Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
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:CLNS1A-PAK1 (FusionGDB2 ID:HG1207TG5058)

Fusion Gene Summary for CLNS1A-PAK1

check button Fusion gene summary
Fusion gene informationFusion gene name: CLNS1A-PAK1
Fusion gene ID: hg1207tg5058
HgeneTgene
Gene symbol

CLNS1A

PAK1

Gene ID

1207

5058

Gene namechloride nucleotide-sensitive channel 1Ap21 (RAC1) activated kinase 1
SynonymsCLCI|CLNS1B|IClnIDDMSSD|PAKalpha|alpha-PAK|p65-PAK
Cytomap('CLNS1A')('PAK1')

11q14.1

11q13.5-q14.1

Type of geneprotein-codingprotein-coding
Descriptionmethylosome subunit pIClnchloride channel regulatory proteinchloride channel, nucleotide sensitive 1Achloride conductance regulatory protein IClnchloride ion current inducer proteini(Cln)reticulocyte pIClnreticulocyte protein IClnserine/threonine-protein kinase PAK 1STE20 homolog, yeastp21 protein (Cdc42/Rac)-activated kinase 1p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000263309, ENST00000525064, 
ENST00000525428, ENST00000528364, 
ENST00000532069, ENST00000533957, 
Fusion gene scores* DoF score13 X 12 X 5=78022 X 17 X 10=3740
# samples 1626
** MAII scorelog2(16/780*10)=-2.28540221886225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(26/3740*10)=-3.84645474174655
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLNS1A [Title/Abstract] AND PAK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLNS1A(77322360)-PAK1(77103586), # samples:1
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
HgeneCLNS1A

GO:0000387

spliceosomal snRNP assembly

18984161

TgenePAK1

GO:0000165

MAPK cascade

8805275

TgenePAK1

GO:0006338

chromatin remodeling

23260667

TgenePAK1

GO:0006468

protein phosphorylation

9852149|23260667

TgenePAK1

GO:0006974

cellular response to DNA damage stimulus

23260667

TgenePAK1

GO:0030335

positive regulation of cell migration

25766321

TgenePAK1

GO:0031532

actin cytoskeleton reorganization

9395435

TgenePAK1

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19667065

TgenePAK1

GO:0033148

positive regulation of intracellular estrogen receptor signaling pathway

16278681

TgenePAK1

GO:0046777

protein autophosphorylation

8805275



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
ChimerDB4HNSCTCGA-CV-6948CLNS1Achr11

77322360

-PAK1chr11

77103586

-


Top

Fusion Gene ORF analysis for CLNS1A-PAK1

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
intron-5UTRENST00000263309ENST00000278568CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000263309ENST00000356341CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000263309ENST00000530617CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000525064ENST00000278568CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000525064ENST00000356341CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000525064ENST00000530617CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000525428ENST00000278568CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000525428ENST00000356341CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000525428ENST00000530617CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000528364ENST00000278568CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000528364ENST00000356341CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000528364ENST00000530617CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000532069ENST00000278568CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000532069ENST00000356341CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000532069ENST00000530617CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000533957ENST00000278568CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000533957ENST00000356341CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-5UTRENST00000533957ENST00000530617CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000263309ENST00000525542CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000263309ENST00000528203CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000525064ENST00000525542CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000525064ENST00000528203CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000525428ENST00000525542CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000525428ENST00000528203CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000528364ENST00000525542CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000528364ENST00000528203CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000532069ENST00000525542CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000532069ENST00000528203CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000533957ENST00000525542CLNS1Achr11

77322360

-PAK1chr11

77103586

-
intron-intronENST00000533957ENST00000528203CLNS1Achr11

77322360

-PAK1chr11

77103586

-

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 CLNS1A-PAK1


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)


Top

Fusion Protein Features for CLNS1A-PAK1


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/:77322360/:77103586)
- 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
..
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: 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}.

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 CLNS1A-PAK1


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 CLNS1A-PAK1


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 CLNS1A-PAK1


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 CLNS1A-PAK1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLNS1AC0025202melanoma1CTD_human
TgeneC4748428INTELLECTUAL DEVELOPMENTAL DISORDER WITH MACROCEPHALY, SEIZURES, AND SPEECH DELAY2GENOMICS_ENGLAND;UNIPROT
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0033687Proteinuria1CTD_human
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1535926Neurodevelopmental Disorders1GENOMICS_ENGLAND
TgeneC4704874Mammary Carcinoma, Human1CTD_human