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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:SMG1-MUSK (FusionGDB2 ID:83488)

Fusion Gene Summary for SMG1-MUSK

check button Fusion gene summary
Fusion gene informationFusion gene name: SMG1-MUSK
Fusion gene ID: 83488
HgeneTgene
Gene symbol

SMG1

MUSK

Gene ID

23049

4593

Gene nameSMG1 nonsense mediated mRNA decay associated PI3K related kinasemuscle associated receptor tyrosine kinase
Synonyms61E3.4|ATX|LIPCMS9|FADS|FADS1
Cytomap

16p12.3

9q31.3

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase SMG1PI-3-kinase-related kinase SMG-1SMG1 phosphatidylinositol 3-kinase-related kinaselambda-interacting proteinlambda/iota protein kinase C-interacting proteinsmg-1 homolog, phosphatidylinositol 3-kinase-related kinasemuscle, skeletal receptor tyrosine-protein kinasemuscle, skeletal, receptor tyrosine kinasemuscle-specific kinase receptormuscle-specific tyrosine-protein kinase receptor
Modification date2020031320200313
UniProtAcc.

O15146

Ensembl transtripts involved in fusion geneENST00000389467, ENST00000446231, 
ENST00000565224, ENST00000567737, 
ENST00000189978, ENST00000374448, 
ENST00000416899, ENST00000374440, 
ENST00000374439, ENST00000374438, 
Fusion gene scores* DoF score28 X 23 X 9=57965 X 6 X 2=60
# samples 317
** MAII scorelog2(31/5796*10)=-4.22471747428269
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/60*10)=0.222392421336448
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SMG1 [Title/Abstract] AND MUSK [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMG1(18888452)-MUSK(113496530), # samples:1
Anticipated loss of major functional domain due to fusion event.SMG1-MUSK seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
SMG1-MUSK seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
SMG1-MUSK seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
SMG1-MUSK seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
SMG1-MUSK seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
HgeneSMG1

GO:0000184

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

11544179

HgeneSMG1

GO:0018105

peptidyl-serine phosphorylation

11544179|15175154

HgeneSMG1

GO:0046777

protein autophosphorylation

11331269|11544179

HgeneSMG1

GO:0046854

phosphatidylinositol phosphorylation

11331269

HgeneSMG1

GO:2001020

regulation of response to DNA damage stimulus

15175154

TgeneMUSK

GO:0007528

neuromuscular junction development

25537362


check buttonFusion gene breakpoints across SMG1 (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 MUSK (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
ChimerDB4STADTCGA-IN-AB1XSMG1chr16

18888452

-MUSKchr9

113496530

+


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Fusion Gene ORF analysis for SMG1-MUSK

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
Frame-shiftENST00000389467ENST00000189978SMG1chr16

18888452

-MUSKchr9

113496530

+
Frame-shiftENST00000389467ENST00000374448SMG1chr16

18888452

-MUSKchr9

113496530

+
Frame-shiftENST00000389467ENST00000416899SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000389467ENST00000374440SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000389467ENST00000374439SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000389467ENST00000374438SMG1chr16

18888452

-MUSKchr9

113496530

+
Frame-shiftENST00000446231ENST00000189978SMG1chr16

18888452

-MUSKchr9

113496530

+
Frame-shiftENST00000446231ENST00000374448SMG1chr16

18888452

-MUSKchr9

113496530

+
Frame-shiftENST00000446231ENST00000416899SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000446231ENST00000374440SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000446231ENST00000374439SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000446231ENST00000374438SMG1chr16

18888452

-MUSKchr9

113496530

+
Frame-shiftENST00000565224ENST00000189978SMG1chr16

18888452

-MUSKchr9

113496530

+
Frame-shiftENST00000565224ENST00000374448SMG1chr16

18888452

-MUSKchr9

113496530

+
Frame-shiftENST00000565224ENST00000416899SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000565224ENST00000374440SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000565224ENST00000374439SMG1chr16

18888452

-MUSKchr9

113496530

+
5CDS-intronENST00000565224ENST00000374438SMG1chr16

18888452

-MUSKchr9

113496530

+
intron-3CDSENST00000567737ENST00000189978SMG1chr16

18888452

-MUSKchr9

113496530

+
intron-3CDSENST00000567737ENST00000374448SMG1chr16

18888452

-MUSKchr9

113496530

+
intron-3CDSENST00000567737ENST00000416899SMG1chr16

18888452

-MUSKchr9

113496530

+
intron-intronENST00000567737ENST00000374440SMG1chr16

18888452

-MUSKchr9

113496530

+
intron-intronENST00000567737ENST00000374439SMG1chr16

18888452

-MUSKchr9

113496530

+
intron-intronENST00000567737ENST00000374438SMG1chr16

18888452

-MUSKchr9

113496530

+

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 SMG1-MUSK


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)
SMG1chr1618888452-MUSKchr9113496530+0.74889970.25110036
SMG1chr1618888452-MUSKchr9113496530+0.74889970.25110036

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 SMG1-MUSK


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
.MUSK

O15146

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.FUNCTION: Receptor tyrosine kinase which plays a central role in the formation and the maintenance of the neuromuscular junction (NMJ), the synapse between the motor neuron and the skeletal muscle (PubMed:25537362). Recruitment of AGRIN by LRP4 to the MUSK signaling complex induces phosphorylation and activation of MUSK, the kinase of the complex. The activation of MUSK in myotubes regulates the formation of NMJs through the regulation of different processes including the specific expression of genes in subsynaptic nuclei, the reorganization of the actin cytoskeleton and the clustering of the acetylcholine receptors (AChR) in the postsynaptic membrane. May regulate AChR phosphorylation and clustering through activation of ABL1 and Src family kinases which in turn regulate MUSK. DVL1 and PAK1 that form a ternary complex with MUSK are also important for MUSK-dependent regulation of AChR clustering. May positively regulate Rho family GTPases through FNTA. Mediates the phosphorylation of FNTA which promotes prenylation, recruitment to membranes and activation of RAC1 a regulator of the actin cytoskeleton and of gene expression. Other effectors of the MUSK signaling include DNAJA3 which functions downstream of MUSK. May also play a role within the central nervous system by mediating cholinergic responses, synaptic plasticity and memory formation (By similarity). {ECO:0000250, ECO:0000269|PubMed:25537362}.

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 SMG1-MUSK


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 SMG1-MUSK


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 SMG1-MUSK


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneMUSKO15146DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for SMG1-MUSK


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneMUSKC4225368MYASTHENIC SYNDROME, CONGENITAL, 9, ASSOCIATED WITH ACETYLCHOLINE RECEPTOR DEFICIENCY6GENOMICS_ENGLAND;UNIPROT
TgeneMUSKC0026896Myasthenia Gravis2CTD_human
TgeneMUSKC0751339Myasthenia Gravis, Generalized2CTD_human
TgeneMUSKC0751340Myasthenia Gravis, Ocular2CTD_human
TgeneMUSKC1276035Pena-Shokeir syndrome type I2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneMUSKC0751882Myasthenic Syndromes, Congenital1GENOMICS_ENGLAND