain-containing guanine nucleotide exchange factor IRap guanine nucleotide exchangeglutamate receptor ionotropic, NMDA 2AN-methyl D-aspartate receptor subtype 2AN-methyl-D-aspartate receptor channel, subunit epsilon-1N-methyl-D-aspartate receptor subunit 2Aglutamate receptor, ionotropic, N-methyl D-aspartate 2A
Modification date2020031320200313
UniProtAcc.

Q12879

Ensembl transtripts involved in fusion geneENST00000296859, ENST00000307984, 
ENST00000308008, ENST00000503398, 
ENST00000507093, ENST00000509018, 
ENST00000510071, ENST00000512052, 
ENST00000330684, ENST00000396573, 
ENST00000396575, ENST00000404927, 
ENST00000535259, ENST00000562109, 
ENST00000566670, 
Fusion gene scores* DoF score10 X 10 X 6=6008 X 7 X 5=280
# samples 108
** MAII scorelog2(10/600*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/280*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAPGEF6 [Title/Abstract] AND GRIN2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRAPGEF6(130804675)-GRIN2A(9897492), # 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
TgeneGRIN2A

GO:0045471

response to ethanol

18445116

TgeneGRIN2A

GO:0097553

calcium ion transmembrane import into cytosol

26875626


check buttonFusion gene breakpoints across RAPGEF6 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across GRIN2A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChiTaRS5.0N/AFN104730RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+


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Fusion Gene ORF analysis for RAPGEF6-GRIN2A

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
intron-intronENST00000296859ENST00000330684RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000296859ENST00000396573RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000296859ENST00000396575RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000296859ENST00000404927RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000296859ENST00000535259RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000296859ENST00000562109RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000296859ENST00000566670RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000307984ENST00000330684RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000307984ENST00000396573RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000307984ENST00000396575RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000307984ENST00000404927RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000307984ENST00000535259RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000307984ENST00000562109RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000307984ENST00000566670RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000308008ENST00000330684RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000308008ENST00000396573RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000308008ENST00000396575RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000308008ENST00000404927RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000308008ENST00000535259RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000308008ENST00000562109RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000308008ENST00000566670RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000503398ENST00000330684RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000503398ENST00000396573RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000503398ENST00000396575RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000503398ENST00000404927RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000503398ENST00000535259RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000503398ENST00000562109RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000503398ENST00000566670RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000507093ENST00000330684RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000507093ENST00000396573RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000507093ENST00000396575RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000507093ENST00000404927RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000507093ENST00000535259RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000507093ENST00000562109RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000507093ENST00000566670RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000509018ENST00000330684RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000509018ENST00000396573RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000509018ENST00000396575RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000509018ENST00000404927RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000509018ENST00000535259RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000509018ENST00000562109RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000509018ENST00000566670RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000510071ENST00000330684RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000510071ENST00000396573RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000510071ENST00000396575RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000510071ENST00000404927RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000510071ENST00000535259RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000510071ENST00000562109RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000510071ENST00000566670RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000512052ENST00000330684RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000512052ENST00000396573RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000512052ENST00000396575RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000512052ENST00000404927RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000512052ENST00000535259RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000512052ENST00000562109RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+
intron-intronENST00000512052ENST00000566670RAPGEF6chr5

130804675

-GRIN2Achr16

9897492

+

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 RAPGEF6-GRIN2A


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for RAPGEF6-GRIN2A


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/:130804675/:9897492)
- 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
.GRIN2A

Q12879

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: Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg(2+) (PubMed:8768735, PubMed:26919761, PubMed:26875626, PubMed:28105280). Sensitivity to glutamate and channel kinetics depend on the subunit composition; channels containing GRIN1 and GRIN2A have lower sensitivity to glutamate and faster deactivation kinetics than channels formed by GRIN1 and GRIN2B (PubMed:26919761, PubMed:26875626). Contributes to the slow phase of excitatory postsynaptic current, long-term synaptic potentiation, and learning (By similarity). {ECO:0000250|UniProtKB:P35436, ECO:0000250|UniProtKB:Q00959, ECO:0000269|PubMed:26875626, ECO:0000269|PubMed:26919761, ECO:0000269|PubMed:28105280, ECO:0000269|PubMed:8768735}.

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 RAPGEF6-GRIN2A


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 RAPGEF6-GRIN2A


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 RAPGEF6-GRIN2A


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 RAPGEF6-GRIN2A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource