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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:RFC2-LIMK1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RFC2-LIMK1
	FusionPDB ID: 73625
	FusionGDB2.0 ID: 73625
		Hgene	Tgene
	Gene symbol	RFC2	LIMK1
	Gene ID	5982	3984
	Gene name	replication factor C subunit 2	LIM domain kinase 1
	Synonyms	RFC40	LIMK\|LIMK-1
	Cytomap	7q11.23	7q11.23
	Type of gene	protein-coding	protein-coding
	Description	replication factor C subunit 2A1 40 kDa subunitRF-C 40 kDa subunitactivator 1 subunit 2replication factor C (activator 1) 2, 40kDa	LIM domain kinase 1LIM motif-containing protein kinase
	Modification date	20200313	20200313
	UniProtAcc	.	P53667
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000055077, ENST00000352131,	ENST00000491052, ENST00000336180, ENST00000418310, ENST00000538333,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 6 X 2=60	4 X 5 X 4=80
	# samples	6	5
	** MAII score	log2(6/60*10)=0	log2(5/80*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: RFC2 [Title/Abstract] AND LIMK1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RFC2(73664068)-LIMK1(73530131), # samples:1
Anticipated loss of major functional domain due to fusion event.	RFC2-LIMK1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. RFC2-LIMK1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	RFC2	GO:1900264	positive regulation of DNA-directed DNA polymerase activity	12930902
Tgene	LIMK1	GO:0006468	protein phosphorylation	17512523\|22328514
Tgene	LIMK1	GO:0032233	positive regulation of actin filament bundle assembly	17512523
Tgene	LIMK1	GO:0051444	negative regulation of ubiquitin-protein transferase activity	17512523

Fusion gene breakpoints across RFC2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across LIMK1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	OV	TCGA-24-1616	RFC2	chr7	73664068	-	LIMK1	chr7	73530131	+

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000352131	RFC2	chr7	73664068	-	ENST00000418310	LIMK1	chr7	73530131	+	1989	231	1091	183	302
ENST00000352131	RFC2	chr7	73664068	-	ENST00000336180	LIMK1	chr7	73530131	+	1989	231	1091	183	302
ENST00000352131	RFC2	chr7	73664068	-	ENST00000538333	LIMK1	chr7	73530131	+	922	231	6	764	252
ENST00000055077	RFC2	chr7	73664068	-	ENST00000418310	LIMK1	chr7	73530131	+	2044	286	1146	238	302
ENST00000055077	RFC2	chr7	73664068	-	ENST00000336180	LIMK1	chr7	73530131	+	2044	286	1146	238	302
ENST00000055077	RFC2	chr7	73664068	-	ENST00000538333	LIMK1	chr7	73530131	+	977	286	61	819	252

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000352131	ENST00000418310	RFC2	chr7	73664068	-	LIMK1	chr7	73530131	+	0.016280683	0.9837193
ENST00000352131	ENST00000336180	RFC2	chr7	73664068	-	LIMK1	chr7	73530131	+	0.016280683	0.9837193
ENST00000352131	ENST00000538333	RFC2	chr7	73664068	-	LIMK1	chr7	73530131	+	0.026743283	0.97325677
ENST00000055077	ENST00000418310	RFC2	chr7	73664068	-	LIMK1	chr7	73530131	+	0.012664544	0.9873354
ENST00000055077	ENST00000336180	RFC2	chr7	73664068	-	LIMK1	chr7	73530131	+	0.012664544	0.9873354
ENST00000055077	ENST00000538333	RFC2	chr7	73664068	-	LIMK1	chr7	73530131	+	0.021178098	0.9788219

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>73625_73625_1_RFC2-LIMK1_RFC2_chr7_73664068_ENST00000055077_LIMK1_chr7_73530131_ENST00000336180_length(amino acids)=302AA_BP=1
MLGQRRVERGVTHTGPPAHARRSKRGQPCQDRGYSRARAWCVCAAGPALGHGREKAGEAVHGVGEGKSGPGSEEKPGSPLSQLRATSRGG
IWWGWILQRWGQGQLSGPGSVGDLRVGRQSALAAPVGLPETSVQLLQLWAQWQVAGQVHAEGLQPVFQLHKGWPLLGVQIATAHGDGEEA
RGAVWGAVAVQESSHVEAKVHGAGQVVRVCVHPPDDLAQDDPKGEHIHLLIIAAAVDHLRCHPVGVAHHGVALLAVWLLEAPQALRLSLL

