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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:CACNA2D3-SCAF11 (FusionGDB2 ID:HG55799TG9169)

Fusion Gene Summary for CACNA2D3-SCAF11

check button Fusion gene summary
Fusion gene informationFusion gene name: CACNA2D3-SCAF11
Fusion gene ID: hg55799tg9169
HgeneTgene
Gene symbol

CACNA2D3

SCAF11

Gene ID

55799

9169

Gene namecalcium voltage-gated channel auxiliary subunit alpha2delta 3SR-related CTD associated factor 11
SynonymsHSA272268CASP11|SFRS2IP|SIP1|SRRP129|SRSF2IP
Cytomap('CACNA2D3')('SCAF11')

3p21.1-p14.3

12q12

Type of geneprotein-codingprotein-coding
Descriptionvoltage-dependent calcium channel subunit alpha-2/delta-3calcium channel alpha2-delta3 subunitcalcium channel, voltage-dependent, alpha 2/delta 3 subunitcalcium channel, voltage-dependent, alpha 2/delta subunit 3voltage-gated calcium channel subunit aprotein SCAF11CTD-associated SR protein 11SC35-interacting protein 1SFRS2-interacting proteinSR-related and CTD-associated factor 11SRSF2-interacting proteinrenal carcinoma antigen NY-REN-40serine/arginine-rich splicing factor 2-interacting protein
Modification date2020031320200313
UniProtAcc

Q8IZS8

.
Ensembl transtripts involved in fusion geneENST00000288197, ENST00000415676, 
ENST00000474759, ENST00000490478, 
ENST00000478261, 
Fusion gene scores* DoF score14 X 12 X 6=10089 X 6 X 8=432
# samples 1510
** MAII scorelog2(15/1008*10)=-2.74846123300404
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/432*10)=-2.11103131238874
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CACNA2D3 [Title/Abstract] AND SCAF11 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCACNA2D3(54604131)-SCAF11(46357971), # samples:2
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
TgeneSCAF11

GO:0000245

spliceosomal complex assembly

9447963

TgeneSCAF11

GO:0000375

RNA splicing, via transesterification reactions

9447963

TgeneSCAF11

GO:0008380

RNA splicing

9447963



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
ChimerDB4MESOTCGA-UT-A88E-01BCACNA2D3chr3

54604131

-SCAF11chr12

46357971

-
ChimerDB4MESOTCGA-UT-A88E-01BCACNA2D3chr3

54604131

+SCAF11chr12

46357971

-


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Fusion Gene ORF analysis for CACNA2D3-SCAF11

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-5UTRENST00000288197ENST00000369367CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000288197ENST00000395453CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000288197ENST00000395454CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000288197ENST00000419565CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000415676ENST00000369367CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000415676ENST00000395453CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000415676ENST00000395454CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000415676ENST00000419565CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000474759ENST00000369367CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000474759ENST00000395453CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000474759ENST00000395454CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000474759ENST00000419565CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000490478ENST00000369367CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000490478ENST00000395453CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000490478ENST00000395454CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-5UTRENST00000490478ENST00000419565CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000288197ENST00000465950CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000288197ENST00000549162CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000288197ENST00000550629CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000415676ENST00000465950CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000415676ENST00000549162CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000415676ENST00000550629CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000474759ENST00000465950CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000474759ENST00000549162CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000474759ENST00000550629CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000490478ENST00000465950CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000490478ENST00000549162CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
5CDS-intronENST00000490478ENST00000550629CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
intron-5UTRENST00000478261ENST00000369367CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
intron-5UTRENST00000478261ENST00000395453CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
intron-5UTRENST00000478261ENST00000395454CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
intron-5UTRENST00000478261ENST00000419565CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
intron-intronENST00000478261ENST00000465950CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
intron-intronENST00000478261ENST00000549162CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-
intron-intronENST00000478261ENST00000550629CACNA2D3chr3

54604131

+SCAF11chr12

46357971

-

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 CACNA2D3-SCAF11


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 CACNA2D3-SCAF11


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/:54604131/:46357971)
- 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
CACNA2D3

Q8IZS8

.
FUNCTION: The alpha-2/delta subunit of voltage-dependent calcium channels regulates calcium current density and activation/inactivation kinetics of the calcium channel. Acts as a regulatory subunit for P/Q-type calcium channel (CACNA1A), N-type (CACNA1B), L-type (CACNA1C OR CACNA1D) but not T-type (CACNA1G) (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 CACNA2D3-SCAF11


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 CACNA2D3-SCAF11


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 CACNA2D3-SCAF11


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCACNA2D3Q8IZS8DB00381AmlodipineInhibitorSmall moleculeApproved
HgeneCACNA2D3Q8IZS8DB06712NilvadipineInhibitorSmall moleculeApproved|Investigational

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Related Diseases for CACNA2D3-SCAF11


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCACNA2D3C1535926Neurodevelopmental Disorders1CTD_human