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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:CNIH2-MS4A4A (FusionGDB2 ID:HG254263TG51338)

Fusion Gene Summary for CNIH2-MS4A4A

check button Fusion gene summary
Fusion gene informationFusion gene name: CNIH2-MS4A4A
Fusion gene ID: hg254263tg51338
HgeneTgene
Gene symbol

CNIH2

MS4A4A

Gene ID

254263

51338

Gene namecornichon family AMPA receptor auxiliary protein 2membrane spanning 4-domains A4A
SynonymsCNIH-2|Cnil4SPAN1|CD20-L1|CD20L1|HDCME31P|MS4A4|MS4A7
Cytomap('CNIH2')('MS4A4A')

11q13.2

11q12.2

Type of geneprotein-codingprotein-coding
Descriptionprotein cornichon homolog 2cornichon homolog 2membrane-spanning 4-domains subfamily A member 4ACD20 antigen-like 1Fc epsilon receptor beta subunit homologepididymis secretory sperm binding proteinfour-span transmembrane protein 1membrane-spanning 4-domains, subfamily A, member 4
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000530519, ENST00000311445, 
ENST00000528852, 
Fusion gene scores* DoF score1 X 1 X 1=14 X 2 X 4=32
# samples 14
** MAII scorelog2(1/1*10)=3.32192809488736log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CNIH2 [Title/Abstract] AND MS4A4A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCNIH2(66046008)-MS4A4A(60059698), # samples:2
Anticipated loss of major functional domain due to fusion event.CNIH2-MS4A4A seems lost the major protein functional domain in Hgene 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
HgeneCNIH2

GO:2000311

regulation of AMPA receptor activity

20805473



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
ChimerDB4SKCMTCGA-D9-A4Z5-01ACNIH2chr11

66046008

-MS4A4Achr11

60059698

+
ChimerDB4SKCMTCGA-D9-A4Z5-01ACNIH2chr11

66046008

+MS4A4Achr11

60059698

+


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Fusion Gene ORF analysis for CNIH2-MS4A4A

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-3CDSENST00000530519ENST00000337908CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
3UTR-3CDSENST00000530519ENST00000532114CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
3UTR-5UTRENST00000530519ENST00000355131CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
3UTR-5UTRENST00000530519ENST00000395016CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
5CDS-5UTRENST00000311445ENST00000355131CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
5CDS-5UTRENST00000311445ENST00000395016CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
5CDS-5UTRENST00000528852ENST00000355131CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
5CDS-5UTRENST00000528852ENST00000395016CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
Frame-shiftENST00000311445ENST00000337908CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
Frame-shiftENST00000311445ENST00000532114CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
Frame-shiftENST00000528852ENST00000337908CNIH2chr11

66046008

+MS4A4Achr11

60059698

+
Frame-shiftENST00000528852ENST00000532114CNIH2chr11

66046008

+MS4A4Achr11

60059698

+

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 CNIH2-MS4A4A


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)
CNIH2chr1166046008+MS4A4Achr1160059697+0.0337012670.9662987
CNIH2chr1166046008+MS4A4Achr1160059697+0.0337012670.9662987


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 CNIH2-MS4A4A


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/:66046008/:60059698)
- 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 CNIH2-MS4A4A


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 CNIH2-MS4A4A


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 CNIH2-MS4A4A


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 CNIH2-MS4A4A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0002395Alzheimer's Disease1CTD_human
TgeneC0011265Presenile dementia1CTD_human
TgeneC0087031Juvenile-Onset Still Disease1CTD_human
TgeneC0276496Familial Alzheimer Disease (FAD)1CTD_human
TgeneC0494463Alzheimer Disease, Late Onset1CTD_human
TgeneC0546126Acute Confusional Senile Dementia1CTD_human
TgeneC0750900Alzheimer's Disease, Focal Onset1CTD_human
TgeneC0750901Alzheimer Disease, Early Onset1CTD_human
TgeneC3495559Juvenile arthritis1CTD_human
TgeneC3714758Juvenile psoriatic arthritis1CTD_human
TgeneC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
TgeneC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human