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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:FRMD4B-LMOD3 (FusionGDB2 ID:31342)

Fusion Gene Summary for FRMD4B-LMOD3

Fusion gene summary

Fusion gene information	Fusion gene name: FRMD4B-LMOD3
	Fusion gene ID: 31342
		Hgene	Tgene
	Gene symbol	FRMD4B	LMOD3
	Gene ID	23150	56203
	Gene name	FERM domain containing 4B	leiomodin 3
	Synonyms	6030440G05Rik\|GRSP1	NEM10
	Cytomap	3p14.1	3p14.1
	Type of gene	protein-coding	protein-coding
	Description	FERM domain-containing protein 4BGRP1-binding protein GRSP1	leiomodin-3leiomodin 3 (fetal)leiomodin, fetal form
	Modification date	20200313	20200329
	UniProtAcc	Q9Y2L6	Q0VAK6
	Ensembl transtripts involved in fusion gene	ENST00000398540, ENST00000542259, ENST00000478263, ENST00000497757,	ENST00000420581, ENST00000489031, ENST00000475434,
Fusion gene scores	* DoF score	13 X 10 X 8=1040	3 X 2 X 3=18
	# samples	14	3
	** MAII score	log2(14/1040*10)=-2.89308479608349 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: FRMD4B [Title/Abstract] AND LMOD3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	FRMD4B(69336903)-LMOD3(69158272), # samples:1
Anticipated loss of major functional domain due to fusion event.	FRMD4B-LMOD3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted 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

Fusion gene breakpoints across FRMD4B (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 LMOD3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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	KIRC	TCGA-EU-5907-01A	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-

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Fusion Gene ORF analysis for FRMD4B-LMOD3

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
Frame-shift	ENST00000398540	ENST00000420581	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
Frame-shift	ENST00000398540	ENST00000489031	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
Frame-shift	ENST00000542259	ENST00000420581	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
Frame-shift	ENST00000542259	ENST00000475434	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
In-frame	ENST00000398540	ENST00000475434	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
In-frame	ENST00000542259	ENST00000489031	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
intron-3CDS	ENST00000478263	ENST00000420581	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
intron-3CDS	ENST00000478263	ENST00000475434	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
intron-3CDS	ENST00000478263	ENST00000489031	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
intron-3CDS	ENST00000497757	ENST00000420581	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
intron-3CDS	ENST00000497757	ENST00000475434	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-
intron-3CDS	ENST00000497757	ENST00000489031	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)
ENST00000398540	FRMD4B	chr3	69336903	-	ENST00000475434	LMOD3	chr3	69158272	-	983	585	84	611	175
ENST00000542259	FRMD4B	chr3	69336903	-	ENST00000489031	LMOD3	chr3	69158272	-	1241	791	11	817	268

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
ENST00000398540	ENST00000475434	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-	0.007350599	0.9926494
ENST00000542259	ENST00000489031	FRMD4B	chr3	69336903	-	LMOD3	chr3	69158272	-	0.010039243	0.9899608

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Fusion Genomic Features for FRMD4B-LMOD3

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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.

Distribution 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.

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Fusion Protein Features for FRMD4B-LMOD3

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:69336903/chr3:69158272)
- 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
FRMD4B Q9Y2L6	LMOD3 Q0VAK6
FUNCTION: Member of GRP1 signaling complexes that are acutely recruited to plasma membrane ruffles in response to insulin receptor signaling. May function as a scaffolding protein that regulates epithelial cell polarity by connecting ARF6 activation with the PAR3 complex. Plays a redundant role with FRMD4A in epithelial polarization. {ECO:0000250\|UniProtKB:Q920B0}.	FUNCTION: Essential for the organization of sarcomeric actin thin filaments in skeletal muscle (PubMed:25250574). Increases the rate of actin polymerization (PubMed:25250574). {ECO:0000269\|PubMed:25250574}.

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.

