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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:CACNA1A-PPIF (FusionGDB2 ID:HG773TG10105)

Fusion Gene Summary for CACNA1A-PPIF

check button Fusion gene summary
Fusion gene informationFusion gene name: CACNA1A-PPIF
Fusion gene ID: hg773tg10105
HgeneTgene
Gene symbol

CACNA1A

PPIF

Gene ID

773

10105

Gene namecalcium voltage-gated channel subunit alpha1 Apeptidylprolyl isomerase F
SynonymsAPCA|BI|CACNL1A4|CAV2.1|EA2|EIEE42|FHM|HPCA|MHP|MHP1|SCA6CYP3|CyP-M|Cyp-D|CypD
Cytomap('CACNA1A')('PPIF')

19p13.13

10q22.3

Type of geneprotein-codingprotein-coding
Descriptionvoltage-dependent P/Q-type calcium channel subunit alpha-1Abrain calcium channel 1brain calcium channel Icalcium channel, L type, alpha-1 polypeptidecalcium channel, voltage-dependent, P/Q type, alpha 1A subunitfetal brain Ca2+ voltage-gated channel peptidyl-prolyl cis-trans isomerase F, mitochondrialPPIase Fcyclophilin 3cyclophilin Dcyclophilin Fmitochondrial cyclophilinpeptidyl-prolyl cis-trans isomerase, mitochondrialrotamase F
Modification date2020032920200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000360228, ENST00000573710, 
ENST00000574822, ENST00000592864, 
Fusion gene scores* DoF score14 X 14 X 3=5883 X 3 X 1=9
# samples 143
** MAII scorelog2(14/588*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CACNA1A [Title/Abstract] AND PPIF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCACNA1A(13599795)-PPIF(81113571), # 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
HgeneCACNA1A

GO:0007204

positive regulation of cytosolic calcium ion concentration

10753886

HgeneCACNA1A

GO:0008219

cell death

16595610

HgeneCACNA1A

GO:0050804

modulation of chemical synaptic transmission

23376566

HgeneCACNA1A

GO:0070588

calcium ion transmembrane transport

24836863|26716990

HgeneCACNA1A

GO:1904645

response to amyloid-beta

18216187|23376566

HgeneCACNA1A

GO:1904646

cellular response to amyloid-beta

21883149

TgenePPIF

GO:0000413

protein peptidyl-prolyl isomerization

20676357

TgenePPIF

GO:0043066

negative regulation of apoptotic process

19228691

TgenePPIF

GO:0090201

negative regulation of release of cytochrome c from mitochondria

19228691



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


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Fusion Gene ORF analysis for CACNA1A-PPIF

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

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 CACNA1A-PPIF


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 CACNA1A-PPIF


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/:13599795/:81113571)
- 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 CACNA1A-PPIF


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 CACNA1A-PPIF


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 CACNA1A-PPIF


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 CACNA1A-PPIF


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCACNA1AC1720416Episodic ataxia type 2 (disorder)21CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCACNA1AC1832884Hemiplegic migraine, familial type 115CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCACNA1AC0752124Spinocerebellar Ataxia Type 6 (disorder)12CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCACNA1AC4310716EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 424CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCACNA1AC0014553Absence Epilepsy2CTD_human;GENOMICS_ENGLAND
HgeneCACNA1AC0087012Ataxia, Spinocerebellar2CTD_human
HgeneCACNA1AC0752120Spinocerebellar Ataxia Type 12CTD_human
HgeneCACNA1AC0752121Spinocerebellar Ataxia Type 22CTD_human
HgeneCACNA1AC0752122Spinocerebellar Ataxia Type 42CTD_human
HgeneCACNA1AC0752123Spinocerebellar Ataxia Type 52CTD_human
HgeneCACNA1AC0752125Spinocerebellar Ataxia Type 72CTD_human
HgeneCACNA1AC0001890Akinetic Petit Mal1CTD_human
HgeneCACNA1AC0004134Ataxia1CTD_human
HgeneCACNA1AC0005586Bipolar Disorder1PSYGENET
HgeneCACNA1AC0013421Dystonia1GENOMICS_ENGLAND
HgeneCACNA1AC0206368Exfoliation Syndrome1CTD_human
HgeneCACNA1AC0240991Ataxia, Sensory1CTD_human
HgeneCACNA1AC0270816epilepsy and migraine1GENOMICS_ENGLAND
HgeneCACNA1AC0278161Ataxia, Motor1CTD_human
HgeneCACNA1AC0338488Alternating hemiplegia of childhood1ORPHANET
HgeneCACNA1AC0427190Ataxia, Truncal1CTD_human
HgeneCACNA1AC0520966Abnormal coordination1CTD_human
HgeneCACNA1AC0543888Epileptic encephalopathy1GENOMICS_ENGLAND
HgeneCACNA1AC0750937Ataxia, Appendicular1CTD_human
HgeneCACNA1AC0750940Tremor, Rubral1CTD_human
HgeneCACNA1AC0751124Epilepsy, Absence, Atypical1CTD_human
HgeneCACNA1AC3494934Benign paroxysmal torticollis of infancy1ORPHANET
HgeneCACNA1AC4281785Childhood Absence Epilepsy1CTD_human
HgeneCACNA1AC4317339Juvenile Absence Epilepsy1CTD_human
HgeneCACNA1AC4552765Epilepsy, Minor1CTD_human
HgeneCACNA1AC4553705Absence Seizure Disorder1CTD_human
TgeneC0021831Intestinal Diseases1CTD_human
TgeneC0041582Ulcer1CTD_human