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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:LFNG-MAD1L1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LFNG-MAD1L1
	FusionPDB ID: 44499
	FusionGDB2.0 ID: 44499
		Hgene	Tgene
	Gene symbol	LFNG	MAD1L1
	Gene ID	3955	8379
	Gene name	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	mitotic arrest deficient 1 like 1
	Synonyms	SCDO3	MAD1\|PIG9\|TP53I9\|TXBP181
	Cytomap	7p22.3	7p22.3
	Type of gene	protein-coding	protein-coding
	Description	beta-1,3-N-acetylglucosaminyltransferase lunatic fringe	mitotic spindle assembly checkpoint protein MAD1MAD1 mitotic arrest deficient like 1MAD1-like protein 1mitotic arrest deficient 1-like protein 1mitotic checkpoint MAD1 protein homologmitotic-arrest deficient 1, yeast, homolog-like 1tax-binding prote
	Modification date	20200313	20200313
	UniProtAcc	Q8NES3	Q9Y6D9
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000222725, ENST00000359574, ENST00000338732, ENST00000402045, ENST00000402506,	ENST00000486340, ENST00000265854, ENST00000399654, ENST00000402746, ENST00000406869,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 2 X 2=8	23 X 16 X 12=4416
	# samples	2	37
	** MAII score	log2(2/8*10)=1.32192809488736	log2(37/4416*10)=-3.57714299626186 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: LFNG [Title/Abstract] AND MAD1L1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LFNG(2559927)-MAD1L1(1976533), # samples:1
Anticipated loss of major functional domain due to fusion event.	LFNG-MAD1L1 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. LFNG-MAD1L1 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	MAD1L1	GO:0007094	mitotic spindle assembly checkpoint	18981471
Tgene	MAD1L1	GO:0090235	regulation of metaphase plate congression	20133940

Fusion gene breakpoints across LFNG (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 MAD1L1 (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-13-0919	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-

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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)
ENST00000222725	LFNG	chr7	2559927	+	ENST00000402746	MAD1L1	chr7	1976533	-	1289	452	20	1012	330
ENST00000222725	LFNG	chr7	2559927	+	ENST00000399654	MAD1L1	chr7	1976533	-	1289	452	20	1012	330
ENST00000222725	LFNG	chr7	2559927	+	ENST00000406869	MAD1L1	chr7	1976533	-	1289	452	20	1012	330
ENST00000222725	LFNG	chr7	2559927	+	ENST00000265854	MAD1L1	chr7	1976533	-	1272	452	20	1012	330
ENST00000359574	LFNG	chr7	2559927	+	ENST00000402746	MAD1L1	chr7	1976533	-	1269	432	0	992	330
ENST00000359574	LFNG	chr7	2559927	+	ENST00000399654	MAD1L1	chr7	1976533	-	1269	432	0	992	330
ENST00000359574	LFNG	chr7	2559927	+	ENST00000406869	MAD1L1	chr7	1976533	-	1269	432	0	992	330
ENST00000359574	LFNG	chr7	2559927	+	ENST00000265854	MAD1L1	chr7	1976533	-	1252	432	0	992	330

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
ENST00000222725	ENST00000402746	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-	0.018587176	0.98141277
ENST00000222725	ENST00000399654	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-	0.018587176	0.98141277
ENST00000222725	ENST00000406869	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-	0.018587176	0.98141277
ENST00000222725	ENST00000265854	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-	0.018096391	0.9819036
ENST00000359574	ENST00000402746	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-	0.01891516	0.9810848
ENST00000359574	ENST00000399654	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-	0.01891516	0.9810848
ENST00000359574	ENST00000406869	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-	0.01891516	0.9810848
ENST00000359574	ENST00000265854	LFNG	chr7	2559927	+	MAD1L1	chr7	1976533	-	0.018260032	0.98174

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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

