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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:CACNG4-VMP1 (FusionGDB2 ID:12418)

Fusion Gene Summary for CACNG4-VMP1

check button Fusion gene summary
Fusion gene informationFusion gene name: CACNG4-VMP1
Fusion gene ID: 12418
HgeneTgene
Gene symbol

CACNG4

VMP1

Gene ID

27092

81671

Gene namecalcium voltage-gated channel auxiliary subunit gamma 4vacuole membrane protein 1
Synonyms-EPG3|TANGO5|TMEM49
Cytomap

17q24.2

17q23.1

Type of geneprotein-codingprotein-coding
Descriptionvoltage-dependent calcium channel gamma-4 subunitTARP gamma-4calcium channel, voltage-dependent, gamma subunit 4neuronal voltage-gated calcium channel gamma-4 subunittransmembrane AMPAR regulatory protein gamma-4vacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homolog
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000262138, ENST00000536180, 
ENST00000537567, ENST00000545362, 
ENST00000539763, ENST00000588617, 
ENST00000262291, 
Fusion gene scores* DoF score5 X 2 X 3=3042 X 34 X 19=27132
# samples 6151
** MAII scorelog2(6/30*10)=1
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(151/27132*10)=-4.16737494326024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CACNG4 [Title/Abstract] AND VMP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCACNG4(64961247)-VMP1(57812699), # samples:2
CACNG4(64961247)-VMP1(57851115), # samples:2
Anticipated loss of major functional domain due to fusion event.CACNG4-VMP1 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
HgeneCACNG4

GO:2000311

regulation of AMPA receptor activity

21172611


check buttonFusion gene breakpoints across CACNG4 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across VMP1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BRCATCGA-C8-A12M-01ACACNG4chr17

64961247

-VMP1chr17

57812699

+
ChimerDB4BRCATCGA-C8-A12M-01ACACNG4chr17

64961247

+VMP1chr17

57812699

+
ChimerDB4PAADTCGA-2L-AAQE-01ACACNG4chr17

64961247

-VMP1chr17

57851115

+
ChimerDB4PAADTCGA-2L-AAQECACNG4chr17

64961247

+VMP1chr17

57851115

+
ChimerDB4PAADTCGA-2L-AAQECACNG4chr17

64961247

+VMP1chr17

57886157

+


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Fusion Gene ORF analysis for CACNG4-VMP1

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-5UTRENST00000262138ENST00000536180CACNG4chr17

64961247

+VMP1chr17

57812699

+
5CDS-5UTRENST00000262138ENST00000537567CACNG4chr17

64961247

+VMP1chr17

57812699

+
5CDS-5UTRENST00000262138ENST00000545362CACNG4chr17

64961247

+VMP1chr17

57812699

+
5CDS-intronENST00000262138ENST00000539763CACNG4chr17

64961247

+VMP1chr17

57812699

+
5CDS-intronENST00000262138ENST00000588617CACNG4chr17

64961247

+VMP1chr17

57812699

+
5CDS-intronENST00000262138ENST00000588617CACNG4chr17

64961247

+VMP1chr17

57851115

+
5CDS-intronENST00000262138ENST00000588617CACNG4chr17

64961247

+VMP1chr17

57886157

+
Frame-shiftENST00000262138ENST00000262291CACNG4chr17

64961247

+VMP1chr17

57851115

+
Frame-shiftENST00000262138ENST00000262291CACNG4chr17

64961247

+VMP1chr17

57886157

+
Frame-shiftENST00000262138ENST00000536180CACNG4chr17

64961247

+VMP1chr17

57851115

+
Frame-shiftENST00000262138ENST00000536180CACNG4chr17

64961247

+VMP1chr17

57886157

+
Frame-shiftENST00000262138ENST00000537567CACNG4chr17

64961247

+VMP1chr17

57851115

+
Frame-shiftENST00000262138ENST00000537567CACNG4chr17

64961247

+VMP1chr17

57886157

+
Frame-shiftENST00000262138ENST00000539763CACNG4chr17

64961247

+VMP1chr17

57851115

+
Frame-shiftENST00000262138ENST00000539763CACNG4chr17

64961247

+VMP1chr17

57886157

+
Frame-shiftENST00000262138ENST00000545362CACNG4chr17

64961247

+VMP1chr17

57851115

+
Frame-shiftENST00000262138ENST00000545362CACNG4chr17

64961247

+VMP1chr17

57886157

+
In-frameENST00000262138ENST00000262291CACNG4chr17

64961247

+VMP1chr17

57812699

+

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)
ENST00000262138CACNG4chr1764961247+ENST00000262291VMP1chr1757812699+254822221366454

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
ENST00000262138ENST00000262291CACNG4chr1764961247+VMP1chr1757812699+0.0003071150.9996929

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Fusion Genomic Features for CACNG4-VMP1


