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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:ATAD1-LIPF

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ATAD1-LIPF
	FusionPDB ID: 7330
	FusionGDB2.0 ID: 7330
		Hgene	Tgene
	Gene symbol	ATAD1	LIPF
	Gene ID	84896	8513
	Gene name	ATPase family AAA domain containing 1	lipase F, gastric type
	Synonyms	AFDC1\|FNP001\|HKPX4\|Msp1\|THORASE	GL\|HGL\|HLAL
	Cytomap	10q23.31	10q23.31
	Type of gene	protein-coding	protein-coding
	Description	ATPase family AAA domain-containing protein 1	gastric triacylglycerol lipasegastric lipaselipase, gastric
	Modification date	20200313	20200313
	UniProtAcc	Q8NBU5	P07098
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000308448, ENST00000328142, ENST00000400215, ENST00000541004, ENST00000495903,	ENST00000238983, ENST00000355843, ENST00000608620, ENST00000394375,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 8 X 7=616	17 X 18 X 7=2142
	# samples	12	18
	** MAII score	log2(12/616*10)=-2.35989594508638 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: ATAD1 [Title/Abstract] AND LIPF [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ATAD1(89550067)-LIPF(90427044), # samples:3
Anticipated loss of major functional domain due to fusion event.	ATAD1-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. ATAD1-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. ATAD1-LIPF seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. ATAD1-LIPF seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. ATAD1-LIPF seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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 ATAD1 (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	LGG	TCGA-E1-A7YN-01A	ATAD1	chr10	89550067	-	LIPF	chr10	90427044	+
ChimerDB4	LGG	TCGA-E1-A7YN	ATAD1	chr10	89550066	-	LIPF	chr10	90427043	+
ChimerDB4	LGG	TCGA-E1-A7YN	ATAD1	chr10	89550067	-	LIPF	chr10	90427044	+

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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)
ENST00000328142	ATAD1	chr10	89550067	-	ENST00000394375	LIPF	chr10	90427044	+	2003	665	253	1872	539
ENST00000400215	ATAD1	chr10	89550067	-	ENST00000394375	LIPF	chr10	90427044	+	1560	222	14	1429	471
ENST00000328142	ATAD1	chr10	89550066	-	ENST00000394375	LIPF	chr10	90427043	+	2003	665	253	1872	539
ENST00000400215	ATAD1	chr10	89550066	-	ENST00000394375	LIPF	chr10	90427043	+	1560	222	14	1429	471

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
ENST00000328142	ENST00000394375	ATAD1	chr10	89550067	-	LIPF	chr10	90427044	+	0.000210786	0.9997892
ENST00000400215	ENST00000394375	ATAD1	chr10	89550067	-	LIPF	chr10	90427044	+	0.002047304	0.9979527
ENST00000328142	ENST00000394375	ATAD1	chr10	89550066	-	LIPF	chr10	90427043	+	0.000210786	0.9997892
ENST00000400215	ENST00000394375	ATAD1	chr10	89550066	-	LIPF	chr10	90427043	+	0.002047304	0.9979527

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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

>7330_7330_1_ATAD1-LIPF_ATAD1_chr10_89550066_ENST00000328142_LIPF_chr10_90427043_ENST00000394375_length(amino acids)=539AA_BP=176
MFVFLRLTFKMVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKNVKLSEYEMSIAAHL
VDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGRSKMWLLLTMASLISVLGTTHGLFGKLHPGSPEVTMNISQMI
TYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSGNTGQRPVVFLQHGLLASATNWISNLPNNSLAFILADAGYDVWLGNSRGNTWARRNLY
YSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVPQ
SLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDWG

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

>7330_7330_2_ATAD1-LIPF_ATAD1_chr10_89550066_ENST00000400215_LIPF_chr10_90427043_ENST00000394375_length(amino acids)=471AA_BP=108
MKQIGVKNVKLSEYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGRSKMWLLLTMASLISVLGTT
HGLFGKLHPGSPEVTMNISQMITYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSGNTGQRPVVFLQHGLLASATNWISNLPNNSLAFILA
DAGYDVWLGNSRGNTWARRNLYYSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYA
LAPVATVKYTKSLINKLRFVPQSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTS
VQNMFHWTQAVKSGKFQAYDWGSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIW

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

>7330_7330_3_ATAD1-LIPF_ATAD1_chr10_89550067_ENST00000328142_LIPF_chr10_90427044_ENST00000394375_length(amino acids)=539AA_BP=176
MFVFLRLTFKMVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKNVKLSEYEMSIAAHL
VDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGRSKMWLLLTMASLISVLGTTHGLFGKLHPGSPEVTMNISQMI
TYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSGNTGQRPVVFLQHGLLASATNWISNLPNNSLAFILADAGYDVWLGNSRGNTWARRNLY
YSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVPQ
SLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDWG

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

>7330_7330_4_ATAD1-LIPF_ATAD1_chr10_89550067_ENST00000400215_LIPF_chr10_90427044_ENST00000394375_length(amino acids)=471AA_BP=108
MKQIGVKNVKLSEYEMSIAAHLVDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGRSKMWLLLTMASLISVLGTT
HGLFGKLHPGSPEVTMNISQMITYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSGNTGQRPVVFLQHGLLASATNWISNLPNNSLAFILA
DAGYDVWLGNSRGNTWARRNLYYSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYA
LAPVATVKYTKSLINKLRFVPQSLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTS
VQNMFHWTQAVKSGKFQAYDWGSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPNLIYHKEIPFYNHLDFIW

