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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:PVT1-CACNA2D2 (FusionGDB2 ID:70337)

Fusion Gene Summary for PVT1-CACNA2D2

check button Fusion gene summary
Fusion gene informationFusion gene name: PVT1-CACNA2D2
Fusion gene ID: 70337
HgeneTgene
Gene symbol

PVT1

CACNA2D2

Gene ID

5820

9254

Gene namePvt1 oncogenecalcium voltage-gated channel auxiliary subunit alpha2delta 2
SynonymsLINC00079|MIR1204HG|NCRNA00079|onco-lncRNA-100CACNA2D|CASVDD
Cytomap

8q24.21

3p21.31

Type of genencRNAprotein-coding
DescriptionCXCR4/PVT1 fusionHIST1H2BD/PVT1 fusionMIR1204, MIR1205, MIR1206 and MIR1207 hostOncogene PVT-1 (MYC activator)PVT1/CASC8 fusionPVT1/CCDC26 fusionPVT1/IFRD1 fusionPVT1/IRF2BP2 fusionPVT1/LINC00824 fusionPVT1/MYC fusionPVT1/NFIL3 fusionPVT1/NSMCEvoltage-dependent calcium channel subunit alpha-2/delta-2alpha 2 delta calcium channel subunitcalcium channel, voltage-dependent, alpha 2/delta subunit 2gene 26voltage-gated calcium channel subunit alpha-2/delta-2
Modification date2020032220200313
UniProtAcc.

Q9NY47

Ensembl transtripts involved in fusion geneENST00000408388, ENST00000423994, 
ENST00000429770, ENST00000435965, 
ENST00000266039, ENST00000395083, 
ENST00000360963, ENST00000424201, 
ENST00000479441, ENST00000487413, 
Fusion gene scores* DoF score75 X 36 X 19=513009 X 8 X 5=360
# samples 10910
** MAII scorelog2(109/51300*10)=-5.55655878571749
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/360*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PVT1 [Title/Abstract] AND CACNA2D2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPVT1(128808254)-CACNA2D2(50421768), # 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

check buttonFusion gene breakpoints across PVT1 (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 CACNA2D2 (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
ChimerDB4READTCGA-AG-3732-01APVT1chr8

128808254

+CACNA2D2chr3

50421768

-
ChimerDB4READTCGA-AG-3732PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
ChimerDB4READTCGA-AG-3732PVT1chr8

128808317

+CACNA2D2chr3

50421768

-


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Fusion Gene ORF analysis for PVT1-CACNA2D2

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
3UTR-3CDSENST00000408388ENST00000423994PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
3UTR-3CDSENST00000408388ENST00000429770PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
3UTR-3CDSENST00000408388ENST00000435965PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
3UTR-3CDSENST00000408388ENST00000266039PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
3UTR-3CDSENST00000408388ENST00000395083PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
3UTR-3CDSENST00000408388ENST00000360963PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
3UTR-3CDSENST00000408388ENST00000424201PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
3UTR-3CDSENST00000408388ENST00000479441PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
3UTR-intronENST00000408388ENST00000487413PVT1chr8

128808254

+CACNA2D2chr3

50421768

-
intron-3CDSENST00000408388ENST00000423994PVT1chr8

128808317

+CACNA2D2chr3

50421768

-
intron-3CDSENST00000408388ENST00000429770PVT1chr8

128808317

+CACNA2D2chr3

50421768

-
intron-3CDSENST00000408388ENST00000435965PVT1chr8

128808317

+CACNA2D2chr3

50421768

-
intron-3CDSENST00000408388ENST00000266039PVT1chr8

128808317

+CACNA2D2chr3

50421768

-
intron-3CDSENST00000408388ENST00000395083PVT1chr8

128808317

+CACNA2D2chr3

50421768

-
intron-3CDSENST00000408388ENST00000360963PVT1chr8

128808317

+CACNA2D2chr3

50421768

-
intron-3CDSENST00000408388ENST00000424201PVT1chr8

128808317

+CACNA2D2chr3

50421768

-
intron-3CDSENST00000408388ENST00000479441PVT1chr8

128808317

+CACNA2D2chr3

50421768

-
intron-intronENST00000408388ENST00000487413PVT1chr8

128808317

+CACNA2D2chr3

50421768

-

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 PVT1-CACNA2D2


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 PVT1-CACNA2D2


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CACNA2D2

Q9NY47

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.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) and possibly T-type (CACNA1G) (PubMed:15111129, PubMed:23339110). Overexpression induces apoptosis. {ECO:0000269|PubMed:12555074, ECO:0000269|PubMed:15111129, ECO:0000269|PubMed:23339110}.

