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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:CREBRF-CSNK1A1 (FusionGDB2 ID:HG153222TG1452)

Fusion Gene Summary for CREBRF-CSNK1A1

check button Fusion gene summary
Fusion gene informationFusion gene name: CREBRF-CSNK1A1
Fusion gene ID: hg153222tg1452
HgeneTgene
Gene symbol

CREBRF

CSNK1A1

Gene ID

153222

1452

Gene nameCREB3 regulatory factorcasein kinase 1 alpha 1
SynonymsC5orf41|LRFCK1|CK1a|CKIa|HEL-S-77p|HLCDGP1|PRO2975
Cytomap('CREBRF')('CSNK1A1')

5q35.1

5q32

Type of geneprotein-codingprotein-coding
DescriptionCREB3 regulatory factorUPF0474 protein C5orf41adult retina proteinluman recruitment factorluman-recruiting factorluman/CREB3 recruitment factorcasein kinase I isoform alphaCKI-alphaclock regulator kinasedown-regulated in lung cancerepididymis secretory sperm binding protein Li 77p
Modification date2020031320200313
UniProtAcc.

P48729

Ensembl transtripts involved in fusion geneENST00000296953, ENST00000520420, 
ENST00000522692, ENST00000540014, 
ENST00000517882, 
Fusion gene scores* DoF score5 X 3 X 3=4512 X 13 X 6=936
# samples 515
** MAII scorelog2(5/45*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(15/936*10)=-2.64154602908752
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CREBRF [Title/Abstract] AND CSNK1A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCREBRF(172483482)-CSNK1A1(148899951), # samples:2
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
HgeneCREBRF

GO:0045944

positive regulation of transcription by RNA polymerase II

16940180

TgeneCSNK1A1

GO:0006468

protein phosphorylation

18305108

TgeneCSNK1A1

GO:0018105

peptidyl-serine phosphorylation

25500533

TgeneCSNK1A1

GO:0032436

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

19364825



check button Fusion gene information
* 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
ChimerDB4LGGTCGA-HT-7860-01ACREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
ChimerDB4LGGTCGA-HT-7860CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-


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Fusion Gene ORF analysis for CREBRF-CSNK1A1

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
5UTR-3CDSENST00000296953ENST00000261798CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000296953ENST00000377843CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000296953ENST00000504676CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000296953ENST00000515435CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000296953ENST00000515768CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000520420ENST00000261798CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000520420ENST00000377843CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000520420ENST00000504676CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000520420ENST00000515435CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000520420ENST00000515768CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000522692ENST00000261798CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000522692ENST00000377843CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000522692ENST00000504676CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000522692ENST00000515435CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000522692ENST00000515768CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000540014ENST00000261798CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000540014ENST00000377843CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000540014ENST00000504676CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000540014ENST00000515435CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-3CDSENST00000540014ENST00000515768CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000296953ENST00000515748CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000296953ENST00000606299CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000296953ENST00000606719CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000520420ENST00000515748CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000520420ENST00000606299CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000520420ENST00000606719CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000522692ENST00000515748CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000522692ENST00000606299CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000522692ENST00000606719CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000540014ENST00000515748CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000540014ENST00000606299CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
5UTR-intronENST00000540014ENST00000606719CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
intron-3CDSENST00000517882ENST00000261798CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
intron-3CDSENST00000517882ENST00000377843CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
intron-3CDSENST00000517882ENST00000504676CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
intron-3CDSENST00000517882ENST00000515435CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
intron-3CDSENST00000517882ENST00000515768CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
intron-intronENST00000517882ENST00000515748CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
intron-intronENST00000517882ENST00000606299CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-
intron-intronENST00000517882ENST00000606719CREBRFchr5

172483482

+CSNK1A1chr5

148899951

-

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 CREBRF-CSNK1A1


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 CREBRF-CSNK1A1


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/:172483482/:148899951)
- 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
.CSNK1A1

P48729

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: Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. It can phosphorylate a large number of proteins. Participates in Wnt signaling. Phosphorylates CTNNB1 at 'Ser-45'. May phosphorylate PER1 and PER2. May play a role in segregating chromosomes during mitosis (PubMed:11955436, PubMed:1409656, PubMed:18305108). May play a role in keratin cytoskeleton disassembly and thereby, it may regulate epithelial cell migration (PubMed:23902688). {ECO:0000269|PubMed:11955436, ECO:0000269|PubMed:1409656, ECO:0000269|PubMed:18305108, ECO:0000269|PubMed:23902688}.

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 CREBRF-CSNK1A1


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 CREBRF-CSNK1A1


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 CREBRF-CSNK1A1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCSNK1A1P48729DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for CREBRF-CSNK1A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0023493Adult T-Cell Lymphoma/Leukemia1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human