--------------------------------------------------------------

>73625_73625_2_RFC2-LIMK1_RFC2_chr7_73664068_ENST00000055077_LIMK1_chr7_73530131_ENST00000418310_length(amino acids)=302AA_BP=1
MLGQRRVERGVTHTGPPAHARRSKRGQPCQDRGYSRARAWCVCAAGPALGHGREKAGEAVHGVGEGKSGPGSEEKPGSPLSQLRATSRGG
IWWGWILQRWGQGQLSGPGSVGDLRVGRQSALAAPVGLPETSVQLLQLWAQWQVAGQVHAEGLQPVFQLHKGWPLLGVQIATAHGDGEEA
RGAVWGAVAVQESSHVEAKVHGAGQVVRVCVHPPDDLAQDDPKGEHIHLLIIAAAVDHLRCHPVGVAHHGVALLAVWLLEAPQALRLSLL

--------------------------------------------------------------

>73625_73625_3_RFC2-LIMK1_RFC2_chr7_73664068_ENST00000055077_LIMK1_chr7_73530131_ENST00000538333_length(amino acids)=252AA_BP=75
MEVEAVCGGAGEVEAQDSDPAPAFSKAPGSAGHYELPWVEKYRPVKLNEIVGNEDTVSRLEVFAREGNVPNIIIANKNVVVADFGLARLM
VDEKTQPEGLRSLKKPDRKKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNC

--------------------------------------------------------------

>73625_73625_4_RFC2-LIMK1_RFC2_chr7_73664068_ENST00000352131_LIMK1_chr7_73530131_ENST00000336180_length(amino acids)=302AA_BP=1
MLGQRRVERGVTHTGPPAHARRSKRGQPCQDRGYSRARAWCVCAAGPALGHGREKAGEAVHGVGEGKSGPGSEEKPGSPLSQLRATSRGG
IWWGWILQRWGQGQLSGPGSVGDLRVGRQSALAAPVGLPETSVQLLQLWAQWQVAGQVHAEGLQPVFQLHKGWPLLGVQIATAHGDGEEA
RGAVWGAVAVQESSHVEAKVHGAGQVVRVCVHPPDDLAQDDPKGEHIHLLIIAAAVDHLRCHPVGVAHHGVALLAVWLLEAPQALRLSLL

--------------------------------------------------------------

>73625_73625_5_RFC2-LIMK1_RFC2_chr7_73664068_ENST00000352131_LIMK1_chr7_73530131_ENST00000418310_length(amino acids)=302AA_BP=1
MLGQRRVERGVTHTGPPAHARRSKRGQPCQDRGYSRARAWCVCAAGPALGHGREKAGEAVHGVGEGKSGPGSEEKPGSPLSQLRATSRGG
IWWGWILQRWGQGQLSGPGSVGDLRVGRQSALAAPVGLPETSVQLLQLWAQWQVAGQVHAEGLQPVFQLHKGWPLLGVQIATAHGDGEEA
RGAVWGAVAVQESSHVEAKVHGAGQVVRVCVHPPDDLAQDDPKGEHIHLLIIAAAVDHLRCHPVGVAHHGVALLAVWLLEAPQALRLSLL

--------------------------------------------------------------

>73625_73625_6_RFC2-LIMK1_RFC2_chr7_73664068_ENST00000352131_LIMK1_chr7_73530131_ENST00000538333_length(amino acids)=252AA_BP=75
MEVEAVCGGAGEVEAQDSDPAPAFSKAPGSAGHYELPWVEKYRPVKLNEIVGNEDTVSRLEVFAREGNVPNIIIANKNVVVADFGLARLM
VDEKTQPEGLRSLKKPDRKKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNC

--------------------------------------------------------------

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:73664068/chr7:73530131)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	LIMK1 P53667
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.	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}.

Retention 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.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

RFC2

chr7:73664068

chr7:73530131

ENST00000055077

76_83

75.0

355.0

Nucleotide binding

ATP

Hgene

RFC2

chr7:73664068

chr7:73530131

ENST00000352131

76_83

75.0

321.0

Nucleotide binding

ATP

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000336180

165_258

470.0

648.0

Domain

PDZ

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000336180

25_75

470.0

648.0

Domain

LIM zinc-binding 1

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000336180

339_604

470.0

648.0

Domain

Protein kinase

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000336180

84_137

470.0

648.0

Domain

LIM zinc-binding 2

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000538333

165_258

436.0

614.0

Domain

PDZ

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000538333

25_75

436.0

614.0

Domain

LIM zinc-binding 1

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000538333

339_604

436.0

614.0

Domain

Protein kinase

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000538333

84_137

436.0

614.0

Domain

LIM zinc-binding 2

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000336180

345_353

470.0

648.0

Nucleotide binding

ATP

Tgene

LIMK1

chr7:73664068

chr7:73530131

ENST00000538333

345_353

436.0

614.0

Nucleotide binding

ATP

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
RFC2
LIMK1

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to RFC2-LIMK1

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to RFC2-LIMK1

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source