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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:CHMP1A-SPIRE2 (FusionGDB2 ID:HG5119TG84501)

Fusion Gene Summary for CHMP1A-SPIRE2

check button Fusion gene summary
Fusion gene informationFusion gene name: CHMP1A-SPIRE2
Fusion gene ID: hg5119tg84501
HgeneTgene
Gene symbol

CHMP1A

SPIRE2

Gene ID

5119

84501

Gene namecharged multivesicular body protein 1Aspire type actin nucleation factor 2
SynonymsCHMP1|PCH8|PCOLN3|PRSM1|VPS46-1|VPS46ASpir-2
Cytomap('CHMP1A')('SPIRE2')

16q24.3

16q24.3

Type of geneprotein-codingprotein-coding
Descriptioncharged multivesicular body protein 1acharged multivesicular body protein 1/chromatin modifying protein 1chromatin modifying protein 1Aprocollagen (type III) N-endopeptidaseprotease, metallo, 1, 33kDvacuolar protein sorting-associated protein 46-1protein spire homolog 2spire actin nucleation factor 2spire family actin nucleation factor 2spire homolog 2
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000253475, ENST00000397901, 
ENST00000535997, ENST00000547614, 
ENST00000550102, 
Fusion gene scores* DoF score6 X 9 X 5=2708 X 8 X 6=384
# samples 910
** MAII scorelog2(9/270*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/384*10)=-1.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHMP1A [Title/Abstract] AND SPIRE2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHMP1A(89715759)-SPIRE2(89924746), # samples:3
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
HgeneCHMP1A

GO:0007076

mitotic chromosome condensation

11559747

HgeneCHMP1A

GO:0016192

vesicle-mediated transport

11559748

HgeneCHMP1A

GO:0016458

gene silencing

11559747

HgeneCHMP1A

GO:0045892

negative regulation of transcription, DNA-templated

11559747



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
ChimerDB4GBMTCGA-06-0210-01ACHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
ChimerDB4GBMTCGA-06-0210-02ACHMP1Achr16

89715759

-SPIRE2chr16

89924746

+


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Fusion Gene ORF analysis for CHMP1A-SPIRE2

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-intronENST00000253475ENST00000378247CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000253475ENST00000393062CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000253475ENST00000563972CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000253475ENST00000564878CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000397901ENST00000378247CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000397901ENST00000393062CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000397901ENST00000563972CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000397901ENST00000564878CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000535997ENST00000378247CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000535997ENST00000393062CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000535997ENST00000563972CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5CDS-intronENST00000535997ENST00000564878CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5UTR-intronENST00000547614ENST00000378247CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5UTR-intronENST00000547614ENST00000393062CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5UTR-intronENST00000547614ENST00000563972CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
5UTR-intronENST00000547614ENST00000564878CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
intron-intronENST00000550102ENST00000378247CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
intron-intronENST00000550102ENST00000393062CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
intron-intronENST00000550102ENST00000563972CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+
intron-intronENST00000550102ENST00000564878CHMP1Achr16

89715759

-SPIRE2chr16

89924746

+

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 CHMP1A-SPIRE2


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)
CHMP1Achr1689715758-SPIRE2chr1689924745+0.0067917590.9932082
CHMP1Achr1689715758-SPIRE2chr1689924745+0.0067917590.9932082
CHMP1Achr1689715758-SPIRE2chr1689924745+0.0067917590.9932082
CHMP1Achr1689715758-SPIRE2chr1689924745+0.0067917590.9932082


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 CHMP1A-SPIRE2


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/:89715759/:89924746)
- 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 CHMP1A-SPIRE2


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 CHMP1A-SPIRE2


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 CHMP1A-SPIRE2


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 CHMP1A-SPIRE2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCHMP1AC0266468Congenital pontocerebellar hypoplasia1GENOMICS_ENGLAND
HgeneCHMP1AC3554209Congenital pontocerebellar hypoplasia type 81CTD_human;GENOMICS_ENGLAND;ORPHANET