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)
CACNG4chr1764961247+VMP1chr1757812698+8.05E-060.999992
CACNG4chr1764961247+VMP1chr1757886156+1.05E-060.9999989
CACNG4chr1764961247+VMP1chr1757851114+7.53E-070.9999993
CACNG4chr1764961247+VMP1chr1757812698+8.05E-060.999992
CACNG4chr1764961247+VMP1chr1757886156+1.05E-060.9999989
CACNG4chr1764961247+VMP1chr1757851114+7.53E-070.9999993

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for CACNG4-VMP1


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/chr17:64961247/chr17:57812699)
- 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
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+141_973328.0Topological domainCytoplasmic
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+1410_3073328.0TransmembraneHelical
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112173_31625407.0RegionVTT domain
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112131_25025407.0Topological domainExtracellular
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112272_27325407.0Topological domainCytoplasmic
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112295_30525407.0Topological domainExtracellular
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112327_36325407.0Topological domainCytoplasmic
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112385_40625407.0Topological domainExtracellular
TgeneVMP1chr17:64961247chr17:57812699ENST0000026229111265_7725407.0Topological domainExtracellular
TgeneVMP1chr17:64961247chr17:57812699ENST0000026229111299_10925407.0Topological domainCytoplasmic
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112110_13025407.0TransmembraneHelical
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112251_27125407.0TransmembraneHelical
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112274_29425407.0TransmembraneHelical
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112306_32625407.0TransmembraneHelical
TgeneVMP1chr17:64961247chr17:57812699ENST00000262291112364_38425407.0TransmembraneHelical
TgeneVMP1chr17:64961247chr17:57812699ENST0000026229111244_6425407.0TransmembraneHelical
TgeneVMP1chr17:64961247chr17:57812699ENST0000026229111278_9825407.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+14129_13673328.0Topological domainCytoplasmic
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+14158_18673328.0Topological domainExtracellular
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+14208_32773328.0Topological domainCytoplasmic
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+1431_10773328.0Topological domainExtracellular
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+14108_12873328.0TransmembraneHelical
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+14137_15773328.0TransmembraneHelical
HgeneCACNG4chr17:64961247chr17:57812699ENST00000262138+14187_20773328.0TransmembraneHelical
TgeneVMP1chr17:64961247chr17:57812699ENST000002622911122_4325407.0Topological domainCytoplasmic


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Fusion Gene Sequence for CACNG4-VMP1


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.
>12418_12418_1_CACNG4-VMP1_CACNG4_chr17_64961247_ENST00000262138_VMP1_chr17_57812699_ENST00000262291_length(transcript)=2548nt_BP=222nt
CCATGGTGCGATGCGACCGCGGGCTGCAGATGCTGCTGACCACGGCCGGAGCCTTCGCCGCCTTCTCGCTCATGGCCATCGCCATCGGCA
CCGACTACTGGCTGTACTCCAGCGCGCACATCTGCAACGGCACCAACCTGACCATGGACGACGGGCCCCCGCCCCGCCGCGCCCGCGGCG
ACCTCACCCACTCTGGTCTGTGGCGGGTGTGCTGCATCGAAGACCCCTCTTCAGTGAATGAAAAGAAGAGGAGGGAGCGGGAAGAAAGGC
AGAATATTGTCCTGTGGAGACAGCCGCTCATTACCTTGCAGTATTTTTCTCTGGAAATCCTTGTAATCTTGAAGGAATGGACCTCAAAAT
TATGGCATCGTCAAAGCATTGTGGTGTCTTTTTTACTGCTGCTTGCTGTGCTTATAGCTACGTATTATGTTGAAGGAGTGCATCAACAGT
ATGTGCAACGTATAGAGAAACAGTTTCTTTTGTATGCCTACTGGATAGGCTTAGGAATTTTGTCTTCTGTTGGGCTTGGAACAGGGCTGC
ACACCTTTCTGCTTTATCTGGGTCCACATATAGCCTCAGTTACATTAGCTGCTTATGAATGCAATTCAGTTAATTTTCCCGAACCACCCT
ATCCTGATCAGATTATTTGTCCAGATGAAGAGGGCACTGAAGGAACCATTTCTTTGTGGAGTATCATCTCAAAAGTTAGGATTGAAGCCT
GCATGTGGGGTATCGGTACAGCAATCGGAGAGCTGCCTCCATATTTCATGGCCAGAGCAGCTCGCCTCTCAGGTGCTGAACCAGATGATG
AAGAGTATCAGGAATTTGAAGAGATGCTGGAACATGCAGAGTCTGCACAAGACTTTGCCTCCCGGGCCAAACTGGCAGTTCAAAAACTAG
TACAGAAAGTTGGATTTTTTGGAATTTTGGCCTGTGCTTCAATTCCAAATCCTTTATTTGATCTGGCTGGAATAACGTGTGGACACTTTC
TGGTACCTTTTTGGACCTTCTTTGGTGCAACCCTAATTGGAAAAGCAATAATAAAAATGCATATCCAGAAAATTTTTGTTATAATAACAT
TCAGCAAGCACATAGTGGAGCAAATGGTGGCTTTCATTGGTGCTGTCCCCGGCATAGGTCCATCTCTGCAGAAGCCATTTCAGGAGTACC
TGGAGGCTCAACGGCAGAAGCTTCACCACAAAAGCGAAATGGGCACACCACAGGGAGAAAACTGGTTGTCCTGGATGTTTGAAAAGTTGG
TCGTTGTCATGGTGTGTTACTTCATCCTATCTATCATTAACTCCATGGCACAAAGTTATGCCAAACGAATCCAGCAGCGGTTGAACTCAG
AGGAGAAAACTAAATAAGTAGAGAAAGTTTTAAACTGCAGAAATTGGAGTGGATGGGTTCTGCCTTAAATTGGGAGGACTCCAAGCCGGG
AAGGAAAATTCCCTTTTCCAACCTGTATCAATTTTTACAACTTTTTTCCTGAAAGCAGTTTAGTCCATACTTTGCACTGACATACTTTTT
CCTTCTGTGCTAAGGTAAGGTATCCACCCTCGATGCAATCCACCTTGTGTTTTCTTAGGGTGGAATGTGATGTTCAGCAGCAAACTTGCA
ACAGACTGGCCTTCTGTTTGTTACTTTCAAAAGGCCCACATGATACAATTAGAGAATTCCCACCGCACAAAAAAAGTTCCTAAGTATGTT
AAATATGTCAAGCTTTTTAGGCTTGTCACAAATGATTGCTTTGTTTTCCTAAGTCATCAAAATGTATATAAATTATCTAGATTGGATAAC
AGTCTTGCATGTTTATCATGTTACAATTTAATATTCCATCCTGCCCAACCCTTCCTCTCCCATCCTCAAAAAAGGGCCATTTTATGATGC
ATTGCACACCCTCTGGGGAAATTGATCTTTAAATTTTGAGACAGTATAAGGAAAATCTGGTTGGTGTCTTACAAGTGAGCTGACACCATT
TTTTATTCTGTGTATTTAGAATGAAGTCTTGAAAAAAACTTTATAAAGACATCTTTAATCATTCCAAAATTGTGTCCGTTTTCTTGAGCG
TTTTGATTTTTTACTTTTAGCTTATACCAGCTGAATGGCAGCCTTGCCTAATCCACCTACAACAAGAATTTCTTAAGCTTTCTTTTATTT
GCATGAGAGAGCCACTACCAAGGCATGTTTTGTTATGCTGAAACTGGGCTGCTGCATACTGCTAAATGGCACCTCTGGGATTGGCCTACC
TGGGGATTTCTTGGTTTGTGAAAACAGGAGAGGAGAAATATCTCATACAAGTGAAAGGATACTGGAGAGAGAAATTACCCATTTCTAAAA
AAAAACCACACTCTGTCGTATCTGTGTTAATGTTTTCTAGCATGTACTCTGGTTTCAACAGACACAAATTTATATGTTAACCCAGTTTTC
TTGCCGTTCTGTAAGTGTTTTATTCTTAGTGTGATTTTTTTCCATTGGGATGTTTTTGATTGAACTTGTTCATTTTGTTTTGCTTGGGAG

>12418_12418_1_CACNG4-VMP1_CACNG4_chr17_64961247_ENST00000262138_VMP1_chr17_57812699_ENST00000262291_length(amino acids)=454AA_BP=73
MVRCDRGLQMLLTTAGAFAAFSLMAIAIGTDYWLYSSAHICNGTNLTMDDGPPPRRARGDLTHSGLWRVCCIEDPSSVNEKKRREREERQ
NIVLWRQPLITLQYFSLEILVILKEWTSKLWHRQSIVVSFLLLLAVLIATYYVEGVHQQYVQRIEKQFLLYAYWIGLGILSSVGLGTGLH
TFLLYLGPHIASVTLAAYECNSVNFPEPPYPDQIICPDEEGTEGTISLWSIISKVRIEACMWGIGTAIGELPPYFMARAARLSGAEPDDE
EYQEFEEMLEHAESAQDFASRAKLAVQKLVQKVGFFGILACASIPNPLFDLAGITCGHFLVPFWTFFGATLIGKAIIKMHIQKIFVIITF
SKHIVEQMVAFIGAVPGIGPSLQKPFQEYLEAQRQKLHHKSEMGTPQGENWLSWMFEKLVVVMVCYFILSIINSMAQSYAKRIQQRLNSE

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Fusion Gene PPI Analysis for CACNG4-VMP1


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 CACNG4-VMP1


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 CACNG4-VMP1


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