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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:MAGED2-CNTNAP2 (FusionGDB2 ID:HG10916TG26047)

Fusion Gene Summary for MAGED2-CNTNAP2

check button Fusion gene summary
Fusion gene informationFusion gene name: MAGED2-CNTNAP2
Fusion gene ID: hg10916tg26047
HgeneTgene
Gene symbol

MAGED2

CNTNAP2

Gene ID

10916

26047

Gene nameMAGE family member D2contactin associated protein 2
Synonyms11B6|BARTS5|BCG-1|BCG1|HCA10|MAGE-D2AUTS15|CASPR2|CDFE|NRXN4|PTHSL1
Cytomap('MAGED2')('CNTNAP2')

Xp11.21

7q35-q36.1

Type of geneprotein-codingprotein-coding
Descriptionmelanoma-associated antigen D2MAGE-D2 antigenbreast cancer-associated gene 1 proteinhepatocellular carcinoma-associated protein JCL-1melanoma antigen family D, 2melanoma antigen family D2contactin-associated protein-like 2cell recognition molecule Caspr2contactin associated protein like 2homolog of Drosophila neurexin IV
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000347546, ENST00000375058, 
ENST00000375060, ENST00000375068, 
ENST00000218439, ENST00000375053, 
ENST00000375062, ENST00000396224, 
ENST00000497484, 
Fusion gene scores* DoF score13 X 9 X 4=46830 X 34 X 9=9180
# samples 1336
** MAII scorelog2(13/468*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(36/9180*10)=-4.6724253419715
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MAGED2 [Title/Abstract] AND CNTNAP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMAGED2(54842443)-CNTNAP2(147991953), # 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


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
ChiTaRS5.0N/AEC578199MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+


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Fusion Gene ORF analysis for MAGED2-CNTNAP2

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-intronENST00000347546ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000347546ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000347546ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375058ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375058ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375058ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375060ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375060ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375060ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375068ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375068ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
5CDS-intronENST00000375068ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000218439ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000218439ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000218439ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000375053ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000375053ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000375053ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000375062ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000375062ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000375062ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000396224ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000396224ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000396224ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000497484ENST00000361727MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000497484ENST00000463592MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+
intron-intronENST00000497484ENST00000538075MAGED2chrX

54842443

+CNTNAP2chr7

147991953

+

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 MAGED2-CNTNAP2


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 MAGED2-CNTNAP2


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/:54842443/:147991953)
- 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 MAGED2-CNTNAP2


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 MAGED2-CNTNAP2


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 MAGED2-CNTNAP2


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 MAGED2-CNTNAP2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMAGED2C1866495Bartter syndrome, antenatal type 11ORPHANET
HgeneMAGED2C4310820BARTTER SYNDROME, TYPE 5, ANTENATAL, TRANSIENT1CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0004352Autistic Disorder4CTD_human
TgeneC1510586Autism Spectrum Disorders4CTD_human
TgeneC0023012Language Delay3CTD_human
TgeneC0023014Language Development Disorders3CTD_human
TgeneC0241210Speech Delay3CTD_human
TgeneC0454655Semantic-Pragmatic Disorder3CTD_human
TgeneC0751257Auditory Processing Disorder, Central3CTD_human
TgeneC0014544Epilepsy2CTD_human
TgeneC0086237Epilepsy, Cryptogenic2CTD_human
TgeneC0236018Aura2CTD_human
TgeneC0751111Awakening Epilepsy2CTD_human
TgeneC2750246Pitt-Hopkins-Like Syndrome 12CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneC0005586Bipolar Disorder1PSYGENET
TgeneC0030567Parkinson Disease1CTD_human
TgeneC0036341Schizophrenia1CTD_human
TgeneC0038131Stammering1CTD_human
TgeneC0038506Stuttering1CTD_human
TgeneC0041696Unipolar Depression1PSYGENET
TgeneC0149925Small cell carcinoma of lung1CTD_human
TgeneC0454542Stuttering, Acquired1CTD_human
TgeneC0751217Hyperkinesia, Generalized1CTD_human
TgeneC0751527Stuttering, Adult1CTD_human
TgeneC0751528Stuttering, Childhood1CTD_human
TgeneC0751529Stuttering, Developmental1CTD_human
TgeneC1269683Major Depressive Disorder1PSYGENET
TgeneC1970431PITT-HOPKINS SYNDROME1CTD_human
TgeneC3489627Stuttering, Familial Persistent 11CTD_human
TgeneC3887506Hyperkinesia1CTD_human
TgeneC4552043Cortical dysplasia with focal epilepsy syndrome1CTD_human;GENOMICS_ENGLAND;ORPHANET