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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:MTAP-CDKN2A (FusionGDB2 ID:55503)

Fusion Gene Summary for MTAP-CDKN2A

check button Fusion gene summary
Fusion gene informationFusion gene name: MTAP-CDKN2A
Fusion gene ID: 55503
HgeneTgene
Gene symbol

MTAP

CDKN2A

Gene ID

4507

1029

Gene namemethylthioadenosine phosphorylasecyclin dependent kinase inhibitor 2A
SynonymsBDMF|DMSFH|DMSMFH|HEL-249|LGMBF|MSAP|c86fusARF|CDK4I|CDKN2|CMM2|INK4|INK4A|MLM|MTS-1|MTS1|P14|P14ARF|P16|P16-INK4A|P16INK4|P16INK4A|P19|P19ARF|TP16
Cytomap

9p21.3

9p21.3

Type of geneprotein-codingprotein-coding
DescriptionS-methyl-5'-thioadenosine phosphorylase5'-methylthioadenosine phosphorylaseMTA phosphorylaseMTAPaseMeSAdo phosphorylaseepididymis luminal protein 249epididymis secretory sperm binding proteincyclin-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 1
Modification date2020031320200329
UniProtAcc

Q13126

Q96HQ2

Ensembl transtripts involved in fusion geneENST00000427788, ENST00000380172, 
ENST00000460874, ENST00000580900, 
ENST00000304494, ENST00000361570, 
ENST00000579122, ENST00000579755, 
ENST00000494262, ENST00000498124, 
ENST00000498628, ENST00000530628, 
ENST00000578845, ENST00000446177, 
ENST00000479692, ENST00000497750, 
ENST00000470819, 
Fusion gene scores* DoF score13 X 9 X 9=105313 X 5 X 10=650
# samples 1716
** MAII scorelog2(17/1053*10)=-2.63089878488802
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/650*10)=-2.02236781302845
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointMTAP(21818201)-CDKN2A(21971207), # samples:2
MTAP(21815518)-CDKN2A(21968241), # samples:2
CDKN2A(21974677)-MTAP(21815432), # samples:3
Anticipated loss of major functional domain due to fusion event.MTAP-CDKN2A seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
MTAP-CDKN2A seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
MTAP-CDKN2A seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
MTAP-CDKN2A seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
MTAP-CDKN2A seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
HgeneMTAP

GO:0006738

nicotinamide riboside catabolic process

19001417

TgeneCDKN2A

GO:0000082

G1/S transition of mitotic cell cycle

10208428

TgeneCDKN2A

GO:0007050

cell cycle arrest

15149599

TgeneCDKN2A

GO:0008285

negative regulation of cell proliferation

15149599

TgeneCDKN2A

GO:0030308

negative regulation of cell growth

10208428

TgeneCDKN2A

GO:0032088

negative regulation of NF-kappaB transcription factor activity

10353611

TgeneCDKN2A

GO:0042326

negative regulation of phosphorylation

8259215|10208428

TgeneCDKN2A

GO:0045736

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

7739547|8259215


check buttonFusion gene breakpoints across MTAP (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 CDKN2A (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
ChimerDB4BRCATCGA-A2-A04Q-01AMTAPchr9

21818201

-CDKN2Achr9

21971207

-
ChimerDB4BRCATCGA-A2-A04Q-01AMTAPchr9

21818201

+CDKN2Achr9

21971207

-
ChimerDB4MESOTCGA-3H-AB3M-01AMTAPchr9

21815518

-CDKN2Achr9

21968241

-
ChimerDB4MESOTCGA-3H-AB3MMTAPchr9

21815518

+CDKN2Achr9

21968241

-


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Fusion Gene ORF analysis for MTAP-CDKN2A