- In-frame and 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

- In-frame and 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

FRMD4B

chr3:69336903

chr3:69158272

ENST00000398540

417_450

167

1035.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

FRMD4B

chr3:69336903

chr3:69158272

ENST00000398540

531_561

167

1035.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

FRMD4B

chr3:69336903

chr3:69158272

ENST00000398540

59_361

167

1035.0

Domain

FERM

Hgene

FRMD4B

chr3:69336903

chr3:69158272

ENST00000398540

542_971

167

1035.0

Region

Necessary for adherens junction and tight junction localization

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000420581

16_42

552

561.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000420581

386_425

552

561.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000475434

16_42

552

561.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000475434

386_425

552

561.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000489031

16_42

552

561.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000489031

386_425

552

561.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000420581

449_457

552

561.0

Compositional bias

Note=Poly-Pro

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000420581

86_179

552

561.0

Compositional bias

Note=Glu-rich

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000475434

449_457

552

561.0

Compositional bias

Note=Poly-Pro

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000475434

86_179

552

561.0

Compositional bias

Note=Glu-rich

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000489031

449_457

552

561.0

Compositional bias

Note=Poly-Pro

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000489031

86_179

552

561.0

Compositional bias

Note=Glu-rich

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000420581

534_553

552

561.0

Domain

WH2

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000475434

534_553

552

561.0

Domain

WH2

Tgene

LMOD3

chr3:69336903

chr3:69158272

ENST00000489031

534_553

552

561.0

Domain

WH2

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Fusion Gene Sequence for FRMD4B-LMOD3

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.

>31342_31342_1_FRMD4B-LMOD3_FRMD4B_chr3_69336903_ENST00000398540_LMOD3_chr3_69158272_ENST00000475434_length(transcript)=983nt_BP=585nt
CGGGAGCCCAGGCGGGCAGGCCGCTGGGGTCGGGGCTGCACGTACGAGAGCCGGGACGCCCGGGTTCAGAGCGAAGGAGGAGGCATGGCT
TCGGTGTTCATGTGTGGCGTGGAGGACCTGCTGTTCAGCGGCAGCCGCTTCGTATGGAACTTGACCGTGTCCACGCTGCGGAGATGGTAC
ACGGAGAGGCTGCGGGCTTGCCACCAGGTGCTGCGGACGTGGTGCGGGCTGCAGGACGTGTACCAGATGACAGAAGGCAGGCACTGCCAG
GTGCACCTCCTGGATGATAGGAGACTGGAGCTGCTGGTTCAGCCCAAACTTCTAGCAAGAGAGTTGCTGGACCTAGTGGCTTCACATTTC
AACCTGAAAGAAAAGGAGTATTTTGGAATAACATTCATAGATGACACAGGTCAGCAGAACTGGCTGCAGTTAGATCACCGAGTTCTTGAC
CACGATTTGCCCAAGAAACCAGGCCCAACCATTTTGCACTTTGCTGTGAGGTTTTACATTGAGAGCATATCGTTTTTAAAGGATAAAACC
ACCGTGGAGCTGTTTTTCCTGAATGCAAAGGCCTGTGTGCACAAGGTGCAACTGCCAAAAGAACTGGCGTAAGAGGCAACAGAGCCATCT
AGAAGAACAAGAAATGGAAATAGTGACTCTTGGATTACAGCATGGAGACTATGTCAGCAGCAATACTTTAGGATCCACGTGGCAGAACTG
GAAACAATGCTACCATCTGATAAGGGTATTTGTAAAAGGCAGAATGTTTGGGCCATGAAGAAGTAGGGGCTGAAGAGGAAGGTGGAAGGA
GATAAAATATAATATTTAGAGGCAATATTTTCTACTTGCAATCAATTTGAGTGACTCAGGTGAAATTTAGAGTCATATTTCCCGAAGCAG

>31342_31342_1_FRMD4B-LMOD3_FRMD4B_chr3_69336903_ENST00000398540_LMOD3_chr3_69158272_ENST00000475434_length(amino acids)=175AA_BP=0
MASVFMCGVEDLLFSGSRFVWNLTVSTLRRWYTERLRACHQVLRTWCGLQDVYQMTEGRHCQVHLLDDRRLELLVQPKLLARELLDLVAS