>44499_44499_1_LFNG-MAD1L1_LFNG_chr7_2559927_ENST00000222725_MAD1L1_chr7_1976533_ENST00000265854_length(amino acids)=330AA_BP=6
MLKRCGRRLLLALAGALLACLLVLTADPPPPPLPAERGRRALRSLAGPAGAAPAPGLGAAAAAPGALVRDVHSLSEYFSLLTRARRDAGP
PPGAAPRPADGHPRPLAEPLAPRDVFIAVKTTKKFHRARLDLLLETWISRHKEMGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAEC
ERLRGLLRAMERGGTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEH

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

>44499_44499_2_LFNG-MAD1L1_LFNG_chr7_2559927_ENST00000222725_MAD1L1_chr7_1976533_ENST00000399654_length(amino acids)=330AA_BP=6
MLKRCGRRLLLALAGALLACLLVLTADPPPPPLPAERGRRALRSLAGPAGAAPAPGLGAAAAAPGALVRDVHSLSEYFSLLTRARRDAGP
PPGAAPRPADGHPRPLAEPLAPRDVFIAVKTTKKFHRARLDLLLETWISRHKEMGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAEC
ERLRGLLRAMERGGTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEH

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

>44499_44499_3_LFNG-MAD1L1_LFNG_chr7_2559927_ENST00000222725_MAD1L1_chr7_1976533_ENST00000402746_length(amino acids)=330AA_BP=6
MLKRCGRRLLLALAGALLACLLVLTADPPPPPLPAERGRRALRSLAGPAGAAPAPGLGAAAAAPGALVRDVHSLSEYFSLLTRARRDAGP
PPGAAPRPADGHPRPLAEPLAPRDVFIAVKTTKKFHRARLDLLLETWISRHKEMGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAEC
ERLRGLLRAMERGGTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEH

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

>44499_44499_4_LFNG-MAD1L1_LFNG_chr7_2559927_ENST00000222725_MAD1L1_chr7_1976533_ENST00000406869_length(amino acids)=330AA_BP=6
MLKRCGRRLLLALAGALLACLLVLTADPPPPPLPAERGRRALRSLAGPAGAAPAPGLGAAAAAPGALVRDVHSLSEYFSLLTRARRDAGP
PPGAAPRPADGHPRPLAEPLAPRDVFIAVKTTKKFHRARLDLLLETWISRHKEMGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAEC
ERLRGLLRAMERGGTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEH

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

>44499_44499_5_LFNG-MAD1L1_LFNG_chr7_2559927_ENST00000359574_MAD1L1_chr7_1976533_ENST00000265854_length(amino acids)=330AA_BP=6
MLKRCGRRLLLALAGALLACLLVLTADPPPPPLPAERGRRALRSLAGPAGAAPAPGLGAAAAAPGALVRDVHSLSEYFSLLTRARRDAGP
PPGAAPRPADGHPRPLAEPLAPRDVFIAVKTTKKFHRARLDLLLETWISRHKEMGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAEC
ERLRGLLRAMERGGTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEH

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

>44499_44499_6_LFNG-MAD1L1_LFNG_chr7_2559927_ENST00000359574_MAD1L1_chr7_1976533_ENST00000399654_length(amino acids)=330AA_BP=6
MLKRCGRRLLLALAGALLACLLVLTADPPPPPLPAERGRRALRSLAGPAGAAPAPGLGAAAAAPGALVRDVHSLSEYFSLLTRARRDAGP
PPGAAPRPADGHPRPLAEPLAPRDVFIAVKTTKKFHRARLDLLLETWISRHKEMGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAEC
ERLRGLLRAMERGGTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEH

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

>44499_44499_7_LFNG-MAD1L1_LFNG_chr7_2559927_ENST00000359574_MAD1L1_chr7_1976533_ENST00000402746_length(amino acids)=330AA_BP=6
MLKRCGRRLLLALAGALLACLLVLTADPPPPPLPAERGRRALRSLAGPAGAAPAPGLGAAAAAPGALVRDVHSLSEYFSLLTRARRDAGP
PPGAAPRPADGHPRPLAEPLAPRDVFIAVKTTKKFHRARLDLLLETWISRHKEMGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAEC
ERLRGLLRAMERGGTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEH

