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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:LIPF-MUC6

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LIPF-MUC6
	FusionPDB ID: 45644
	FusionGDB2.0 ID: 45644
		Hgene	Tgene
	Gene symbol	LIPF	MUC6
	Gene ID	8513	4588
	Gene name	lipase F, gastric type	mucin 6, oligomeric mucus/gel-forming
	Synonyms	GL\|HGL\|HLAL	MUC-6
	Cytomap	10q23.31	11p15.5
	Type of gene	protein-coding	protein-coding
	Description	gastric triacylglycerol lipasegastric lipaselipase, gastric	mucin-6gastric mucin-6
	Modification date	20200313	20200313
	UniProtAcc	P07098	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000238983, ENST00000355843, ENST00000394375, ENST00000608620,	ENST00000421673,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 28 X 4=1568	6 X 8 X 4=192
	# samples	16	5
	** MAII score	log2(16/1568*10)=-3.29278174922785 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/192*10)=-1.94110631094643 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: LIPF [Title/Abstract] AND MUC6 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LIPF(90438314)-MUC6(1017565), # samples:1
Anticipated loss of major functional domain due to fusion event.	LIPF-MUC6 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. LIPF-MUC6 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. LIPF-MUC6 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. LIPF-MUC6 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

Fusion gene breakpoints across LIPF (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 MUC6 (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	ESCA	TCGA-JY-A939	LIPF	chr10	90438314	+	MUC6	chr11	1017565	-

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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)
ENST00000394375	LIPF	chr10	90438314	+	ENST00000421673	MUC6	chr11	1017565	-	4077	1357	2255	4075	607
ENST00000608620	LIPF	chr10	90438314	+	ENST00000421673	MUC6	chr11	1017565	-	3897	1177	2075	3895	607
ENST00000238983	LIPF	chr10	90438314	+	ENST00000421673	MUC6	chr11	1017565	-	3983	1263	2161	3981	607
ENST00000355843	LIPF	chr10	90438314	+	ENST00000421673	MUC6	chr11	1017565	-	3964	1244	2142	3962	607

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
ENST00000394375	ENST00000421673	LIPF	chr10	90438314	+	MUC6	chr11	1017565	-	0.1610373	0.83896273
ENST00000608620	ENST00000421673	LIPF	chr10	90438314	+	MUC6	chr11	1017565	-	0.17234045	0.8276596
ENST00000238983	ENST00000421673	LIPF	chr10	90438314	+	MUC6	chr11	1017565	-	0.15274131	0.8472587
ENST00000355843	ENST00000421673	LIPF	chr10	90438314	+	MUC6	chr11	1017565	-	0.17085986	0.8291401

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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

>45644_45644_1_LIPF-MUC6_LIPF_chr10_90438314_ENST00000238983_MUC6_chr11_1017565_ENST00000421673_length(amino acids)=607AA_BP=6
MHFRCQSTSLHSHTSSTHHPEVTSTSTTSITPNHTSTGTRTPVAHTTSATSSRLPTPFTTHSPPTGTTPISSTGPVTATSFQTTTTYPTP
SHPHTTLPTHVPSFSTSLVTPSTHTVIIPTHTQMATSASIHSMPTGTIPPPTTIKATGSTHTAPPMTPTTSGTSQSPSSFSTAKTSTSLP
YHTSSTHHPEVTPTSTTNITPKHTSTGTRTPVAHTTSASSSRLPTPFTTHSPPTGSSPFSSTGPMTATSFQTTTTYPTPSHPQTTLPTHV
PPFSTSLVTPSTHTVIITTHTQMATSASIHSTPTGTVPPPTTLKATGSTHTAPPMTVTTSGTSQTHSSFSTATASSSFISSSSWLPQNSS
SRPPSSPITTQLPHLSSATTPVSTTNQLSSSFSPSPSAPSTVSSYVPSSHSSPQTSSPSVGTSSSFVSAPVHSTTLSSGSHSSLSTHPTT
ASVSASPLFPSSPAASTTIRATLPHTISSPFTLSALLPISTVTVSPTPSSHLASSTIAFPSTPRTTASTHTAPAFSSQSTTSRSTSLTTR

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

>45644_45644_2_LIPF-MUC6_LIPF_chr10_90438314_ENST00000355843_MUC6_chr11_1017565_ENST00000421673_length(amino acids)=607AA_BP=6
MHFRCQSTSLHSHTSSTHHPEVTSTSTTSITPNHTSTGTRTPVAHTTSATSSRLPTPFTTHSPPTGTTPISSTGPVTATSFQTTTTYPTP
SHPHTTLPTHVPSFSTSLVTPSTHTVIIPTHTQMATSASIHSMPTGTIPPPTTIKATGSTHTAPPMTPTTSGTSQSPSSFSTAKTSTSLP
YHTSSTHHPEVTPTSTTNITPKHTSTGTRTPVAHTTSASSSRLPTPFTTHSPPTGSSPFSSTGPMTATSFQTTTTYPTPSHPQTTLPTHV
PPFSTSLVTPSTHTVIITTHTQMATSASIHSTPTGTVPPPTTLKATGSTHTAPPMTVTTSGTSQTHSSFSTATASSSFISSSSWLPQNSS
SRPPSSPITTQLPHLSSATTPVSTTNQLSSSFSPSPSAPSTVSSYVPSSHSSPQTSSPSVGTSSSFVSAPVHSTTLSSGSHSSLSTHPTT
ASVSASPLFPSSPAASTTIRATLPHTISSPFTLSALLPISTVTVSPTPSSHLASSTIAFPSTPRTTASTHTAPAFSSQSTTSRSTSLTTR

