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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:RAD50-LIPF

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RAD50-LIPF
	FusionPDB ID: 71726
	FusionGDB2.0 ID: 71726
		Hgene	Tgene
	Gene symbol	RAD50	LIPF
	Gene ID	10111	8513
	Gene name	RAD50 double strand break repair protein	lipase F, gastric type
	Synonyms	NBSLD\|RAD502\|hRad50	GL\|HGL\|HLAL
	Cytomap	5q31.1	10q23.31
	Type of gene	protein-coding	protein-coding
	Description	DNA repair protein RAD50RAD50 homolog, double strand break repair protein	gastric triacylglycerol lipasegastric lipaselipase, gastric
	Modification date	20200320	20200313
	UniProtAcc	RINT1	P07098
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000265335, ENST00000378823, ENST00000487596,	ENST00000238983, ENST00000355843, ENST00000394375, ENST00000608620,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 7 X 7=441	17 X 18 X 7=2142
	# samples	10	18
	** MAII score	log2(10/441*10)=-2.1407786557828 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(18/2142*10)=-3.57288966842058 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: RAD50 [Title/Abstract] AND LIPF [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RAD50(131915194)-LIPF(90429593), # samples:1
Anticipated loss of major functional domain due to fusion event.	RAD50-LIPF 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. RAD50-LIPF 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
Hgene	RAD50	GO:0000019	regulation of mitotic recombination	8756642
Hgene	RAD50	GO:0006281	DNA repair	9705271
Hgene	RAD50	GO:0006310	DNA recombination	9705271
Hgene	RAD50	GO:0006974	cellular response to DNA damage stimulus	17500065
Hgene	RAD50	GO:0007004	telomere maintenance via telomerase	9705271
Hgene	RAD50	GO:0031954	positive regulation of protein autophosphorylation	15790808
Hgene	RAD50	GO:0033674	positive regulation of kinase activity	15790808
Hgene	RAD50	GO:1904354	negative regulation of telomere capping	17694070

Fusion gene breakpoints across RAD50 (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 LIPF (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	Non-Cancer	131Nd	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+

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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)
ENST00000378823	RAD50	chr5	131915194	+	ENST00000394375	LIPF	chr10	90429593	+	1857	952	374	1726	450
ENST00000378823	RAD50	chr5	131915194	+	ENST00000608620	LIPF	chr10	90429593	+	1857	952	374	1726	450
ENST00000378823	RAD50	chr5	131915194	+	ENST00000238983	LIPF	chr10	90429593	+	1860	952	374	1726	450
ENST00000378823	RAD50	chr5	131915194	+	ENST00000355843	LIPF	chr10	90429593	+	1860	952	374	1726	450
ENST00000265335	RAD50	chr5	131915194	+	ENST00000394375	LIPF	chr10	90429593	+	1843	938	360	1712	450
ENST00000265335	RAD50	chr5	131915194	+	ENST00000608620	LIPF	chr10	90429593	+	1843	938	360	1712	450
ENST00000265335	RAD50	chr5	131915194	+	ENST00000238983	LIPF	chr10	90429593	+	1846	938	360	1712	450
ENST00000265335	RAD50	chr5	131915194	+	ENST00000355843	LIPF	chr10	90429593	+	1846	938	360	1712	450

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
ENST00000378823	ENST00000394375	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+	0.000358167	0.9996418
ENST00000378823	ENST00000608620	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+	0.000358167	0.9996418
ENST00000378823	ENST00000238983	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+	0.000352192	0.99964786
ENST00000378823	ENST00000355843	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+	0.000352192	0.99964786
ENST00000265335	ENST00000394375	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+	0.000354206	0.9996458
ENST00000265335	ENST00000608620	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+	0.000354206	0.9996458
ENST00000265335	ENST00000238983	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+	0.000348644	0.9996513
ENST00000265335	ENST00000355843	RAD50	chr5	131915194	+	LIPF	chr10	90429593	+	0.000348644	0.9996513

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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

>71726_71726_1_RAD50-LIPF_RAD50_chr5_131915194_ENST00000265335_LIPF_chr10_90429593_ENST00000238983_length(amino acids)=450AA_BP=192
MVRLETFANMSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQ
IRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKA
LKQKFDEIFSATSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVP
QSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDW
GSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK