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

>44499_44499_8_LFNG-MAD1L1_LFNG_chr7_2559927_ENST00000359574_MAD1L1_chr7_1976533_ENST00000406869_length(amino acids)=330AA_BP=6
MLKRCGRRLLLALAGALLACLLVLTADPPPPPLPAERGRRALRSLAGPAGAAPAPGLGAAAAAPGALVRDVHSLSEYFSLLTRARRDAGP
PPGAAPRPADGHPRPLAEPLAPRDVFIAVKTTKKFHRARLDLLLETWISRHKEMGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAEC
ERLRGLLRAMERGGTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEH

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

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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/chr7:2559927/chr7:1976533)
- 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
LFNG Q8NES3	MAD1L1 Q9Y6D9
FUNCTION: Glycosyltransferase that initiates the elongation of O-linked fucose residues attached to EGF-like repeats in the extracellular domain of Notch molecules. Modulates NOTCH1 activity by modifying O-fucose residues at specific EGF-like domains resulting in inhibition of NOTCH1 activation by JAG1 and enhancement of NOTCH1 activation by DLL1 via an increase in its binding to DLL1 (By similarity). Decreases the binding of JAG1 to NOTCH2 but not that of DLL1 (PubMed:11346656). Essential mediator of somite segmentation and patterning (By similarity). {ECO:0000250\|UniProtKB:O09010, ECO:0000269\|PubMed:11346656}.	FUNCTION: Component of the spindle-assembly checkpoint that prevents the onset of anaphase until all chromosomes are properly aligned at the metaphase plate (PubMed:10049595, PubMed:20133940, PubMed:29162720). Forms a heterotetrameric complex with the closed conformation form of MAD2L1 (C-MAD2) at unattached kinetochores during prometaphase, recruits an open conformation of MAD2L1 (O-MAD2) and promotes the conversion of O-MAD2 to C-MAD2, which ensures mitotic checkpoint signaling (PubMed:29162720). {ECO:0000269\|PubMed:10049595, ECO:0000269\|PubMed:20133940, ECO:0000269\|PubMed:29162720}.

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

LFNG

chr7:2559927

chr7:1976533

ENST00000222725

1_8

144.0

380.0

Topological domain

Cytoplasmic

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000359574

1_8

144.0

362.0

Topological domain

Cytoplasmic

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000222725

9_29

144.0

380.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000359574

9_29

144.0

362.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

- 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

LFNG

chr7:2559927

chr7:1976533

ENST00000222725

30_379

144.0

380.0

Topological domain

Lumenal

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000338732

1_8

0.0

251.0

Topological domain

Cytoplasmic

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000338732

30_379

0.0

251.0

Topological domain

Lumenal

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000359574

30_379

144.0

362.0

Topological domain

Lumenal

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000402045

1_8

251.0

Topological domain

Cytoplasmic

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000402045

30_379

251.0

Topological domain

Lumenal

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000402506

1_8

309.0

Topological domain

Cytoplasmic

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000402506

30_379

309.0

Topological domain

Lumenal

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000338732

9_29

0.0

251.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000402045

9_29

251.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

LFNG

chr7:2559927

chr7:1976533

ENST00000402506

9_29

309.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

MAD1L1

chr7:2559927

chr7:1976533

ENST00000265854

46_632

532.0

719.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

MAD1L1

chr7:2559927

chr7:1976533

ENST00000399654

46_632

532.0

719.0

Coiled coil

Ontology_term=ECO:0000255

Tgene

MAD1L1

chr7:2559927

chr7:1976533

ENST00000406869

46_632

532.0

719.0

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
LFNG
MAD1L1

- 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 LFNG-MAD1L1

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 LFNG-MAD1L1

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