--------------------------------------------------------------
>31342_31342_2_FRMD4B-LMOD3_FRMD4B_chr3_69336903_ENST00000542259_LMOD3_chr3_69158272_ENST00000489031_length(transcript)=1241nt_BP=791nt
CGAGGGCCAGCTTGGTGGAGCTTAGCACAGCTTGCTCGGCGCTGCGAGCGGGCGGGGGTGGACACTGGGCTTCTGTGTGCCAGTCGCAGC
CGTTGGCTGGCGGGCACCCAATCCCAGGGCATGCCGCCGGAGCCTGGCCAGGACGCACGGTGAAAGACGAGTTTGGTGGCAGGCTTGACC
CCCCGGCTGCCAGCAGAAGCCGGCGTCGGGAGCCCAGGCGGGCAGGCCGCTGGGGTCGGGGCTGCACGTACGAGAGCCGGGACGCCCGGG
TTCAGAGCGAAGGAGGAGGCATGGCTTCGGTGTTCATGTGTGGCGTGGAGGACCTGCTGTTCAGCGGCAGCCGCTTCGTATGGAACTTGA
CCGTGTCCACGCTGCGGAGATGGTACACGGAGAGGCTGCGGGCTTGCCACCAGGTGCTGCGGACGTGGTGCGGGCTGCAGGACGTGTACC
AGATGACAGAAGGCAGGCACTGCCAGGTGCACCTCCTGGATGATAGGAGACTGGAGCTGCTGGTTCAGCCCAAACTTCTAGCAAGAGAGT
TGCTGGACCTAGTGGCTTCACATTTCAACCTGAAAGAAAAGGAGTATTTTGGAATAACATTCATAGATGACACAGGTCAGCAGAACTGGC
TGCAGTTAGATCACCGAGTTCTTGACCACGATTTGCCCAAGAAACCAGGCCCAACCATTTTGCACTTTGCTGTGAGGTTTTACATTGAGA
GCATATCGTTTTTAAAGGATAAAACCACCGTGGAGCTGTTTTTCCTGAATGCAAAGGCCTGTGTGCACAAGGTGCAACTGCCAAAAGAAC
TGGCGTAAGAGGCAACAGAGCCATCTAGAAGAACAAGAAATGGAAATAGTGACTCTTGGATTACAGCATGGAGACTATGTCAGCAGCAAT
ACTTTAGGATCCACGTGGCAGAACTGGAAACAATGCTACCATCTGATAAGGGTATTTGTAAAAGGCAGAATGTTTGGGCCATGAAGAAGT
AGGGGCTGAAGAGGAAGGTGGAAGGAGATAAAATATAATATTTAGAGGCAATATTTTCTACTTGCAATCAATTTGAGTGACTCAGGTGAA
ATTTAGAGTCATATTTCCCGAAGCAGAAGTTAAAGAAAATTTTTTAAACATTTGCTTTATTATTGTTTTCTTCTGGTAAATAATAAATAT

>31342_31342_2_FRMD4B-LMOD3_FRMD4B_chr3_69336903_ENST00000542259_LMOD3_chr3_69158272_ENST00000489031_length(amino acids)=268AA_BP=1
MVELSTACSALRAGGGGHWASVCQSQPLAGGHPIPGHAAGAWPGRTVKDEFGGRLDPPAASRSRRREPRRAGRWGRGCTYESRDARVQSE
GGGMASVFMCGVEDLLFSGSRFVWNLTVSTLRRWYTERLRACHQVLRTWCGLQDVYQMTEGRHCQVHLLDDRRLELLVQPKLLARELLDL

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

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Fusion Gene PPI Analysis for FRMD4B-LMOD3

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Tgene	LMOD3	chr3:69336903	chr3:69158272	ENST00000420581		1	3	1_49	552.0	561.0	tropomyosin alpha
Tgene	LMOD3	chr3:69336903	chr3:69158272	ENST00000475434		2	4	1_49	552.0	561.0	tropomyosin alpha
Tgene	LMOD3	chr3:69336903	chr3:69158272	ENST00000489031		2	4	1_49	552.0	561.0	tropomyosin alpha

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for FRMD4B-LMOD3

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for FRMD4B-LMOD3

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source