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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:PPFIBP1-ALK (FusionGDB2 ID:67450)

Fusion Gene Summary for PPFIBP1-ALK

check button Fusion gene summary
Fusion gene informationFusion gene name: PPFIBP1-ALK
Fusion gene ID: 67450
HgeneTgene
Gene symbol

PPFIBP1

ALK

Gene ID

8496

238

Gene namePPFIA binding protein 1ALK receptor tyrosine kinase
SynonymsL2|SGT2|hSGT2|hSgt2pCD246|NBLST3
Cytomap

12p11.23-p11.22

2p23.2-p23.1

Type of geneprotein-codingprotein-coding
Descriptionliprin-beta-1PTPRF interacting protein, binding protein 1 (liprin beta 1)PTPRF-interacting protein-binding protein 1liprin related proteinprotein-tyrosine phosphatase receptor-type f polypeptide-interacting protein-binding protein 1ALK tyrosine kinase receptorCD246 antigenanaplastic lymphoma receptor tyrosine kinasemutant anaplastic lymphoma kinase
Modification date2020031320200329
UniProtAcc.

Q96BT7

Ensembl transtripts involved in fusion geneENST00000228425, ENST00000318304, 
ENST00000537927, ENST00000542629, 
ENST00000535047, ENST00000541633, 
ENST00000545334, 		ENST00000389048, 
ENST00000431873, ENST00000498037, 
Fusion gene scores* DoF score20 X 14 X 13=364056 X 74 X 20=82880
# samples 2657
** MAII scorelog2(26/3640*10)=-3.8073549220576
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: PPFIBP1 [Title/Abstract] AND ALK [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPPFIBP1(27807749)-ALK(29447593), # samples:2
Anticipated loss of major functional domain due to fusion event.PPFIBP1-ALK seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
PPFIBP1-ALK seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PPFIBP1-ALK seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
PPFIBP1-ALK seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PPFIBP1-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
TgeneALK

GO:0016310

phosphorylation

9174053

TgeneALK

GO:0046777

protein autophosphorylation

9174053


check buttonFusion gene breakpoints across PPFIBP1 (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 ALK (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
ChimerDB4myofibroblastic sarcomaAB600939PPFIBP1chr12

27807749

ALKchr2

29416073
ChimerKB3..PPFIBP1chr12

27807747

+ALKchr2

29446394

-
ChimerKB3..PPFIBP1chr12

27807749

+ALKchr2

29416073

-
ChimerKB3..PPFIBP1chr12

27807749

+ALKchr2

29416080

-
ChiTaRS5.0N/AAB600939PPFIBP1chr12

27807749

+ALKchr2

29447593

-
ChiTaRS5.0N/AAB795401PPFIBP1chr12

27807749

+ALKchr2

29447593

-


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Fusion Gene ORF analysis for PPFIBP1-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-3UTRENST00000228425ENST00000389048PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-3UTRENST00000228425ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-3UTRENST00000228425ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-3UTRENST00000318304ENST00000389048PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-3UTRENST00000318304ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-3UTRENST00000318304ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-3UTRENST00000537927ENST00000389048PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-3UTRENST00000537927ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-3UTRENST00000537927ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-3UTRENST00000542629ENST00000389048PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-3UTRENST00000542629ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-3UTRENST00000542629ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000228425ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000228425ENST00000431873PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-intronENST00000228425ENST00000431873PPFIBP1chr12

27807747

+ALKchr2

29446394

-
5CDS-intronENST00000228425ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-intronENST00000228425ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000228425ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000228425ENST00000498037PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-intronENST00000228425ENST00000498037PPFIBP1chr12

27807747

+ALKchr2

29446394

-
5CDS-intronENST00000228425ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-intronENST00000228425ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000228425ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000318304ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000318304ENST00000431873PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-intronENST00000318304ENST00000431873PPFIBP1chr12

27807747

+ALKchr2

29446394

-
5CDS-intronENST00000318304ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-intronENST00000318304ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000318304ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000318304ENST00000498037PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-intronENST00000318304ENST00000498037PPFIBP1chr12

27807747

+ALKchr2

29446394

-
5CDS-intronENST00000318304ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-intronENST00000318304ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000318304ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000537927ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000537927ENST00000431873PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-intronENST00000537927ENST00000431873PPFIBP1chr12

27807747

+ALKchr2

29446394

-
5CDS-intronENST00000537927ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-intronENST00000537927ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000537927ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000537927ENST00000498037PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-intronENST00000537927ENST00000498037PPFIBP1chr12

27807747

+ALKchr2

29446394

-
5CDS-intronENST00000537927ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-intronENST00000537927ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000537927ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000542629ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000542629ENST00000431873PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-intronENST00000542629ENST00000431873PPFIBP1chr12

27807747

+ALKchr2

29446394

-
5CDS-intronENST00000542629ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-intronENST00000542629ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000542629ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29447593

