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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:LPCAT1-SDHA (FusionGDB2 ID:49492)

Fusion Gene Summary for LPCAT1-SDHA

Fusion gene summary

Fusion gene information	Fusion gene name: LPCAT1-SDHA
	Fusion gene ID: 49492
		Hgene	Tgene
	Gene symbol	LPCAT1	SDHA
	Gene ID	79888	6389
	Gene name	lysophosphatidylcholine acyltransferase 1	succinate dehydrogenase complex flavoprotein subunit A
	Synonyms	AGPAT10\|AGPAT9\|AYTL2\|LPCAT-1\|PFAAP3\|lpcat\|lysoPAFAT	CMD1GG\|FP\|PGL5\|SDH1\|SDH2\|SDHF
	Cytomap	5p15.33	5p15.33
	Type of gene	protein-coding	protein-coding
	Description	lysophosphatidylcholine acyltransferase 11-acylglycerophosphocholine O-acyltransferase1-alkylglycerophosphocholine O-acetyltransferaseLPC acyltransferase 1acetyl-CoA:lyso-PAF acetyltransferaseacetyl-CoA:lyso-platelet-activating factor acetyltransfera	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrialflavoprotein subunit of complex IIsuccinate dehydrogenase complex, subunit A, flavoprotein (Fp)
	Modification date	20200313	20200313
	UniProtAcc	Q8NF37	Q5VUM1
	Ensembl transtripts involved in fusion gene	ENST00000283415, ENST00000503252,	ENST00000504309, ENST00000507522, ENST00000510361, ENST00000264932,
Fusion gene scores	* DoF score	9 X 8 X 6=432	5 X 7 X 5=175
	# samples	12	7
	** MAII score	log2(12/432*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/175*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: LPCAT1 [Title/Abstract] AND SDHA [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	LPCAT1(1488506)-SDHA(251453), # samples:1
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
Hgene	LPCAT1	GO:0036151	phosphatidylcholine acyl-chain remodeling	21498505
Tgene	SDHA	GO:0006105	succinate metabolic process	7550341
Tgene	SDHA	GO:0022904	respiratory electron transport chain	7550341
Tgene	SDHA	GO:0055114	oxidation-reduction process	7550341

Fusion gene breakpoints across LPCAT1 (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 SDHA (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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	LUAD	TCGA-55-8506-01A	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+

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Fusion Gene ORF analysis for LPCAT1-SDHA

Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-intron	ENST00000283415	ENST00000504309	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+
5CDS-intron	ENST00000283415	ENST00000507522	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+
5CDS-intron	ENST00000283415	ENST00000510361	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+
In-frame	ENST00000283415	ENST00000264932	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+
intron-3CDS	ENST00000503252	ENST00000264932	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+
intron-intron	ENST00000503252	ENST00000504309	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+
intron-intron	ENST00000503252	ENST00000507522	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+
intron-intron	ENST00000503252	ENST00000510361	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

ENST00000283415

LPCAT1

chr5

1488506

ENST00000264932

SDHA

chr5

251453

1412

800

106

1131

341

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
ENST00000283415	ENST00000264932	LPCAT1	chr5	1488506	-	SDHA	chr5	251453	+	0.012495583	0.9875044

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Fusion Genomic Features for LPCAT1-SDHA

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
LPCAT1	chr5	1488505	-	SDHA	chr5	251455	+	3.89E-05	0.999961
LPCAT1	chr5	1488505	-	SDHA	chr5	251455	+	3.89E-05	0.999961

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for LPCAT1-SDHA

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:1488506/chr5:251453)
- 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
LPCAT1 Q8NF37	SDHA Q5VUM1
FUNCTION: Exhibits acyltransferase activity (PubMed:21498505, PubMed:18156367). Exhibits acetyltransferase activity (By similarity). Activity is calcium-independent (By similarity). Catalyzes the conversion of lysophosphatidylcholine (1-acyl-sn-glycero-3-phosphocholine or LPC) into phosphatidylcholine (1,2-diacyl-sn-glycero-3-phosphocholine or PC) (PubMed:21498505, PubMed:18156367). Catalyzes the conversion 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid or LPA) into 1,2-diacyl-sn-glycerol-3-phosphate (phosphatidic acid or PA) by incorporating an acyl moiety at the sn-2 position of the glycerol backbone (By similarity). Displays a clear preference for saturated fatty acyl-CoAs, and 1-myristoyl or 1-palmitoyl LPC as acyl donors and acceptors, respectively (By similarity). Involved in platelet-activating factor (PAF) biosynthesis by catalyzing the conversion of the PAF precursor, 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF) into 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (PAF) (By similarity). May synthesize phosphatidylcholine in pulmonary surfactant, thereby playing a pivotal role in respiratory physiology (By similarity). Involved in the regulation of lipid droplet number and size (PubMed:25491198). {ECO:0000250\|UniProtKB:Q3TFD2, ECO:0000269\|PubMed:18156367, ECO:0000269\|PubMed:21498505, ECO:0000269\|PubMed:25491198}.	FUNCTION: Plays an essential role in the assembly of succinate dehydrogenase (SDH), an enzyme complex (also referred to as respiratory complex II) that is a component of both the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol (PubMed:24954416). Binds to the flavoprotein subunit SDHA in its FAD-bound form, blocking the generation of excess reactive oxigen species (ROS) and facilitating its assembly with the iron-sulfur protein subunit SDHB into the SDH catalytic dimer (By similarity). {ECO:0000250\|UniProtKB:P38345, ECO:0000269\|PubMed:24954416}.

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.