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 PVT1-CACNA2D2


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 PVT1-CACNA2D2


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 PVT1-CACNA2D2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCACNA2D2Q9NY47DB00270IsradipineInhibitorSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB00270IsradipineInhibitorSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB00996GabapentinInhibitorSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB00996GabapentinInhibitorSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB01023FelodipineInhibitorSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB01023FelodipineInhibitorSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB01054NitrendipineInhibitorSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB01054NitrendipineInhibitorSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB08872Gabapentin enacarbilSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB08872Gabapentin enacarbilSmall moleculeApproved|Investigational
TgeneCACNA2D2Q9NY47DB01244BepridilInhibitorSmall moleculeApproved|Withdrawn
TgeneCACNA2D2Q9NY47DB01244BepridilInhibitorSmall moleculeApproved|Withdrawn

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Related Diseases for PVT1-CACNA2D2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePVT1C0019829Hodgkin Disease1CTD_human
HgenePVT1C0152266Mixed Cellularity Hodgkin Lymphoma1CTD_human
HgenePVT1C0152267Hodgkin lymphoma, lymphocyte depletion1CTD_human
HgenePVT1C0162538Immunoglobulin A deficiency (disorder)1CTD_human
HgenePVT1C0220597Adult Hodgkin Lymphoma1CTD_human
HgenePVT1C1266194Lymphocyte Rich Classical Hodgkin Lymphoma1CTD_human
HgenePVT1C1334968Nodular Lymphocyte Predominant Hodgkin Lymphoma1CTD_human
TgeneCACNA2D2C0004134Ataxia2CTD_human;GENOMICS_ENGLAND
TgeneCACNA2D2C0014553Absence Epilepsy2CTD_human;GENOMICS_ENGLAND
TgeneCACNA2D2C0001890Akinetic Petit Mal1CTD_human
TgeneCACNA2D2C0008489Chorea1CTD_human
TgeneCACNA2D2C0014544Epilepsy1GENOMICS_ENGLAND
TgeneCACNA2D2C0021361Female infertility1CTD_human
TgeneCACNA2D2C0038279Sterility, Postpartum1CTD_human
TgeneCACNA2D2C0152113Rheumatic Chorea1CTD_human
TgeneCACNA2D2C0238056Chorea, Senile1CTD_human
TgeneCACNA2D2C0240991Ataxia, Sensory1CTD_human
TgeneCACNA2D2C0278161Ataxia, Motor1CTD_human
TgeneCACNA2D2C0341869Subfertility, Female1CTD_human
TgeneCACNA2D2C0393584Benign Hereditary Chorea1CTD_human
TgeneCACNA2D2C0424605Developmental delay (disorder)1GENOMICS_ENGLAND
TgeneCACNA2D2C0427190Ataxia, Truncal1CTD_human
TgeneCACNA2D2C0520966Abnormal coordination1CTD_human
TgeneCACNA2D2C0557874Global developmental delay1GENOMICS_ENGLAND
TgeneCACNA2D2C0699728Chronic progressive chorea1CTD_human
TgeneCACNA2D2C0699731Hereditary Chorea1CTD_human
TgeneCACNA2D2C0740279Cerebellar atrophy1GENOMICS_ENGLAND
TgeneCACNA2D2C0750937Ataxia, Appendicular1CTD_human
TgeneCACNA2D2C0750940Tremor, Rubral1CTD_human
TgeneCACNA2D2C0751124Epilepsy, Absence, Atypical1CTD_human
TgeneCACNA2D2C0752210Dyskinesias, Paroxysmal1CTD_human
TgeneCACNA2D2C0917730Female sterility1CTD_human
TgeneCACNA2D2C1384666hearing impairment1CTD_human
TgeneCACNA2D2C4281785Childhood Absence Epilepsy1CTD_human
TgeneCACNA2D2C4317339Juvenile Absence Epilepsy1CTD_human
TgeneCACNA2D2C4552765Epilepsy, Minor1CTD_human
TgeneCACNA2D2C4553705Absence Seizure Disorder1CTD_human