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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:MSN-ALK (FusionGDB2 ID:HG4478TG238)

Fusion Gene Summary for MSN-ALK

check button Fusion gene summary
Fusion gene informationFusion gene name: MSN-ALK
Fusion gene ID: hg4478tg238
HgeneTgene
Gene symbol

MSN

ALK

Gene ID

4478

238

Gene namemoesinALK receptor tyrosine kinase
SynonymsHEL70|IMD50CD246|NBLST3
Cytomap('MSN')('ALK')

Xq12

2p23.2-p23.1

Type of geneprotein-codingprotein-coding
Descriptionmoesinepididymis luminal protein 70membrane-organizing extension spike proteinALK tyrosine kinase receptorCD246 antigenanaplastic lymphoma receptor tyrosine kinasemutant anaplastic lymphoma kinase
Modification date2020032720200329
UniProtAcc

P26038

Q9UM73

Ensembl transtripts involved in fusion geneENST00000360270, ENST00000609205, 
ENST00000360270, ENST00000609205, 
Fusion gene scores* DoF score10 X 11 X 5=55056 X 74 X 20=82880
# samples 1257
** MAII scorelog2(12/550*10)=-2.1963972128035
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(57/82880*10)=-7.18391827352181
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MSN [Title/Abstract] AND ALK [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMSN(64958831)-ALK(29446322), # samples:1
MSN(64958831)-ALK(29446377), # samples:1
MSN(64958479)-ALK(29446377), # samples:1
Anticipated loss of major functional domain due to fusion event.MSN-ALK seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
MSN-ALK seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
MSN-ALK seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
MSN-ALK seems lost the major protein functional domain in Tgene partner, which is a kinase 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
HgeneMSN

GO:0001771

immunological synapse formation

27405666

HgeneMSN

GO:0042098

T cell proliferation

27405666

HgeneMSN

GO:0070489

T cell aggregation

27405666

HgeneMSN

GO:0071394

cellular response to testosterone stimulus

24065547

HgeneMSN

GO:0072678

T cell migration

27405666

TgeneALK

GO:0016310

phosphorylation

9174053

TgeneALK

GO:0046777

protein autophosphorylation

9174053



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
ChimerDB4anaplastic large cell lymphomaAF295078MSNchrX

64958831

ALKchr2

29446322
ChimerKB3..MSNchrX

64957200

+ALKchr2

29446394

-
ChimerKB3..MSNchrX

64958479

+ALKchr2

29445405

-
ChimerKB3..MSNchrX

64958479

+ALKchr2

29446394

-
ChimerKB3..MSNchrX

64958831

+ALKchr2

29446322

-
ChiTaRS5.0N/AAF295078MSNchrX

64958831

+ALKchr2

29446377

-
ChiTaRS5.0N/AAF295356MSNchrX

64958479

+ALKchr2

29446377

-


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Fusion Gene ORF analysis for MSN-ALK

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-intronENST00000360270ENST00000431873MSNchrX

