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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:CHD6-LIMK2 (FusionGDB2 ID:HG84181TG3985)

Fusion Gene Summary for CHD6-LIMK2

check button Fusion gene summary
Fusion gene informationFusion gene name: CHD6-LIMK2
Fusion gene ID: hg84181tg3985
HgeneTgene
Gene symbol

CHD6

LIMK2

Gene ID

84181

3985

Gene namechromodomain helicase DNA binding protein 6LIM domain kinase 2
SynonymsCHD-6|CHD5|RIGB-
Cytomap('CHD6')('LIMK2')

20q12

22q12.2

Type of geneprotein-codingprotein-coding
Descriptionchromodomain-helicase-DNA-binding protein 6ATP-dependent helicase CHD6helicase C-terminal domain- and SNF2 N-terminal domain-containing proteinradiation-induced gene B proteinLIM domain kinase 2
Modification date2020031320200313
UniProtAcc.

P53671

Ensembl transtripts involved in fusion geneENST00000309279, ENST00000373222, 
ENST00000373233, ENST00000480022, 
Fusion gene scores* DoF score30 X 18 X 11=59409 X 9 X 5=405
# samples 359
** MAII scorelog2(35/5940*10)=-4.0850361038558
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/405*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHD6 [Title/Abstract] AND LIMK2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHD6(40246978)-LIMK2(31661931), # 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
TgeneLIMK2

GO:0006468

protein phosphorylation

22328514

TgeneLIMK2

GO:0030953

astral microtubule organization

22328514



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
ChimerDB4LUSCTCGA-37-4133CHD6chr20

40246978

-LIMK2chr22

31661931

+


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Fusion Gene ORF analysis for CHD6-LIMK2

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-3CDSENST00000309279ENST00000331728CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000309279ENST00000333611CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000309279ENST00000340552CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000309279ENST00000406516CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000309279ENST00000444929CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373222ENST00000331728CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373222ENST00000333611CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373222ENST00000340552CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373222ENST00000406516CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373222ENST00000444929CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373233ENST00000331728CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373233ENST00000333611CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373233ENST00000340552CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373233ENST00000406516CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-3CDSENST00000373233ENST00000444929CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-intronENST00000309279ENST00000467301CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-intronENST00000373222ENST00000467301CHD6chr20

40246978

-LIMK2chr22

31661931

+
5UTR-intronENST00000373233ENST00000467301CHD6chr20

40246978

-LIMK2chr22

31661931

+
intron-3CDSENST00000480022ENST00000331728CHD6chr20

40246978

-LIMK2chr22

31661931

+
intron-3CDSENST00000480022ENST00000333611CHD6chr20

40246978

-LIMK2chr22

31661931

+
intron-3CDSENST00000480022ENST00000340552CHD6chr20

40246978

-LIMK2chr22

31661931

+
intron-3CDSENST00000480022ENST00000406516CHD6chr20

40246978

-LIMK2chr22

31661931

+
intron-3CDSENST00000480022ENST00000444929CHD6chr20

40246978

-LIMK2chr22

31661931

+
intron-intronENST00000480022ENST00000467301CHD6chr20

40246978

-LIMK2chr22

31661931

+

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 CHD6-LIMK2


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)
CHD6chr2040246978-LIMK2chr2231661931+2.33E-050.99997675
CHD6chr2040246978-LIMK2chr2231661931+2.33E-050.99997675


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.
genomic feature of top 1%

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Fusion Protein Features for CHD6-LIMK2


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/:40246978/:31661931)
- 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
.LIMK2

P53671

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: Serine/threonine-protein kinase that plays an essential role in the regulation of actin filament dynamics (PubMed:10436159, PubMed:11018042). Acts downstream of several Rho family GTPase signal transduction pathways (PubMed:10436159, PubMed:11018042). Involved in astral microtubule organization and mitotic spindle orientation during early stages of mitosis by mediating phosphorylation of TPPP (PubMed:22328514). Displays serine/threonine-specific phosphorylation of myelin basic protein and histone (MBP) in vitro (PubMed:8537403). Suppresses ciliogenesis via multiple pathways; phosphorylation of CFL1, suppression of directional trafficking of ciliary vesicles to the ciliary base, and by facilitating YAP1 nuclear localization where it acts as a transcriptional corepressor of the TEAD4 target genes AURKA and PLK1 (PubMed:25849865). {ECO:0000269|PubMed:10436159, ECO:0000269|PubMed:11018042, ECO:0000269|PubMed:22328514, ECO:0000269|PubMed:25849865, ECO:0000269|PubMed:8537403}.

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 CHD6-LIMK2


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 CHD6-LIMK2


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 CHD6-LIMK2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneLIMK2P53671DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for CHD6-LIMK2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCHD6C0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneCHD6C0005695Bladder Neoplasm1CTD_human
HgeneCHD6C0007138Carcinoma, Transitional Cell1CTD_human
HgeneCHD6C0027819Neuroblastoma1CTD_human
HgeneCHD6C0033578Prostatic Neoplasms1CTD_human
HgeneCHD6C0376358Malignant neoplasm of prostate1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human