FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CDKN2A-FASTKD3 (FusionGDB2 ID:15438)

Fusion Gene Summary for CDKN2A-FASTKD3

check button Fusion gene summary
Fusion gene informationFusion gene name: CDKN2A-FASTKD3
Fusion gene ID: 15438
HgeneTgene
Gene symbol

CDKN2A

FASTKD3

Gene ID

1029

79072

Gene namecyclin dependent kinase inhibitor 2AFAST kinase domains 3
SynonymsARF|CDK4I|CDKN2|CMM2|INK4|INK4A|MLM|MTS-1|MTS1|P14|P14ARF|P16|P16-INK4A|P16INK4|P16INK4A|P19|P19ARF|TP16-
Cytomap

9p21.3

5p15.31

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 1FAST kinase domain-containing protein 3, mitochondrial
Modification date2020032920200313
UniProtAcc

P42771

.
Ensembl transtripts involved in fusion geneENST00000361570, ENST00000304494, 
ENST00000579755, ENST00000579122, 
ENST00000578845, ENST00000530628, 
ENST00000498124, ENST00000498628, 
ENST00000494262, ENST00000446177, 
ENST00000479692, ENST00000497750, 
ENST00000470819, 		ENST00000264669, 
ENST00000513658, 
Fusion gene scores* DoF score14 X 9 X 11=13863 X 1 X 3=9
# samples 173
** MAII scorelog2(17/1386*10)=-3.02732060599951
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CDKN2A [Title/Abstract] AND FASTKD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDKN2A(21994138)-FASTKD3(7866096), # samples:2
Anticipated loss of major functional domain due to fusion event.CDKN2A-FASTKD3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CDKN2A-FASTKD3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
CDKN2A-FASTKD3 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
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

TgeneFASTKD3

GO:0033617

mitochondrial respiratory chain complex IV assembly

27789713

TgeneFASTKD3

GO:0044528

regulation of mitochondrial mRNA stability

27789713

TgeneFASTKD3

GO:0070131

positive regulation of mitochondrial translation

27789713


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 FASTKD3 (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
ChimerDB4MESOTCGA-TS-A7P1-01ACDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
ChimerDB4MESOTCGA-TS-A7P1-01ACDKN2Achr9

21994138

-FASTKD3chr5

7866096

-


Top

Fusion Gene ORF analysis for CDKN2A-FASTKD3

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-shiftENST00000361570ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
5CDS-5UTRENST00000361570ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000304494ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000304494ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
Frame-shiftENST00000579755ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
5CDS-5UTRENST00000579755ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000579122ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000579122ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000578845ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000578845ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
Frame-shiftENST00000530628ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
5CDS-5UTRENST00000530628ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000498124ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000498124ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000498628ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000498628ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000494262ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000494262ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000446177ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000446177ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000479692ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000479692ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000497750ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000497750ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-3CDSENST00000470819ENST00000264669CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-
intron-5UTRENST00000470819ENST00000513658CDKN2Achr9

21994138

-FASTKD3chr5

7866096

-

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

Top

Fusion Genomic Features for CDKN2A-FASTKD3


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.

Top

Fusion Protein Features for CDKN2A-FASTKD3


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
CDKN2A

P42771

.
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: 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


Top

Fusion Gene Sequence for CDKN2A-FASTKD3


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.