64957200

+ALKchr2

29446394

-
5CDS-intronENST00000360270ENST00000431873MSNchrX

64958479

+ALKchr2

29445405

-
5CDS-intronENST00000360270ENST00000431873MSNchrX

64958479

+ALKchr2

29446394

-
5CDS-intronENST00000360270ENST00000431873MSNchrX

64958479

+ALKchr2

29446377

-
5CDS-intronENST00000360270ENST00000498037MSNchrX

64957200

+ALKchr2

29446394

-
5CDS-intronENST00000360270ENST00000498037MSNchrX

64958479

+ALKchr2

29445405

-
5CDS-intronENST00000360270ENST00000498037MSNchrX

64958479

+ALKchr2

29446394

-
5CDS-intronENST00000360270ENST00000498037MSNchrX

64958479

+ALKchr2

29446377

-
Frame-shiftENST00000360270ENST00000389048MSNchrX

64957200

+ALKchr2

29446394

-
Frame-shiftENST00000360270ENST00000389048MSNchrX

64958479

+ALKchr2

29445405

-
Frame-shiftENST00000360270ENST00000389048MSNchrX

64958479

+ALKchr2

29446394

-
Frame-shiftENST00000360270ENST00000389048MSNchrX

64958479

+ALKchr2

29446377

-
intron-3CDSENST00000360270ENST00000389048MSNchrX

64958831

ALKchr2

29446322

intron-3CDSENST00000360270ENST00000389048MSNchrX

64958831

+ALKchr2

29446322

-
intron-3CDSENST00000360270ENST00000389048MSNchrX

64958831

+ALKchr2

29446377

-
intron-3CDSENST00000609205ENST00000389048MSNchrX

64958831

ALKchr2

29446322

intron-3CDSENST00000609205ENST00000389048MSNchrX

64957200

+ALKchr2

29446394

-
intron-3CDSENST00000609205ENST00000389048MSNchrX

64958479

+ALKchr2

29445405

-
intron-3CDSENST00000609205ENST00000389048MSNchrX

64958479

+ALKchr2

29446394

-
intron-3CDSENST00000609205ENST00000389048MSNchrX

64958831

+ALKchr2

29446322

-
intron-3CDSENST00000609205ENST00000389048MSNchrX

64958831

+ALKchr2

29446377

-
intron-3CDSENST00000609205ENST00000389048MSNchrX

64958479

+ALKchr2

29446377

-
intron-intronENST00000360270ENST00000431873MSNchrX

64958831

ALKchr2

29446322

intron-intronENST00000360270ENST00000431873MSNchrX

64958831

+ALKchr2

29446322

-
intron-intronENST00000360270ENST00000431873MSNchrX

64958831

+ALKchr2

29446377

-
intron-intronENST00000360270ENST00000498037MSNchrX

64958831

ALKchr2

29446322

intron-intronENST00000360270ENST00000498037MSNchrX

64958831

+ALKchr2

29446322

-
intron-intronENST00000360270ENST00000498037MSNchrX

64958831

+ALKchr2

29446377

-
intron-intronENST00000609205ENST00000431873MSNchrX

64958831

ALKchr2

29446322

intron-intronENST00000609205ENST00000431873MSNchrX

64957200

+ALKchr2

29446394

-
intron-intronENST00000609205ENST00000431873MSNchrX

64958479

+ALKchr2

29445405

-
intron-intronENST00000609205ENST00000431873MSNchrX

64958479

+ALKchr2

29446394

-
intron-intronENST00000609205ENST00000431873MSNchrX

64958831

+ALKchr2

29446322

-
intron-intronENST00000609205ENST00000431873MSNchrX

64958831

+ALKchr2

29446377

-
intron-intronENST00000609205ENST00000431873MSNchrX

64958479

+ALKchr2

29446377

-
intron-intronENST00000609205ENST00000498037MSNchrX

64958831

ALKchr2

29446322

intron-intronENST00000609205ENST00000498037MSNchrX

64957200

+ALKchr2

29446394

-
intron-intronENST00000609205ENST00000498037MSNchrX

64958479

+ALKchr2

29445405

-
intron-intronENST00000609205ENST00000498037MSNchrX

64958479

+ALKchr2

29446394

-
intron-intronENST00000609205ENST00000498037MSNchrX

64958831

+ALKchr2

29446322

-
intron-intronENST00000609205ENST00000498037MSNchrX

64958831

+ALKchr2

29446377

-
intron-intronENST00000609205ENST00000498037MSNchrX

64958479

+ALKchr2

29446377

-

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 MSN-ALK


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 MSN-ALK


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/:64958831/:29446322)
- 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
MSN

P26038

ALK

Q9UM73

FUNCTION: Ezrin-radixin-moesin (ERM) family protein that connects the actin cytoskeleton to the plasma membrane and thereby regulates the structure and function of specific domains of the cell cortex. Tethers actin filaments by oscillating between a resting and an activated state providing transient interactions between moesin and the actin cytoskeleton (PubMed:10212266). Once phosphorylated on its C-terminal threonine, moesin is activated leading to interaction with F-actin and cytoskeletal rearrangement (PubMed:10212266). These rearrangements regulate many cellular processes, including cell shape determination, membrane transport, and signal transduction (PubMed:12387735, PubMed:15039356). The role of moesin is particularly important in immunity acting on both T and B-cells homeostasis and self-tolerance, regulating lymphocyte egress from lymphoid organs (PubMed:9298994, PubMed:9616160). Modulates phagolysosomal biogenesis in macrophages (By similarity). Participates also in immunologic synapse formation (PubMed:27405666). {ECO:0000250|UniProtKB:P26041, ECO:0000269|PubMed:10212266, ECO:0000269|PubMed:12387735, ECO:0000269|PubMed:15039356, ECO:0000269|PubMed:27405666, ECO:0000269|PubMed:9298994, ECO:0000269|PubMed:9616160}.FUNCTION: Neuronal receptor tyrosine kinase that is essentially and transiently expressed in specific regions of the central and peripheral nervous systems and plays an important role in the genesis and differentiation of the nervous system. Transduces signals from ligands at the cell surface, through specific activation of the mitogen-activated protein kinase (MAPK) pathway. Phosphorylates almost exclusively at the first tyrosine of the Y-x-x-x-Y-Y motif. Following activation by ligand, ALK induces tyrosine phosphorylation of CBL, FRS2, IRS1 and SHC1, as well as of the MAP kinases MAPK1/ERK2 and MAPK3/ERK1. Acts as a receptor for ligands pleiotrophin (PTN), a secreted growth factor, and midkine (MDK), a PTN-related factor, thus participating in PTN and MDK signal transduction. PTN-binding induces MAPK pathway activation, which is important for the anti-apoptotic signaling of PTN and regulation of cell proliferation. MDK-binding induces phosphorylation of the ALK target insulin receptor substrate (IRS1), activates mitogen-activated protein kinases (MAPKs) and PI3-kinase, resulting also in cell proliferation induction. Drives NF-kappa-B activation, probably through IRS1 and the activation of the AKT serine/threonine kinase. Recruitment of IRS1 to activated ALK and the activation of NF-kappa-B are essential for the autocrine growth and survival signaling of MDK. Thinness gene involved in the resistance to weight gain: in hypothalamic neurons, controls energy expenditure acting as a negative regulator of white adipose tissue lipolysis and sympathetic tone to fine-tune energy homeostasis (By similarity). {ECO:0000250|UniProtKB:P97793, ECO:0000269|PubMed:11121404, ECO:0000269|PubMed:11278720, ECO:0000269|PubMed:11387242, ECO:0000269|PubMed:11809760, ECO:0000269|PubMed:12107166, ECO:0000269|PubMed:12122009, ECO:0000269|PubMed:15226403, ECO:0000269|PubMed:15908427, ECO:0000269|PubMed:16317043, ECO:0000269|PubMed:16878150, ECO:0000269|PubMed:17274988}.