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

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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/chr10:89550067/chr10:90427044)
- 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
ATAD1 Q8NBU5	LIPF P07098
FUNCTION: Outer mitochondrial translocase required to remove mislocalized tail-anchored transmembrane proteins on mitochondria (PubMed:24843043). Specifically recognizes and binds tail-anchored transmembrane proteins: acts as a dislocase that mediates the ATP-dependent extraction of mistargeted tail-anchored transmembrane proteins from the mitochondrion outer membrane (By similarity). Also plays a critical role in regulating the surface expression of AMPA receptors (AMPAR), thereby regulating synaptic plasticity and learning and memory (By similarity). Required for NMDA-stimulated AMPAR internalization and inhibition of GRIA1 and GRIA2 recycling back to the plasma membrane; these activities are ATPase-dependent (By similarity). {ECO:0000250\|UniProtKB:P28737, ECO:0000250\|UniProtKB:Q9D5T0, ECO:0000269\|PubMed:24843043}.	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

ATAD1

chr10:89550066

chr10:90427043

ENST00000308448

1_15

127.33333333333333

362.0

Topological domain

Mitochondrial intermembrane

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000328142

1_15

127.33333333333333

362.0

Topological domain

Mitochondrial intermembrane

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000541004

1_15

127.33333333333333

288.0

Topological domain

Mitochondrial intermembrane

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000308448

1_15

127.33333333333333

362.0

Topological domain

Mitochondrial intermembrane

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000328142

1_15

127.33333333333333

362.0

Topological domain

Mitochondrial intermembrane

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000541004

1_15

127.33333333333333

288.0

Topological domain

Mitochondrial intermembrane

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000308448

16_32

127.33333333333333

362.0

Transmembrane

Helical

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000328142

16_32

127.33333333333333

362.0

Transmembrane

Helical

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000541004

16_32

127.33333333333333

288.0

Transmembrane

Helical

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000308448

16_32

127.33333333333333

362.0

Transmembrane

Helical

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000328142

16_32

127.33333333333333

362.0

Transmembrane

Helical

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000541004

16_32

127.33333333333333

288.0

Transmembrane

Helical

Tgene

LIPF

chr10:89550066

chr10:90427043

ENST00000238983

78_377

399.0

Domain

AB hydrolase-1

Tgene

LIPF

chr10:89550066

chr10:90427043

ENST00000355843

78_377

6.333333333333333

376.0

Domain

AB hydrolase-1

Tgene

LIPF

chr10:89550066

chr10:90427043

ENST00000394375

78_377

6.333333333333333

409.0

Domain

AB hydrolase-1

Tgene

LIPF

chr10:89550067

chr10:90427044

ENST00000238983

78_377

399.0

Domain

AB hydrolase-1

Tgene

LIPF

chr10:89550067

chr10:90427044

ENST00000355843

78_377

6.333333333333333

376.0

Domain

AB hydrolase-1

Tgene

LIPF

chr10:89550067

chr10:90427044

ENST00000394375

78_377

6.333333333333333

409.0

Domain

AB hydrolase-1

- 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

ATAD1

chr10:89550066

chr10:90427043

ENST00000308448

133_140

127.33333333333333

362.0

Nucleotide binding

ATP

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000328142

133_140

127.33333333333333

362.0

Nucleotide binding

ATP

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000541004

133_140

127.33333333333333

288.0

Nucleotide binding

ATP

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000308448

133_140

127.33333333333333

362.0

Nucleotide binding

ATP

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000328142

133_140

127.33333333333333

362.0

Nucleotide binding

ATP

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000541004

133_140

127.33333333333333

288.0

Nucleotide binding

ATP

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000308448

33_361

127.33333333333333

362.0

Topological domain

Cytoplasmic

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000328142

33_361

127.33333333333333

362.0

Topological domain

Cytoplasmic

Hgene

ATAD1

chr10:89550066

chr10:90427043

ENST00000541004

33_361

127.33333333333333

288.0

Topological domain

Cytoplasmic

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000308448

33_361

127.33333333333333

362.0

Topological domain

Cytoplasmic

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000328142

33_361

127.33333333333333

362.0

Topological domain

Cytoplasmic

Hgene

ATAD1

chr10:89550067

chr10:90427044

ENST00000541004

33_361

127.33333333333333

288.0

Topological domain

Cytoplasmic

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>1149_ATAD1_89550067_LIPF_90427044_1149_ATAD1_89550067_LIPF_90427044_ranked_0.pdb	ATAD1	89550066	89550067	ENST00000394375	LIPF	chr10	90427044	+	MFVFLRLTFKMVHAEAFSRPLSRNEVVGLIFRLTIFGAVTYFTIKWMVDAIDPTRKQKVEAQKQAEKLMKQIGVKNVKLSEYEMSIAAHL VDPLNMHVTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGRSKMWLLLTMASLISVLGTTHGLFGKLHPGSPEVTMNISQMI TYWGYPNEEYEVVTEDGYILEVNRIPYGKKNSGNTGQRPVVFLQHGLLASATNWISNLPNNSLAFILADAGYDVWLGNSRGNTWARRNLY YSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFIAFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVPQ SLFKFIFGDKIFYPHNFFDQFLATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKSGKFQAYDWG	539

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

ATAD1_pLDDT.png

LIPF_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
ATAD1
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 ATAD1-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 ATAD1-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