Top

Fusion Gene PPI Analysis for CDKN2A-FASTKD3


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


Top

Related Drugs for CDKN2A-FASTKD3


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

Top

Related Diseases for CDKN2A-FASTKD3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCDKN2AC1835044MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 213CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCDKN2AC1838547MELANOMA-PANCREATIC CANCER SYNDROME10CLINGEN;CTD_human
HgeneCDKN2AC0024121Lung Neoplasms4CTD_human;UNIPROT
HgeneCDKN2AC0242379Malignant neoplasm of lung4CTD_human
HgeneCDKN2AC0011570Mental Depression3PSYGENET
HgeneCDKN2AC0011581Depressive disorder3PSYGENET
HgeneCDKN2AC0023903Liver neoplasms3CTD_human
HgeneCDKN2AC0345904Malignant neoplasm of liver3CTD_human
HgeneCDKN2AC0345967Malignant mesothelioma3CTD_human
HgeneCDKN2AC1168401Squamous cell carcinoma of the head and neck3CTD_human
HgeneCDKN2AC0005684Malignant neoplasm of urinary bladder2CTD_human
HgeneCDKN2AC0005695Bladder Neoplasm2CTD_human;UNIPROT
HgeneCDKN2AC0006118Brain Neoplasms2CTD_human
HgeneCDKN2AC0006826Malignant Neoplasms2CGI;CTD_human
HgeneCDKN2AC0007131Non-Small Cell Lung Carcinoma2CTD_human;UNIPROT
HgeneCDKN2AC0017638Glioma2CGI;CTD_human
HgeneCDKN2AC0023452Childhood Acute Lymphoblastic Leukemia2CTD_human;GENOMICS_ENGLAND
HgeneCDKN2AC0025202melanoma2CGI;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCDKN2AC0027651Neoplasms2CTD_human
HgeneCDKN2AC0030297Pancreatic Neoplasm2CGI;CTD_human;UNIPROT
HgeneCDKN2AC0040715Chromosomal translocation2CTD_human
HgeneCDKN2AC0041696Unipolar Depression2PSYGENET
HgeneCDKN2AC0085390Li-Fraumeni Syndrome2ORPHANET
HgeneCDKN2AC0086692Benign Neoplasm2CTD_human
HgeneCDKN2AC0153633Malignant neoplasm of brain2CTD_human
HgeneCDKN2AC0259783mixed gliomas2CTD_human
HgeneCDKN2AC0346647Malignant neoplasm of pancreas2CGI;CTD_human
HgeneCDKN2AC0496899Benign neoplasm of brain, unspecified2CTD_human
HgeneCDKN2AC0555198Malignant Glioma2CTD_human
HgeneCDKN2AC0750974Brain Tumor, Primary2CTD_human
HgeneCDKN2AC0750977Recurrent Brain Neoplasm2CTD_human
HgeneCDKN2AC0750979Primary malignant neoplasm of brain2CTD_human
HgeneCDKN2AC1269683Major Depressive Disorder2PSYGENET
HgeneCDKN2AC1527390Neoplasms, Intracranial2CTD_human
HgeneCDKN2AC2239176Liver carcinoma2CTD_human
HgeneCDKN2AC0001418Adenocarcinoma1CTD_human
HgeneCDKN2AC0001624Adrenal Gland Neoplasms1CTD_human
HgeneCDKN2AC0005940Bone Diseases1CTD_human
HgeneCDKN2AC0006142Malignant neoplasm of breast1CTD_human
HgeneCDKN2AC0006413Burkitt Lymphoma1ORPHANET
HgeneCDKN2AC0007137Squamous cell carcinoma1CTD_human;UNIPROT
HgeneCDKN2AC0008628Chromosome Deletion1CTD_human
HgeneCDKN2AC0014859Esophageal Neoplasms1CTD_human;UNIPROT
HgeneCDKN2AC0016325Fluoride Poisoning1CTD_human
HgeneCDKN2AC0017601Glaucoma1CTD_human
HgeneCDKN2AC0022783Vulvar Lichen Sclerosus1CTD_human
HgeneCDKN2AC0023449Acute lymphocytic leukemia1GENOMICS_ENGLAND
HgeneCDKN2AC0023453L2 Acute Lymphoblastic Leukemia1CTD_human
HgeneCDKN2AC0024232Lymphatic Metastasis1CTD_human
HgeneCDKN2AC0024299Lymphoma1CTD_human
HgeneCDKN2AC0024623Malignant neoplasm of stomach1CTD_human
