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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:CDKN2A-MGA (FusionGDB2 ID:15408)

Fusion Gene Summary for CDKN2A-MGA

check button Fusion gene summary
Fusion gene informationFusion gene name: CDKN2A-MGA
Fusion gene ID: 15408
HgeneTgene
Gene symbol

CDKN2A

MGA

Gene ID

1029

23269

Gene namecyclin dependent kinase inhibitor 2AMAX dimerization protein MGA
SynonymsARF|CDK4I|CDKN2|CMM2|INK4|INK4A|MLM|MTS-1|MTS1|P14|P14ARF|P16|P16-INK4A|P16INK4|P16INK4A|P19|P19ARF|TP16MAD5|MXD5
Cytomap

9p21.3

15q15.1

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase inhibitor 2ACDK4 inhibitor p16-INK4alternative reading framecell cycle negative regulator betacyclin-dependent kinase 4 inhibitor Acyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)multiple tumor suppressor 1MAX gene-associated proteinMAX dimerization protein 5MGA, MAX dimerization protein
Modification date2020032920200313
UniProtAcc

P42771

Q3V5L5

Ensembl transtripts involved in fusion geneENST00000361570, ENST00000579755, 
ENST00000304494, ENST00000446177, 
ENST00000479692, ENST00000494262, 
ENST00000498124, ENST00000498628, 
ENST00000578845, ENST00000470819, 
ENST00000497750, ENST00000530628, 
ENST00000579122, 		ENST00000219905, 
ENST00000389936, ENST00000545763, 
ENST00000566586, ENST00000568630, 
ENST00000570161, 
Fusion gene scores* DoF score14 X 9 X 11=13866 X 7 X 3=126
# samples 177
** MAII scorelog2(17/1386*10)=-3.02732060599951
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/126*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CDKN2A [Title/Abstract] AND MGA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDKN2A(21970901)-MGA(42019378), # samples:3
MGA(42005694)-CDKN2A(21968241), # samples:3
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
HgeneCDKN2A

GO:0000082

G1/S transition of mitotic cell cycle

10208428

HgeneCDKN2A

GO:0007050

cell cycle arrest

15149599

HgeneCDKN2A

GO:0008285

negative regulation of cell proliferation

15149599

HgeneCDKN2A

GO:0030308

negative regulation of cell growth

10208428

HgeneCDKN2A

GO:0032088

negative regulation of NF-kappaB transcription factor activity

10353611

HgeneCDKN2A

GO:0042326

negative regulation of phosphorylation

8259215|10208428

HgeneCDKN2A

GO:0045736

negative regulation of cyclin-dependent protein serine/threonine kinase activity

7739547|8259215


check buttonFusion gene breakpoints across CDKN2A (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 MGA (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-GC-A3RD-01ACDKN2Achr9

21970901

-MGAchr15

42019378

+


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Fusion Gene ORF analysis for CDKN2A-MGA

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-intronENST00000361570ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000361570ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000361570ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000361570ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000361570ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000361570ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000579755ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000579755ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000579755ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000579755ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000579755ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
3UTR-intronENST00000579755ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000304494ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000304494ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000304494ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000304494ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000304494ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000304494ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000446177ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000446177ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000446177ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000446177ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000446177ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000446177ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000479692ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000479692ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000479692ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000479692ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000479692ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000479692ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000494262ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000494262ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000494262ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000494262ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000494262ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000494262ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498124ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498124ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498124ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498124ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498124ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498124ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498628ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498628ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498628ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498628ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498628ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000498628ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000578845ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000578845ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000578845ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000578845ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000578845ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
5CDS-intronENST00000578845ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000470819ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000470819ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000470819ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000470819ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000470819ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000470819ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000497750ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000497750ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000497750ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000497750ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000497750ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000497750ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000530628ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000530628ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000530628ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000530628ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000530628ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000530628ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000579122ENST00000219905CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000579122ENST00000389936CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000579122ENST00000545763CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000579122ENST00000566586CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000579122ENST00000568630CDKN2Achr9

21970901

-MGAchr15

42019378

+
intron-intronENST00000579122ENST00000570161CDKN2Achr9

21970901

-MGAchr15

42019378

+

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 CDKN2A-MGA


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)
CDKN2Achr921970900-MGAchr1542019377+0.0004689540.99953103
CDKN2Achr921970900-MGAchr1542019377+0.0004689540.99953103

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.
genomic feature of top 1%

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Fusion Protein Features for CDKN2A-MGA


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/:21970901/:42019378)
- 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
CDKN2A

P42771

MGA

Q3V5L5

FUNCTION: Acts as a negative regulator of the proliferation of normal cells by interacting strongly with CDK4 and CDK6. This inhibits their ability to interact with cyclins D and to phosphorylate the retinoblastoma protein. {ECO:0000269|PubMed:16782892, ECO:0000269|PubMed:7972006}.FUNCTION: Glycosyltransferase that acts on alpha-linked mannose of N-glycans and O-mannosyl glycans. Catalyzes the transfer of N-acetylglucosamine (GlcNAc) to the beta 1-6 linkage of the mannose residue of GlcNAc-beta1,2-Man-alpha on both the alpha1,3- and alpha1,6-linked mannose arms in the core structure of N-glycan. Also acts on the GlcNAc-beta1,2-Man-alpha1-Ser/Thr moiety, forming a 2,6-branched structure in brain O-mannosyl glycan. Plays an active role in modulating integrin and laminin-dependent adhesion and migration of neuronal cells via its activity in the O-mannosyl glycan pathway. {ECO:0000269|PubMed:12941944, ECO:0000269|PubMed:14617637, ECO:0000269|PubMed:14623122, ECO:0000269|PubMed:16606368, ECO:0000269|PubMed:16857188, ECO:0000269|PubMed:19846580}.

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 CDKN2A-MGA


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 CDKN2A-MGA


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 CDKN2A-MGA


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 CDKN2A-MGA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource