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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:LRRC58-GSK3B

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LRRC58-GSK3B
	FusionPDB ID: 49972
	FusionGDB2.0 ID: 49972
		Hgene	Tgene
	Gene symbol	LRRC58	GSK3B
	Gene ID	116064	2932
	Gene name	leucine rich repeat containing 58	glycogen synthase kinase 3 beta
	Synonyms	-	-
	Cytomap	3q13.33	3q13.33
	Type of gene	protein-coding	protein-coding
	Description	leucine-rich repeat-containing protein 58	glycogen synthase kinase-3 betaGSK-3 betaGSK3beta isoformserine/threonine-protein kinase GSK3B
	Modification date	20200313	20200315
	UniProtAcc	Q96CX6	C14orf129
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000295628,	ENST00000473886, ENST00000264235, ENST00000316626,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 7 X 6=462	3 X 3 X 3=27
	# samples	9	3
	** MAII score	log2(9/462*10)=-2.35989594508638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)	PubMed: LRRC58 [Title/Abstract] AND GSK3B [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LRRC58(120053709)-GSK3B(119721086), # samples:1
Anticipated loss of major functional domain due to fusion event.	LRRC58-GSK3B 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. LRRC58-GSK3B 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
Tgene	GSK3B	GO:0005977	glycogen metabolic process	8638126
Tgene	GSK3B	GO:0006468	protein phosphorylation	11035810\|16315267\|20937854
Tgene	GSK3B	GO:0006983	ER overload response	14744935
Tgene	GSK3B	GO:0018105	peptidyl-serine phosphorylation	8638126\|11104755\|11955436\|14744935\|17139249
Tgene	GSK3B	GO:0018107	peptidyl-threonine phosphorylation	11955436\|17139249\|25897075
Tgene	GSK3B	GO:0031175	neuron projection development	19830702
Tgene	GSK3B	GO:0031334	positive regulation of protein complex assembly	8638126
Tgene	GSK3B	GO:0032091	negative regulation of protein binding	16890161
Tgene	GSK3B	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	19364825
Tgene	GSK3B	GO:0035556	intracellular signal transduction	14749367
Tgene	GSK3B	GO:0043066	negative regulation of apoptotic process	14744935
Tgene	GSK3B	GO:0046777	protein autophosphorylation	23184662
Tgene	GSK3B	GO:0046827	positive regulation of protein export from nucleus	14744935
Tgene	GSK3B	GO:1901215	negative regulation of neuron death	19830702
Tgene	GSK3B	GO:1901216	positive regulation of neuron death	18508033
Tgene	GSK3B	GO:2000300	regulation of synaptic vesicle exocytosis	17989287

Fusion gene breakpoints across LRRC58 (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 GSK3B (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	BLCA	TCGA-LC-A66R-01A	LRRC58	chr3	120053709	-	GSK3B	chr3	119721086	-

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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)
ENST00000295628	LRRC58	chr3	120053709	-	ENST00000264235	GSK3B	chr3	119721086	-	7643	1003	39	2177	712
ENST00000295628	LRRC58	chr3	120053709	-	ENST00000316626	GSK3B	chr3	119721086	-	2319	1003	39	2216	725

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
ENST00000295628	ENST00000264235	LRRC58	chr3	120053709	-	GSK3B	chr3	119721086	-	0.000183887	0.9998161
ENST00000295628	ENST00000316626	LRRC58	chr3	120053709	-	GSK3B	chr3	119721086	-	0.003593509	0.9964065

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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

>49972_49972_1_LRRC58-GSK3B_LRRC58_chr3_120053709_ENST00000295628_GSK3B_chr3_119721086_ENST00000264235_length(amino acids)=712AA_BP=1
MDRARRSGESGATRRAVARMEEAGAAVVTAGEAELNWSRLSVSTETLESELEARGEERRGAREALLRLLLPHNRLVSLPRALGSGFPHLQ
LLDVSGNALTALGPELLALRGLRTLLAKNNRLGGPSALPKGLAQSPLCRSLQVLNLSGNCFQEVPASLLELRALQTLSLGGNQLQSIPAE
IENLQSLECLYLGGNFIKEIPPELGNLPSLNYLVLCDNKIQSIPPQLSQLHSLRSLSLHNNLLTYLPREILNLIHLEELSLRGNPLVVRF
VRDLTYDPPTLLELAARTIKIRNISYTPYDLPGNLLRYLGSASNCPNPKCGGDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFG
VVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYV
KLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLA
ELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHS

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

>49972_49972_2_LRRC58-GSK3B_LRRC58_chr3_120053709_ENST00000295628_GSK3B_chr3_119721086_ENST00000316626_length(amino acids)=725AA_BP=1
MDRARRSGESGATRRAVARMEEAGAAVVTAGEAELNWSRLSVSTETLESELEARGEERRGAREALLRLLLPHNRLVSLPRALGSGFPHLQ
LLDVSGNALTALGPELLALRGLRTLLAKNNRLGGPSALPKGLAQSPLCRSLQVLNLSGNCFQEVPASLLELRALQTLSLGGNQLQSIPAE
IENLQSLECLYLGGNFIKEIPPELGNLPSLNYLVLCDNKIQSIPPQLSQLHSLRSLSLHNNLLTYLPREILNLIHLEELSLRGNPLVVRF
VRDLTYDPPTLLELAARTIKIRNISYTPYDLPGNLLRYLGSASNCPNPKCGGDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFG
VVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYV
KLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLA
ELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKDSSGTGHFTSGVRVFRPRTPPEAIALCSRLLEYTP
TARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQAAASTPTNATAASDANTGDRGQTNNAASAS

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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/chr3:120053709/chr3:119721086)
- 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
LRRC58 Q96CX6	GSK3B C14orf129
	139

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

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

121_143

302.3333333333333

372.0

Repeat

Note=LRR 4

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

144_166

302.3333333333333

372.0

Repeat

Note=LRR 5

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

167_189

302.3333333333333

372.0

Repeat

Note=LRR 6

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

190_211

302.3333333333333

372.0

Repeat

Note=LRR 7

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

213_234

302.3333333333333

372.0

Repeat

Note=LRR 8

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

236_256

302.3333333333333

372.0

Repeat

Note=LRR 9

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

45_66

302.3333333333333

372.0

Repeat

Note=LRR 1

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

69_91

302.3333333333333

372.0

Repeat

Note=LRR 2

Hgene

LRRC58

chr3:120053709

chr3:119721086

ENST00000295628

92_113

302.3333333333333

372.0

Repeat

Note=LRR 3

Tgene

GSK3B

chr3:120053709

chr3:119721086

ENST00000264235

56_340

29.333333333333332

421.0

Domain

Protein kinase

Tgene

GSK3B

chr3:120053709

chr3:119721086

ENST00000316626

56_340

29.333333333333332

434.0

Domain

Protein kinase

Tgene

GSK3B

chr3:120053709

chr3:119721086

ENST00000264235

62_70

29.333333333333332

421.0

Nucleotide binding

ATP

Tgene

GSK3B

chr3:120053709

chr3:119721086

ENST00000316626

62_70

29.333333333333332

434.0

Nucleotide binding

ATP

- 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

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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
LRRC58
GSK3B

- 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 LRRC58-GSK3B

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 LRRC58-GSK3B

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