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-3CDSENST00000427788ENST00000304494MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-3CDSENST00000427788ENST00000361570MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-3CDSENST00000427788ENST00000579122MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-3CDSENST00000427788ENST00000579755MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-3UTRENST00000427788ENST00000304494MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-3UTRENST00000427788ENST00000361570MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-3UTRENST00000427788ENST00000494262MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-3UTRENST00000427788ENST00000498124MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-3UTRENST00000427788ENST00000498628MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-3UTRENST00000427788ENST00000530628MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-3UTRENST00000427788ENST00000578845MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-3UTRENST00000427788ENST00000579122MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-3UTRENST00000427788ENST00000579755MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-5UTRENST00000427788ENST00000446177MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-5UTRENST00000427788ENST00000479692MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-5UTRENST00000427788ENST00000494262MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-5UTRENST00000427788ENST00000497750MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-5UTRENST00000427788ENST00000498124MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-5UTRENST00000427788ENST00000498628MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-5UTRENST00000427788ENST00000530628MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-5UTRENST00000427788ENST00000578845MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-intronENST00000427788ENST00000446177MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-intronENST00000427788ENST00000470819MTAPchr9

21818201

+CDKN2Achr9

21971207

-
3UTR-intronENST00000427788ENST00000470819MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-intronENST00000427788ENST00000479692MTAPchr9

21815518

+CDKN2Achr9

21968241

-
3UTR-intronENST00000427788ENST00000497750MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000304494MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000361570MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000494262MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000498124MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000498628MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000530628MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000578845MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000579122MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000380172ENST00000579755MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000304494MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000361570MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000494262MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000498124MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000498628MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000530628MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000578845MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000579122MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000460874ENST00000579755MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000304494MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000361570MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000494262MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000498124MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000498628MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000530628MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000578845MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000579122MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-3UTRENST00000580900ENST00000579755MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-5UTRENST00000380172ENST00000446177MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000380172ENST00000479692MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000380172ENST00000494262MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000380172ENST00000497750MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000380172ENST00000498124MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000380172ENST00000498628MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000380172ENST00000530628MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000380172ENST00000578845MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000460874ENST00000446177MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000460874ENST00000479692MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000460874ENST00000494262MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000460874ENST00000497750MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000460874ENST00000498124MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000460874ENST00000498628MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000460874ENST00000530628MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000460874ENST00000578845MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000580900ENST00000446177MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000580900ENST00000479692MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000580900ENST00000494262MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000580900ENST00000497750MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000580900ENST00000498124MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000580900ENST00000498628MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000580900ENST00000530628MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-5UTRENST00000580900ENST00000578845MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-intronENST00000380172ENST00000446177MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000380172ENST00000470819MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-intronENST00000380172ENST00000470819MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000380172ENST00000479692MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000380172ENST00000497750MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000460874ENST00000446177MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000460874ENST00000470819MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-intronENST00000460874ENST00000470819MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000460874ENST00000479692MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000460874ENST00000497750MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000580900ENST00000446177MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000580900ENST00000470819MTAPchr9

21818201

+CDKN2Achr9

21971207

-
5CDS-intronENST00000580900ENST00000470819MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000580900ENST00000479692MTAPchr9

21815518

+CDKN2Achr9

21968241

-
5CDS-intronENST00000580900ENST00000497750MTAPchr9

21815518

+CDKN2Achr9

21968241

-
Frame-shiftENST00000380172ENST00000304494MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000380172ENST00000361570MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000380172ENST00000579122MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000380172ENST00000579755MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000460874ENST00000304494MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000460874ENST00000361570MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000460874ENST00000579122MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000460874ENST00000579755MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000580900ENST00000304494MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000580900ENST00000361570MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000580900ENST00000579122MTAPchr9

21818201

+CDKN2Achr9

21971207

-
Frame-shiftENST00000580900ENST00000579755MTAPchr9

21818201

+CDKN2Achr9

21971207

-

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 MTAP-CDKN2A


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.
genomic feature

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 MTAP-CDKN2A


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/:21818201/:21971207)
- 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
MTAP

Q13126

CDKN2A

Q96HQ2

FUNCTION: Catalyzes the reversible phosphorylation of S-methyl-5'-thioadenosine (MTA) to adenine and 5-methylthioribose-1-phosphate. Involved in the breakdown of MTA, a major by-product of polyamine biosynthesis. Responsible for the first step in the methionine salvage pathway after MTA has been generated from S-adenosylmethionine. Has broad substrate specificity with 6-aminopurine nucleosides as preferred substrates. {ECO:0000255|HAMAP-Rule:MF_03155, ECO:0000269|PubMed:3091600}.

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 MTAP-CDKN2A


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 MTAP-CDKN2A


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 MTAP-CDKN2A


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 MTAP-CDKN2A


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