- In-frame and 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

LPCAT1

chr5:1488506

chr5:251453

ENST00000283415

135_140

222

535.0

Motif

HXXXXD motif

Hgene

LPCAT1

chr5:1488506

chr5:251453

ENST00000283415

1_57

222

535.0

Topological domain

Cytoplasmic

Hgene

LPCAT1

chr5:1488506

chr5:251453

ENST00000283415

58_78

222

535.0

Transmembrane

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

- In-frame and 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

LPCAT1

chr5:1488506

chr5:251453

ENST00000283415

392_403

222

535.0

Calcium binding

Hgene

LPCAT1

chr5:1488506

chr5:251453

ENST00000283415

379_414

222

535.0

Domain

EF-hand 1

Hgene

LPCAT1

chr5:1488506

chr5:251453

ENST00000283415

451_486

222

535.0

Domain

EF-hand 2

Hgene

LPCAT1

chr5:1488506

chr5:251453

ENST00000283415

531_534

222

535.0

Motif

Di-lysine motif

Hgene

LPCAT1

chr5:1488506

chr5:251453

ENST00000283415

79_534

222

535.0

Topological domain

Lumenal

Tgene

SDHA

chr5:1488506

chr5:251453

ENST00000264932

456_457

554

665.0

Nucleotide binding

FAD

Tgene

SDHA

chr5:1488506

chr5:251453

ENST00000264932

68_73

554

665.0

Nucleotide binding

FAD

Tgene

SDHA

chr5:1488506

chr5:251453

ENST00000264932

91_106

554

665.0

Nucleotide binding

FAD

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Fusion Gene Sequence for LPCAT1-SDHA

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>49492_49492_1_LPCAT1-SDHA_LPCAT1_chr5_1488506_ENST00000283415_SDHA_chr5_251453_ENST00000264932_length(transcript)=1412nt_BP=800nt
CGCGCCTGCGCGCCCGGCCCGCTCCAGCCGCCGCGCATCCTCGGCCCGCGCCCCGAGACCCGCGCCCAGCTAGCCCCGGCCCCGCTCGGC
GCCCCAGGCAGCTCGGCTGCGCTCGCCGCGGGACGGCGCGGCCATGAGGCTGCGGGGATGCGGACCCCGGGCCGCCCCTGCCTCCAGCGC
AGGGGCCAGCGACGCTCGGCTGCTGGCGCCCCCGGGGCGGAACCCCTTCGTGCACGAGCTGCGCCTCAGCGCCCTGCAGAAGGCCCAGGT
GGCCCTCATGACACTGACGCTCTTCCCGGTCCGGCTCCTGGTTGCCGCTGCCATGATGCTGCTGGCCTGGCCCCTCGCACTTGTCGCATC
CCTGGGCTCTGCGGAGAAGGAACCCGAGCAGCCCCCGGCCCTGTGGAGGAAGGTTGTGGACTTCCTGCTGAAGGCCATCATGCGCACCAT
GTGGTTCGCCGGCGGCTTCCACCGGGTGGCCGTGAAGGGGCGGCAGGCGCTGCCCACCGAGGCGGCCATCCTCACGCTCGCGCCTCACTC
GTCCTACTTCGACGCCATCCCTGTGACCATGACGATGTCCTCCATCGTGATGAAGGCAGAGAGCAGAGACATCCCGATCTGGGGAACTCT
GATCCAGTATATACGGCCTGTGTTCGTGTCCCGGTCAGACCAGGATTCTCGCAGGAAAACAGTAGAAGAAATCAAGAGACGGGCGCAGTC
CAACGGAAAGTGGCCACAGATAATGATTTTTCCAGAAGGAACTTGTACAAACAGGACCTGCCTAATTACCTTCAAACCTGGAATGGTCTG
GAACACGGACCTGGTGGAGACCCTGGAGCTGCAGAACCTGATGCTGTGTGCGCTGCAGACCATCTACGGAGCAGAGGCACGGAAGGAGTC
ACGGGGCGCGCATGCCAGGGAAGACTACAAGGTGCGGATTGATGAGTACGATTACTCCAAGCCCATCCAGGGGCAACAGAAGAAGCCCTT
TGAGGAGCACTGGAGGAAGCACACCCTGTCCTATGTGGACGTTGGCACTGGGAAGGTCACTCTGGAATATAGACCCGTGATCGACAAAAC
TTTGAACGAGGCTGACTGTGCCACCGTCCCGCCAGCCATTCGCTCCTACTGATGAGACAAGATGTGGTGATGACAGAATCAGCTTTTGTA
ATTATGTATAATAGCTCATGCATGTGTCCATGTCATAACTGTCTTCATACGCTTCTGCACTCTGGGGAAGAAGGAGTACATTGAAGGGAG
ATTGGCACCTAGTGGCTGGGAGCTTGCCAGGAACCCAGTGGCCAGGGAGCGTGGCACTTACCTTTGTCCCTTGCTTCATTCTTGTGAGAT

>49492_49492_1_LPCAT1-SDHA_LPCAT1_chr5_1488506_ENST00000283415_SDHA_chr5_251453_ENST00000264932_length(amino acids)=341AA_BP=230
MRSPRDGAAMRLRGCGPRAAPASSAGASDARLLAPPGRNPFVHELRLSALQKAQVALMTLTLFPVRLLVAAAMMLLAWPLALVASLGSAE
KEPEQPPALWRKVVDFLLKAIMRTMWFAGGFHRVAVKGRQALPTEAAILTLAPHSSYFDAIPVTMTMSSIVMKAESRDIPIWGTLIQYIR
PVFVSRSDQDSRRKTVEEIKRRAQSNGKWPQIMIFPEGTCTNRTCLITFKPGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHA

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

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Fusion Gene PPI Analysis for LPCAT1-SDHA

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for LPCAT1-SDHA

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for LPCAT1-SDHA

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source