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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:LMF1-CCDC154

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LMF1-CCDC154
	FusionPDB ID: 45772
	FusionGDB2.0 ID: 45772
		Hgene	Tgene
	Gene symbol	LMF1	CCDC154
	Gene ID	64788	645811
	Gene name	lipase maturation factor 1	coiled-coil domain containing 154
	Synonyms	C16orf26\|HMFN1876\|JFP11\|TMEM112\|TMEM112A	C16orf29
	Cytomap	16p13.3	16p13.3
	Type of gene	protein-coding	protein-coding
	Description	lipase maturation factor 1transmembrane protein 112	coiled-coil domain-containing protein 154
	Modification date	20200313	20200313
	UniProtAcc	Q96S06	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000539379, ENST00000262301, ENST00000399843, ENST00000568897, ENST00000543238, ENST00000568268,	ENST00000389176, ENST00000409671,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	1 X 1 X 1=1	1 X 1 X 1=1
	# samples	1	1
	** MAII score	log2(1/1*10)=3.32192809488736	log2(1/1*10)=3.32192809488736
Context (manual curation of fusion genes in FusionPDB)	PubMed: LMF1 [Title/Abstract] AND CCDC154 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LMF1(960931)-CCDC154(1489127), # 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)

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 LMF1 (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 CCDC154 (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	LGG	TCGA-DU-A6S2-01A	LMF1	chr16	960931	-	CCDC154	chr16	1489127	-

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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)
ENST00000262301	LMF1	chr16	960931	-	ENST00000409671	CCDC154	chr16	1489127	-	2034	682	19	2010	663
ENST00000262301	LMF1	chr16	960931	-	ENST00000389176	CCDC154	chr16	1489127	-	2052	682	19	2031	670
ENST00000399843	LMF1	chr16	960931	-	ENST00000409671	CCDC154	chr16	1489127	-	2017	665	2	1993	663
ENST00000399843	LMF1	chr16	960931	-	ENST00000389176	CCDC154	chr16	1489127	-	2035	665	2	2014	670
ENST00000568897	LMF1	chr16	960931	-	ENST00000409671	CCDC154	chr16	1489127	-	1894	542	386	1870	494
ENST00000568897	LMF1	chr16	960931	-	ENST00000389176	CCDC154	chr16	1489127	-	1912	542	386	1891	501

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
ENST00000262301	ENST00000409671	LMF1	chr16	960931	-	CCDC154	chr16	1489127	-	0.043009564	0.9569905
ENST00000262301	ENST00000389176	LMF1	chr16	960931	-	CCDC154	chr16	1489127	-	0.04437499	0.955625
ENST00000399843	ENST00000409671	LMF1	chr16	960931	-	CCDC154	chr16	1489127	-	0.0427162	0.9572838
ENST00000399843	ENST00000389176	LMF1	chr16	960931	-	CCDC154	chr16	1489127	-	0.04399601	0.95600396
ENST00000568897	ENST00000409671	LMF1	chr16	960931	-	CCDC154	chr16	1489127	-	0.016946755	0.98305327
ENST00000568897	ENST00000389176	LMF1	chr16	960931	-	CCDC154	chr16	1489127	-	0.017507967	0.98249197

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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

>45772_45772_1_LMF1-CCDC154_LMF1_chr16_960931_ENST00000262301_CCDC154_chr16_1489127_ENST00000389176_length(amino acids)=670AA_BP=221
MRPDSPTMAAPAESLRRRKTGYSDPEPESPPAPGRGPAGSPAHLHTGTFWLTRIVLLKALAFVYFVAFLVAFHQNKQLIGDRGLLPCRVF
LKNFQQYFQDRTSWEVFSYMPTILWLMDWSDMNSNLDLLALLGLGISSFVLITGCANMLLMAALWGLYMSLVNVGHVWYSFGWESQLLET
GFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGS
LRGELESRWEKLRGLMEERLRALQGQHEVGPGGRRAEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRAGE
LAAYVQENLEAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSLED
LARWRKEVTEHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKLAT
NQIMKLENCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQAVRW

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

>45772_45772_2_LMF1-CCDC154_LMF1_chr16_960931_ENST00000262301_CCDC154_chr16_1489127_ENST00000409671_length(amino acids)=663AA_BP=221
MRPDSPTMAAPAESLRRRKTGYSDPEPESPPAPGRGPAGSPAHLHTGTFWLTRIVLLKALAFVYFVAFLVAFHQNKQLIGDRGLLPCRVF
LKNFQQYFQDRTSWEVFSYMPTILWLMDWSDMNSNLDLLALLGLGISSFVLITGCANMLLMAALWGLYMSLVNVGHVWYSFGWESQLLET
GFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGS
LRGELESRWEKLRGLMEERLRALQGQHEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRAGELAAYVQENL
EAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSLEDLARWRKEVT
EHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKLATFQNQIMKLE
NCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQAVRWLRWKASL

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

>45772_45772_3_LMF1-CCDC154_LMF1_chr16_960931_ENST00000399843_CCDC154_chr16_1489127_ENST00000389176_length(amino acids)=670AA_BP=221
MRPDSPTMAAPAESLRRRKTGYSDPEPESPPAPGRGPAGSPAHLHTGTFWLTRIVLLKALAFVYFVAFLVAFHQNKQLIGDRGLLPCRVF
LKNFQQYFQDRTSWEVFSYMPTILWLMDWSDMNSNLDLLALLGLGISSFVLITGCANMLLMAALWGLYMSLVNVGHVWYSFRWESQLLET
GFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGS
LRGELESRWEKLRGLMEERLRALQGQHEVGPGGRRAEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRAGE
LAAYVQENLEAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSLED
LARWRKEVTEHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKLAT
NQIMKLENCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQAVRW

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

>45772_45772_4_LMF1-CCDC154_LMF1_chr16_960931_ENST00000399843_CCDC154_chr16_1489127_ENST00000409671_length(amino acids)=663AA_BP=221
MRPDSPTMAAPAESLRRRKTGYSDPEPESPPAPGRGPAGSPAHLHTGTFWLTRIVLLKALAFVYFVAFLVAFHQNKQLIGDRGLLPCRVF
LKNFQQYFQDRTSWEVFSYMPTILWLMDWSDMNSNLDLLALLGLGISSFVLITGCANMLLMAALWGLYMSLVNVGHVWYSFRWESQLLET
GFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKASESSRLKLEGS
LRGELESRWEKLRGLMEERLRALQGQHEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRAGELAAYVQENL
EAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSLEDLARWRKEVT
EHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKLATFQNQIMKLE
NCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQAVRWLRWKASL

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

>45772_45772_5_LMF1-CCDC154_LMF1_chr16_960931_ENST00000568897_CCDC154_chr16_1489127_ENST00000389176_length(amino acids)=501AA_BP=52
MVRWESQLLETGFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKA
SESSRLKLEGSLRGELESRWEKLRGLMEERLRALQGQHEVGPGGRRAEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDA
KGRLEESRAGELAAYVQENLEAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTE
WEGAERKSLEDLARWRKEVTEHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGR
KIAEMQGKLATNQIMKLENCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPM

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

>45772_45772_6_LMF1-CCDC154_LMF1_chr16_960931_ENST00000568897_CCDC154_chr16_1489127_ENST00000409671_length(amino acids)=494AA_BP=52
MVRWESQLLETGFLGIFLCPLWTLSRLPQHTPTSRIVLWGFRWLIFRIMLGAAQVTKLGEEVSLRFLKREAKLCGFLQKSFLALEKRMKA
SESSRLKLEGSLRGELESRWEKLRGLMEERLRALQGQHEESHLLEQCQGLDAAVAQLTKFVQQNQASLNRVLLAEEKAWDAKGRLEESRA
GELAAYVQENLEAAQLAGELARQEMHGELVLLREKSRALEASVAQLAGQLKELSGHLPALSSRLDLQEQMLGLRLSEAKTEWEGAERKSL
EDLARWRKEVTEHLRGVREKVDGLPQQIESVSDKCLLHKSDSDLRISAEGKAREFKVGALRQELATLLSSVQLLKEDNPGRKIAEMQGKL
ATFQNQIMKLENCVQANKTIQNLRFNTEARLRTQEMATLWESVLRLWSEEGPRTPLGSWKALPSLVRPRVFIKDMAPGKVVPMNCWGVYQ

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

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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/chr16:960931/chr16:1489127)
- 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
LMF1 Q96S06	.
FUNCTION: Involved in the maturation of specific proteins in the endoplasmic reticulum. Required for maturation and transport of active lipoprotein lipase (LPL) through the secretory pathway. Each LMF1 molecule chaperones 50 or more molecules of LPL. {ECO:0000250\|UniProtKB:Q3U3R4, ECO:0000269\|PubMed:24909692}.	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.

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

LMF1

chr16:960931

chr16:1489127

ENST00000262301

152_207

221.0

568.0

Topological domain

Cytoplasmic

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

1_49

221.0

568.0

Topological domain

Cytoplasmic

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

73_127

221.0

568.0

Topological domain

Lumenal

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

128_151

221.0

568.0

Transmembrane

Helical

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

208_221

221.0

568.0

Transmembrane

Helical

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

50_72

221.0

568.0

Transmembrane

Helical

Tgene

CCDC154

chr16:960931

chr16:1489127

ENST00000389176

384_410

225.0

675.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

CCDC154

chr16:960931

chr16:1489127

ENST00000389176

457_521

225.0

675.0

Coiled coil

Ontology_term=ECO:0000255

- 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

LMF1

chr16:960931

chr16:1489127

ENST00000262301

222_292

221.0

568.0

Topological domain

Lumenal

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

322_367

221.0

568.0

Topological domain

Cytoplasmic

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

389_567

221.0

568.0

Topological domain

Lumenal

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

293_321

221.0

568.0

Transmembrane

Helical

Hgene

LMF1

chr16:960931

chr16:1489127

ENST00000262301

368_388

221.0

568.0

Transmembrane

Helical

Tgene

CCDC154

chr16:960931

chr16:1489127

ENST00000389176

215_302

225.0

675.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

CCDC154

chr16:960931

chr16:1489127

ENST00000389176

76_182

225.0

675.0

Coiled coil

Ontology_term=ECO:0000255

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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
LMF1
CCDC154

- 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 LMF1-CCDC154

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 LMF1-CCDC154

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