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

>71726_71726_2_RAD50-LIPF_RAD50_chr5_131915194_ENST00000265335_LIPF_chr10_90429593_ENST00000355843_length(amino acids)=450AA_BP=192
MVRLETFANMSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQ
IRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKA
LKQKFDEIFSATSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVP
QSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDW
GSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK

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

>71726_71726_3_RAD50-LIPF_RAD50_chr5_131915194_ENST00000265335_LIPF_chr10_90429593_ENST00000394375_length(amino acids)=450AA_BP=192
MVRLETFANMSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQ
IRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKA
LKQKFDEIFSATSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVP
QSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDW
GSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK

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

>71726_71726_4_RAD50-LIPF_RAD50_chr5_131915194_ENST00000265335_LIPF_chr10_90429593_ENST00000608620_length(amino acids)=450AA_BP=192
MVRLETFANMSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQ
IRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKA
LKQKFDEIFSATSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVP
QSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDW
GSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK

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

>71726_71726_5_RAD50-LIPF_RAD50_chr5_131915194_ENST00000378823_LIPF_chr10_90429593_ENST00000238983_length(amino acids)=450AA_BP=192
MVRLETFANMSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQ
IRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKA
LKQKFDEIFSATSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVP
QSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDW
GSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK

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

>71726_71726_6_RAD50-LIPF_RAD50_chr5_131915194_ENST00000378823_LIPF_chr10_90429593_ENST00000355843_length(amino acids)=450AA_BP=192
MVRLETFANMSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQ
IRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKA
LKQKFDEIFSATSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVP
QSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDW
GSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK

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

>71726_71726_7_RAD50-LIPF_RAD50_chr5_131915194_ENST00000378823_LIPF_chr10_90429593_ENST00000394375_length(amino acids)=450AA_BP=192
MVRLETFANMSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQ
IRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKA
LKQKFDEIFSATSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVP
QSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDW
GSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK

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

>71726_71726_8_RAD50-LIPF_RAD50_chr5_131915194_ENST00000378823_LIPF_chr10_90429593_ENST00000608620_length(amino acids)=450AA_BP=192
MVRLETFANMSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKGNTFVHDPKVAQETDVRAQ
IRLQFRDVNGELIAVQRSMVCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAVLNNVIFCHQEDSNWPLSEGKA
LKQKFDEIFSATSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVP
QSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDW
GSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK

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

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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/chr5:131915194/chr10:90429593)
- 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
RAD50 RINT1	LIPF P07098
792	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}.

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

RAD50

chr5:131915194

chr10:90429593

ENST00000265335

36_43

183.66666666666666

1313.0

Nucleotide binding

ATP

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000378823

36_43

44.666666666666664

1174.0

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

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000265335

228_359

183.66666666666666

1313.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000265335

401_598

183.66666666666666

1313.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000265335

635_673

183.66666666666666

1313.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000265335

706_734

183.66666666666666

1313.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000265335

789_1079

183.66666666666666

1313.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000378823

228_359

44.666666666666664

1174.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000378823

401_598

44.666666666666664

1174.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000378823

635_673

44.666666666666664

1174.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000378823

706_734

44.666666666666664

1174.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000378823

789_1079

44.666666666666664

1174.0

Coiled coil

Ontology_term=ECO:0000255

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000265335

1201_1238

183.66666666666666

1313.0

Compositional bias

Note=Ala/Asp-rich (DA-box)

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000378823

1201_1238

44.666666666666664

1174.0

Compositional bias

Note=Ala/Asp-rich (DA-box)

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000265335

635_734

183.66666666666666

1313.0

Domain

Zinc-hook

Hgene

RAD50

chr5:131915194

chr10:90429593

ENST00000378823

635_734

44.666666666666664

1174.0

Domain

Zinc-hook

Tgene

LIPF

chr5:131915194

chr10:90429593

ENST00000238983

78_377

140.66666666666666

399.0

Domain

AB hydrolase-1

Tgene

LIPF

chr5:131915194

chr10:90429593

ENST00000355843

78_377

117.66666666666667

376.0

Domain

AB hydrolase-1

Tgene

LIPF

chr5:131915194

chr10:90429593

ENST00000394375

78_377

150.66666666666666

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
RAD50
LIPF

- 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 RAD50-LIPF

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 RAD50-LIPF

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