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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:LIMK1-GGA1 (FusionGDB2 ID:44710)

Fusion Gene Summary for LIMK1-GGA1

check button Fusion gene summary
Fusion gene informationFusion gene name: LIMK1-GGA1
Fusion gene ID: 44710
HgeneTgene
Gene symbol

LIMK1

GGA1

Gene ID

3984

26088

Gene nameLIM domain kinase 1golgi associated, gamma adaptin ear containing, ARF binding protein 1
SynonymsLIMK|LIMK-1-
Cytomap

7q11.23

22q13.1

Type of geneprotein-codingprotein-coding
DescriptionLIM domain kinase 1LIM motif-containing protein kinaseADP-ribosylation factor-binding protein GGA1ADP-ribosylation factor binding protein 1gamma-adaptin related protein 1golgi-localized, gamma ear-containing, ARF-binding protein 1
Modification date2020031320200313
UniProtAcc

P53667

Q9UJY5

Ensembl transtripts involved in fusion geneENST00000336180, ENST00000418310, 
ENST00000491052, ENST00000538333, 
ENST00000406772, ENST00000325180, 
ENST00000337437, ENST00000343632, 
ENST00000381756, ENST00000405147, 
ENST00000414350, ENST00000488672, 
Fusion gene scores* DoF score7 X 6 X 4=1686 X 6 X 4=144
# samples 66
** MAII scorelog2(6/168*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LIMK1 [Title/Abstract] AND GGA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIMK1(73500174)-GGA1(38014454), # 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
HgeneLIMK1

GO:0006468

protein phosphorylation

17512523|22328514

HgeneLIMK1

GO:0032233

positive regulation of actin filament bundle assembly

17512523

HgeneLIMK1

GO:0051444

negative regulation of ubiquitin-protein transferase activity

17512523

TgeneGGA1

GO:0006886

intracellular protein transport

15886016

TgeneGGA1

GO:0008104

protein localization

15886016

TgeneGGA1

GO:0034394

protein localization to cell surface

27901063

TgeneGGA1

GO:0042147

retrograde transport, endosome to Golgi

15886016

TgeneGGA1

GO:0043001

Golgi to plasma membrane protein transport

27901063


check buttonFusion gene breakpoints across LIMK1 (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 GGA1 (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
ChimerDB4HNSCTCGA-CN-6019LIMK1chr7

73500174

+GGA1chr22

38014454

+


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Fusion Gene ORF analysis for LIMK1-GGA1

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-5UTRENST00000336180ENST00000406772LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-5UTRENST00000418310ENST00000406772LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000336180ENST00000325180LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000336180ENST00000337437LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000336180ENST00000343632LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000336180ENST00000381756LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000336180ENST00000405147LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000336180ENST00000414350LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000336180ENST00000488672LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000418310ENST00000325180LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000418310ENST00000337437LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000418310ENST00000343632LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000418310ENST00000381756LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000418310ENST00000405147LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000418310ENST00000414350LIMK1chr7

73500174

+GGA1chr22

38014454

+
5CDS-intronENST00000418310ENST00000488672LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-5UTRENST00000491052ENST00000406772LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-5UTRENST00000538333ENST00000406772LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000491052ENST00000325180LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000491052ENST00000337437LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000491052ENST00000343632LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000491052ENST00000381756LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000491052ENST00000405147LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000491052ENST00000414350LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000491052ENST00000488672LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000538333ENST00000325180LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000538333ENST00000337437LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000538333ENST00000343632LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000538333ENST00000381756LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000538333ENST00000405147LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000538333ENST00000414350LIMK1chr7

73500174

+GGA1chr22

38014454

+
intron-intronENST00000538333ENST00000488672LIMK1chr7

73500174

+GGA1chr22

38014454

+

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 LIMK1-GGA1


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)
LIMK1chr773500174+GGA1chr2238014454+1.42E-101
LIMK1chr773500174+GGA1chr2238014454+1.42E-101

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.
genomic feature of top 1%

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Fusion Protein Features for LIMK1-GGA1


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/:73500174/:38014454)
- 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
LIMK1

P53667

GGA1

Q9UJY5

FUNCTION: Serine/threonine-protein kinase that plays an essential role in the regulation of actin filament dynamics. Acts downstream of several Rho family GTPase signal transduction pathways (PubMed:10436159, PubMed:11832213, PubMed:12807904, PubMed:15660133, PubMed:16230460, PubMed:18028908, PubMed:22328514, PubMed:23633677). Activated by upstream kinases including ROCK1, PAK1 and PAK4, which phosphorylate LIMK1 on a threonine residue located in its activation loop (PubMed:10436159). LIMK1 subsequently phosphorylates and inactivates the actin binding/depolymerizing factors cofilin-1/CFL1, cofilin-2/CFL2 and destrin/DSTN, thereby preventing the cleavage of filamentous actin (F-actin), and stabilizing the actin cytoskeleton (PubMed:11832213, PubMed:15660133, PubMed:16230460, PubMed:23633677). In this way LIMK1 regulates several actin-dependent biological processes including cell motility, cell cycle progression, and differentiation (PubMed:11832213, PubMed:15660133, PubMed:16230460, PubMed:23633677). Phosphorylates TPPP on serine residues, thereby promoting microtubule disassembly (PubMed:18028908). Stimulates axonal outgrowth and may be involved in brain development (PubMed:18028908). {ECO:0000269|PubMed:10436159, ECO:0000269|PubMed:11832213, ECO:0000269|PubMed:12807904, ECO:0000269|PubMed:15660133, ECO:0000269|PubMed:16230460, ECO:0000269|PubMed:18028908, ECO:0000269|PubMed:22328514, ECO:0000269|PubMed:23633677}.; FUNCTION: [Isoform 3]: Has a dominant negative effect on actin cytoskeletal changes. Required for atypical chemokine receptor ACKR2-induced phosphorylation of cofilin (CFL1). {ECO:0000269|PubMed:10196227}.FUNCTION: Plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes. Mediates the ARF-dependent recruitment of clathrin to the TGN and binds ubiquitinated proteins and membrane cargo molecules with a cytosolic acidic cluster-dileucine (DXXLL) motif (PubMed:11301005, PubMed:15886016). Mediates export of the GPCR receptor ADRA2B to the cell surface (PubMed:27901063). Required for targeting PKD1:PKD2 complex from the trans-Golgi network to the cilium membrane (By similarity). Regulates retrograde transport of proteins such as phosphorylated form of BACE1 from endosomes to the trans-Golgi network (PubMed:15886016, PubMed:15615712). {ECO:0000250|UniProtKB:Q8R0H9, ECO:0000269|PubMed:11301005, ECO:0000269|PubMed:15615712, ECO:0000269|PubMed:15886016, ECO:0000269|PubMed:27901063}.

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 LIMK1-GGA1


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 LIMK1-GGA1


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 LIMK1-GGA1


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 LIMK1-GGA1


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