-
5CDS-intronENST00000542629ENST00000498037PPFIBP1chr12

27807749

ALKchr2

29416073

5CDS-intronENST00000542629ENST00000498037PPFIBP1chr12

27807747

+ALKchr2

29446394

-
5CDS-intronENST00000542629ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416073

-
5CDS-intronENST00000542629ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416080

-
5CDS-intronENST00000542629ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29447593

-
Frame-shiftENST00000228425ENST00000389048PPFIBP1chr12

27807747

+ALKchr2

29446394

-
Frame-shiftENST00000318304ENST00000389048PPFIBP1chr12

27807747

+ALKchr2

29446394

-
Frame-shiftENST00000537927ENST00000389048PPFIBP1chr12

27807747

+ALKchr2

29446394

-
Frame-shiftENST00000542629ENST00000389048PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-3CDSENST00000535047ENST00000389048PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-3CDSENST00000541633ENST00000389048PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-3CDSENST00000545334ENST00000389048PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-3UTRENST00000535047ENST00000389048PPFIBP1chr12

27807749

ALKchr2

29416073

intron-3UTRENST00000535047ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-3UTRENST00000535047ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-3UTRENST00000541633ENST00000389048PPFIBP1chr12

27807749

ALKchr2

29416073

intron-3UTRENST00000541633ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-3UTRENST00000541633ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-3UTRENST00000545334ENST00000389048PPFIBP1chr12

27807749

ALKchr2

29416073

intron-3UTRENST00000545334ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-3UTRENST00000545334ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-intronENST00000535047ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29447593

-
intron-intronENST00000535047ENST00000431873PPFIBP1chr12

27807749

ALKchr2

29416073

intron-intronENST00000535047ENST00000431873PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-intronENST00000535047ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-intronENST00000535047ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-intronENST00000535047ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29447593

-
intron-intronENST00000535047ENST00000498037PPFIBP1chr12

27807749

ALKchr2

29416073

intron-intronENST00000535047ENST00000498037PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-intronENST00000535047ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-intronENST00000535047ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-intronENST00000535047ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29447593

-
intron-intronENST00000541633ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29447593

-
intron-intronENST00000541633ENST00000431873PPFIBP1chr12

27807749

ALKchr2

29416073

intron-intronENST00000541633ENST00000431873PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-intronENST00000541633ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-intronENST00000541633ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-intronENST00000541633ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29447593

-
intron-intronENST00000541633ENST00000498037PPFIBP1chr12

27807749

ALKchr2

29416073

intron-intronENST00000541633ENST00000498037PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-intronENST00000541633ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-intronENST00000541633ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-intronENST00000541633ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29447593

-
intron-intronENST00000545334ENST00000389048PPFIBP1chr12

27807749

+ALKchr2

29447593

-
intron-intronENST00000545334ENST00000431873PPFIBP1chr12

27807749

ALKchr2

29416073

intron-intronENST00000545334ENST00000431873PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-intronENST00000545334ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-intronENST00000545334ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-intronENST00000545334ENST00000431873PPFIBP1chr12

27807749

+ALKchr2

29447593

-
intron-intronENST00000545334ENST00000498037PPFIBP1chr12

27807749

ALKchr2

29416073

intron-intronENST00000545334ENST00000498037PPFIBP1chr12

27807747

+ALKchr2

29446394

-
intron-intronENST00000545334ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416073

-
intron-intronENST00000545334ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29416080

-
intron-intronENST00000545334ENST00000498037PPFIBP1chr12

27807749

+ALKchr2

29447593

-

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 PPFIBP1-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)

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 PPFIBP1-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/:27807749/:29447593)
- 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
.ALK

Q96BT7

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Catalyzes the methylation of 5-carboxymethyl uridine to 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in tRNA via its methyltransferase domain (PubMed:20123966, PubMed:20308323, PubMed:31079898). Catalyzes the last step in the formation of 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in target tRNA (PubMed:20123966, PubMed:20308323). Has a preference for tRNA(Arg) and tRNA(Glu), and does not bind tRNA(Lys)(PubMed:20308323). Binds tRNA and catalyzes the iron and alpha-ketoglutarate dependent hydroxylation of 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in tRNA via its dioxygenase domain, giving rise to 5-(S)-methoxycarbonylhydroxymethyluridine; has a preference for tRNA(Gly) (PubMed:21285950). Required for normal survival after DNA damage (PubMed:20308323). May inhibit apoptosis and promote cell survival and angiogenesis (PubMed:19293182). {ECO:0000269|PubMed:19293182, ECO:0000269|PubMed:20123966, ECO:0000269|PubMed:20308323, ECO:0000269|PubMed:21285950, ECO:0000269|PubMed:31079898}.

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 PPFIBP1-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 PPFIBP1-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 PPFIBP1-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

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Related Diseases for PPFIBP1-ALK


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