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 MSN-ALK


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 MSN-ALK


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 MSN-ALK


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneALKQ9UM73DB08865CrizotinibInhibitorSmall moleculeApproved
TgeneALKQ9UM73DB09063CeritinibAntagonistSmall moleculeApproved
TgeneALKQ9UM73DB11363AlectinibInhibitorSmall moleculeApproved|Investigational
TgeneALKQ9UM73DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneALKQ9UM73DB12130LorlatinibInhibitorSmall moleculeApproved|Investigational
TgeneALKQ9UM73DB12141GilteritinibInhibitorSmall moleculeApproved|Investigational
TgeneALKQ9UM73DB12267BrigatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for MSN-ALK


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMSNC4310812IMMUNODEFICIENCY 502CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneMSNC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneMSNC0029408Degenerative polyarthritis1CTD_human
HgeneMSNC0086743Osteoarthrosis Deformans1CTD_human
HgeneMSNC0087031Juvenile-Onset Still Disease1CTD_human
HgeneMSNC0151744Myocardial Ischemia1CTD_human
HgeneMSNC0494261Combined immunodeficiency1GENOMICS_ENGLAND
HgeneMSNC3495559Juvenile arthritis1CTD_human
HgeneMSNC3714758Juvenile psoriatic arthritis1CTD_human
HgeneMSNC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneMSNC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneC0007131Non-Small Cell Lung Carcinoma28CGI;CTD_human
TgeneC0027819Neuroblastoma13CGI;CTD_human;ORPHANET
TgeneC0152013Adenocarcinoma of lung (disorder)8CGI;CTD_human
TgeneC2751681NEUROBLASTOMA, SUSCEPTIBILITY TO, 38CLINGEN;UNIPROT
TgeneC0206180Ki-1+ Anaplastic Large Cell Lymphoma6CGI;CTD_human
TgeneC0334121Inflammatory Myofibroblastic Tumor4CGI;CTD_human;ORPHANET
TgeneC0018199Granuloma, Plasma Cell3CTD_human
TgeneC0007621Neoplastic Cell Transformation2CTD_human
TgeneC0027627Neoplasm Metastasis2CTD_human
TgeneC0238463Papillary thyroid carcinoma2ORPHANET
TgeneC0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneC0006118Brain Neoplasms1CGI;CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0011570Mental Depression1PSYGENET
TgeneC0011581Depressive disorder1PSYGENET
TgeneC0027643Neoplasm Recurrence, Local1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0079744Diffuse Large B-Cell Lymphoma1CTD_human
TgeneC0085269Plasma Cell Granuloma, Pulmonary1CTD_human
TgeneC0153633Malignant neoplasm of brain1CGI;CTD_human
TgeneC0278601Inflammatory Breast Carcinoma1CTD_human
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneC0496899Benign neoplasm of brain, unspecified1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0750974Brain Tumor, Primary1CTD_human
TgeneC0750977Recurrent Brain Neoplasm1CTD_human
TgeneC0750979Primary malignant neoplasm of brain1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC1332079Anaplastic Large Cell Lymphoma, ALK-Positive1ORPHANET
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1527390Neoplasms, Intracranial1CTD_human
TgeneC2931189Neural crest tumor1ORPHANET
TgeneC3899155hereditary neuroblastoma1GENOMICS_ENGLAND
TgeneC4704874Mammary Carcinoma, Human1CTD_human