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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:MAGED1-STAMBP (FusionGDB2 ID:50502)

Fusion Gene Summary for MAGED1-STAMBP

check button Fusion gene summary
Fusion gene informationFusion gene name: MAGED1-STAMBP
Fusion gene ID: 50502
HgeneTgene
Gene symbol

MAGED1

STAMBP

Gene ID

9500

10617

Gene nameMAGE family member D1STAM binding protein
SynonymsDLXIN-1|NRAGEAMSH|MICCAP
Cytomap

Xp11.22

2p13.1

Type of geneprotein-codingprotein-coding
Descriptionmelanoma-associated antigen D1MAGE tumor antigen CCFMAGE-D1 antigenmelanoma antigen family D, 1melanoma antigen family D1neurotrophin receptor-interacting MAGE homologSTAM-binding proteinassociated molecule with the SH3 domain of STAMendosome-associated ubiquitin isopeptidasetesticular secretory protein Li 54
Modification date2020032020200313
UniProtAcc

Q9Y5V3

.
Ensembl transtripts involved in fusion geneENST00000375772, ENST00000375722, 
ENST00000326587, ENST00000375695, 
ENST00000494718, 		ENST00000339566, 
ENST00000409707, ENST00000394073, 
ENST00000394070, ENST00000536064, 
ENST00000486458, 
Fusion gene scores* DoF score10 X 6 X 5=3007 X 7 X 5=245
# samples 109
** MAII scorelog2(10/300*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/245*10)=-1.4447848426729
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MAGED1 [Title/Abstract] AND STAMBP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMAGED1(51546213)-STAMBP(74086380), # 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
HgeneMAGED1

GO:0050680

negative regulation of epithelial cell proliferation

15930293


check buttonFusion gene breakpoints across MAGED1 (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 STAMBP (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
ChimerDB4BLCATCGA-KQ-A41OMAGED1chrX

51546213

+STAMBPchr2

74086380

+


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Fusion Gene ORF analysis for MAGED1-STAMBP

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
5UTR-3CDSENST00000375772ENST00000339566MAGED1chrX

51546213

+STAMBPchr2

74086380

+
5UTR-3CDSENST00000375772ENST00000409707MAGED1chrX

51546213

+STAMBPchr2

74086380

+
5UTR-3CDSENST00000375772ENST00000394073MAGED1chrX

51546213

+STAMBPchr2

74086380

+
5UTR-3CDSENST00000375772ENST00000394070MAGED1chrX

51546213

+STAMBPchr2

74086380

+
5UTR-intronENST00000375772ENST00000536064MAGED1chrX

51546213

+STAMBPchr2

74086380

+
5UTR-3UTRENST00000375772ENST00000486458MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000375722ENST00000339566MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000375722ENST00000409707MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000375722ENST00000394073MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000375722ENST00000394070MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-intronENST00000375722ENST00000536064MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3UTRENST00000375722ENST00000486458MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000326587ENST00000339566MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000326587ENST00000409707MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000326587ENST00000394073MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000326587ENST00000394070MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-intronENST00000326587ENST00000536064MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3UTRENST00000326587ENST00000486458MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000375695ENST00000339566MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000375695ENST00000409707MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000375695ENST00000394073MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000375695ENST00000394070MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-intronENST00000375695ENST00000536064MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3UTRENST00000375695ENST00000486458MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000494718ENST00000339566MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000494718ENST00000409707MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000494718ENST00000394073MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3CDSENST00000494718ENST00000394070MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-intronENST00000494718ENST00000536064MAGED1chrX

51546213

+STAMBPchr2

74086380

+
intron-3UTRENST00000494718ENST00000486458MAGED1chrX

51546213

+STAMBPchr2

74086380

+

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 MAGED1-STAMBP


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 MAGED1-STAMBP


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
MAGED1

Q9Y5V3

.
FUNCTION: Involved in the apoptotic response after nerve growth factor (NGF) binding in neuronal cells. Inhibits cell cycle progression, and facilitates NGFR-mediated apoptosis. May act as a regulator of the function of DLX family members. May enhance ubiquitin ligase activity of RING-type zinc finger-containing E3 ubiquitin-protein ligases. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. Plays a role in the circadian rhythm regulation. May act as RORA co-regulator, modulating the expression of core clock genes such as ARNTL/BMAL1 and NFIL3, induced, or NR1D1, repressed. {ECO:0000269|PubMed:20864041}.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.

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 MAGED1-STAMBP


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 MAGED1-STAMBP


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 MAGED1-STAMBP


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 MAGED1-STAMBP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSTAMBPC3280296Microcephaly-capillary malformation syndrome2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneSTAMBPC0006111Brain Diseases1CTD_human
TgeneSTAMBPC0008073Developmental Disabilities1CTD_human
TgeneSTAMBPC0014544Epilepsy1CTD_human
TgeneSTAMBPC0025958Microcephaly1CTD_human
TgeneSTAMBPC0085584Encephalopathies1CTD_human
TgeneSTAMBPC0085996Child Development Deviations1CTD_human
TgeneSTAMBPC0085997Child Development Disorders, Specific1CTD_human
TgeneSTAMBPC0086237Epilepsy, Cryptogenic1CTD_human
TgeneSTAMBPC0236018Aura1CTD_human
TgeneSTAMBPC0751111Awakening Epilepsy1CTD_human
TgeneSTAMBPC1842180CAPILLARY MALFORMATION-ARTERIOVENOUS MALFORMATION (disorder)1CTD_human
TgeneSTAMBPC1956147Microlissencephaly1CTD_human
TgeneSTAMBPC2675370Capillary Malformation Without Arteriovenous Malformation1CTD_human
TgeneSTAMBPC3853041Severe Congenital Microcephaly1CTD_human