HgeneCDKN2AC0025500Mesothelioma1CTD_human
HgeneCDKN2AC0026640Mouth Neoplasms1CTD_human
HgeneCDKN2AC0026764Multiple Myeloma1CTD_human
HgeneCDKN2AC0027626Neoplasm Invasiveness1CTD_human
HgeneCDKN2AC0027819Neuroblastoma1CTD_human
HgeneCDKN2AC0032927Precancerous Conditions1CTD_human
HgeneCDKN2AC0036920Sezary Syndrome1CTD_human
HgeneCDKN2AC0038356Stomach Neoplasms1CTD_human
HgeneCDKN2AC0040100Thymoma1CTD_human
HgeneCDKN2AC0041107Trisomy1CTD_human
HgeneCDKN2AC0042065Genitourinary Neoplasms1CTD_human
HgeneCDKN2AC0079744Diffuse Large B-Cell Lymphoma1CTD_human
HgeneCDKN2AC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
HgeneCDKN2AC0151779Cutaneous Melanoma1CGI;CTD_human
HgeneCDKN2AC0153381Malignant neoplasm of mouth1CTD_human
HgeneCDKN2AC0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneCDKN2AC0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneCDKN2AC0205643Carcinoma, Cribriform1CTD_human
HgeneCDKN2AC0205644Carcinoma, Granular Cell1CTD_human
HgeneCDKN2AC0205645Adenocarcinoma, Tubular1CTD_human
HgeneCDKN2AC0205969Thymic Carcinoma1CTD_human
HgeneCDKN2AC0206686Adrenocortical carcinoma1CTD_human
HgeneCDKN2AC0206727Nerve Sheath Tumors1CTD_human
HgeneCDKN2AC0279626Squamous cell carcinoma of esophagus1CTD_human
HgeneCDKN2AC0279628Adenocarcinoma Of Esophagus1CTD_human
HgeneCDKN2AC0282313Condition, Preneoplastic1CTD_human
HgeneCDKN2AC0376407Granulomatous Slack Skin1CTD_human
HgeneCDKN2AC0546837Malignant neoplasm of esophagus1CTD_human
HgeneCDKN2AC0596263Carcinogenesis1CTD_human
HgeneCDKN2AC0677866Brain Stem Neoplasms1CTD_human
HgeneCDKN2AC0678222Breast Carcinoma1CTD_human
HgeneCDKN2AC0750887Adrenal Cancer1CTD_human
HgeneCDKN2AC0751569Genitourinary Cancer1CTD_human
HgeneCDKN2AC0751606Adult Acute Lymphocytic Leukemia1GENOMICS_ENGLAND
HgeneCDKN2AC0751689Peripheral Nerve Sheath Neoplasm1CTD_human
HgeneCDKN2AC0751691Perineurioma1CTD_human
HgeneCDKN2AC0751886Brain Stem Neoplasms, Primary1CTD_human
HgeneCDKN2AC0751887Medullary Neoplasms1CTD_human
HgeneCDKN2AC0751888Mesencephalic Neoplasms1CTD_human
HgeneCDKN2AC0751889Pontine Tumors1CTD_human
HgeneCDKN2AC0887833Carcinoma, Pancreatic Ductal1CTD_human
HgeneCDKN2AC1257931Mammary Neoplasms, Human1CTD_human
HgeneCDKN2AC1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
HgeneCDKN2AC1297882Partial Trisomy1CTD_human
HgeneCDKN2AC1449861Micronuclei, Chromosome-Defective1CTD_human
HgeneCDKN2AC1449862Micronuclei, Genotoxicant-Induced1CTD_human
HgeneCDKN2AC1458155Mammary Neoplasms1CTD_human
HgeneCDKN2AC1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneCDKN2AC1835042Melanoma astrocytoma syndrome1CTD_human;ORPHANET
HgeneCDKN2AC1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1ORPHANET
HgeneCDKN2AC1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human
HgeneCDKN2AC2314896Familial Atypical Mole Melanoma Syndrome1ORPHANET
HgeneCDKN2AC2930745Partial Monosomy1CTD_human
HgeneCDKN2AC2931038Pancreatic carcinoma, familial1ORPHANET
HgeneCDKN2AC2931822Nasopharyngeal carcinoma1CTD_human
HgeneCDKN2AC4283859Cutaneous Malignant Melanoma 21GENOMICS_ENGLAND
HgeneCDKN2AC4704874Mammary Carcinoma, Human1CTD_human
HgeneCDKN2AC4721453Peripheral Nervous System Diseases1CTD_human