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

>45644_45644_3_LIPF-MUC6_LIPF_chr10_90438314_ENST00000394375_MUC6_chr11_1017565_ENST00000421673_length(amino acids)=607AA_BP=6
MHFRCQSTSLHSHTSSTHHPEVTSTSTTSITPNHTSTGTRTPVAHTTSATSSRLPTPFTTHSPPTGTTPISSTGPVTATSFQTTTTYPTP
SHPHTTLPTHVPSFSTSLVTPSTHTVIIPTHTQMATSASIHSMPTGTIPPPTTIKATGSTHTAPPMTPTTSGTSQSPSSFSTAKTSTSLP
YHTSSTHHPEVTPTSTTNITPKHTSTGTRTPVAHTTSASSSRLPTPFTTHSPPTGSSPFSSTGPMTATSFQTTTTYPTPSHPQTTLPTHV
PPFSTSLVTPSTHTVIITTHTQMATSASIHSTPTGTVPPPTTLKATGSTHTAPPMTVTTSGTSQTHSSFSTATASSSFISSSSWLPQNSS
SRPPSSPITTQLPHLSSATTPVSTTNQLSSSFSPSPSAPSTVSSYVPSSHSSPQTSSPSVGTSSSFVSAPVHSTTLSSGSHSSLSTHPTT
ASVSASPLFPSSPAASTTIRATLPHTISSPFTLSALLPISTVTVSPTPSSHLASSTIAFPSTPRTTASTHTAPAFSSQSTTSRSTSLTTR

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

>45644_45644_4_LIPF-MUC6_LIPF_chr10_90438314_ENST00000608620_MUC6_chr11_1017565_ENST00000421673_length(amino acids)=607AA_BP=6
MHFRCQSTSLHSHTSSTHHPEVTSTSTTSITPNHTSTGTRTPVAHTTSATSSRLPTPFTTHSPPTGTTPISSTGPVTATSFQTTTTYPTP
SHPHTTLPTHVPSFSTSLVTPSTHTVIIPTHTQMATSASIHSMPTGTIPPPTTIKATGSTHTAPPMTPTTSGTSQSPSSFSTAKTSTSLP
YHTSSTHHPEVTPTSTTNITPKHTSTGTRTPVAHTTSASSSRLPTPFTTHSPPTGSSPFSSTGPMTATSFQTTTTYPTPSHPQTTLPTHV
PPFSTSLVTPSTHTVIITTHTQMATSASIHSTPTGTVPPPTTLKATGSTHTAPPMTVTTSGTSQTHSSFSTATASSSFISSSSWLPQNSS
SRPPSSPITTQLPHLSSATTPVSTTNQLSSSFSPSPSAPSTVSSYVPSSHSSPQTSSPSVGTSSSFVSAPVHSTTLSSGSHSSLSTHPTT
ASVSASPLFPSSPAASTTIRATLPHTISSPFTLSALLPISTVTVSPTPSSHLASSTIAFPSTPRTTASTHTAPAFSSQSTTSRSTSLTTR

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

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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/chr10:90438314/chr11:1017565)
- 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
LIPF P07098	.
FUNCTION: Catalyzes the hydrolysis of triacylglycerols to yield free fatty acids, diacylglycerol, monoacylglycerol, and glycerol (PubMed:2243091, PubMed:10358049). Shows a preferential hydrolysis at the sn-3 position of triacylglycerol (PubMed:2243091). {ECO:0000269\|PubMed:10358049, ECO:0000269\|PubMed:2243091}.	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

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

1241_1664

2440.0

Compositional bias

Note=Pro-rich

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

1246_2344

2440.0

Compositional bias

Note=Thr-rich

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

2069_2275

2440.0

Compositional bias

Note=Ser-rich

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

2349_2438

2440.0

Domain

CTCK

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

302_357

2440.0

Domain

Note=TIL

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

396_608

2440.0

Domain

VWFD 2

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

44_246

2440.0

Domain

VWFD 1

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

867_1075

2440.0

Domain

VWFD 3

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

1607_1953

2440.0

Region

Note=Approximate repeats

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

1561_1738

2440.0

Repeat

Note=1%3B truncated

Tgene

MUC6

chr10:90438314

chr11:1017565

ENST00000421673

1785_1953

2440.0

Repeat

Note=2

- 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

LIPF

chr10:90438314

chr11:1017565

ENST00000238983

78_377

399.0

Domain

AB hydrolase-1

Hgene

LIPF

chr10:90438314

chr11:1017565

ENST00000355843

78_377

376.0

Domain

AB hydrolase-1

Hgene

LIPF

chr10:90438314

chr11:1017565

ENST00000394375

78_377

409.0

Domain

AB hydrolase-1

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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
LIPF
MUC6

- 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 LIPF-MUC6

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 LIPF-MUC6

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