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Fusion Protein:LPCAT1-SDHA |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: LPCAT1-SDHA | FusionPDB ID: 49492 | FusionGDB2.0 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 | ENST ids | ENST00000283415, ENST00000503252, | ENST00000504309, ENST00000507522, ENST00000510361, ENST00000264932, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * 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 (manual curation of fusion genes in FusionPDB) | PubMed: LPCAT1 [Title/Abstract] AND SDHA [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | LPCAT1(1488506)-SDHA(251453), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | LPCAT1-SDHA 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. LPCAT1-SDHA 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. LPCAT1-SDHA 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. LPCAT1-SDHA 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 | 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. |
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| 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. |
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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 | LUAD | TCGA-55-8506-01A | LPCAT1 | chr5 | 1488506 | - | SDHA | chr5 | 251453 | + |
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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) |
| 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 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 >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 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/chr5:1488506/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. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LPCAT1 | SDHA |
| 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 * 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 | LPCAT1 | chr5:1488506 | chr5:251453 | ENST00000283415 | - | 5 | 14 | 135_140 | 222.33333333333334 | 535.0 | Motif | HXXXXD motif |
| Hgene | LPCAT1 | chr5:1488506 | chr5:251453 | ENST00000283415 | - | 5 | 14 | 1_57 | 222.33333333333334 | 535.0 | Topological domain | Cytoplasmic |
| Hgene | LPCAT1 | chr5:1488506 | chr5:251453 | ENST00000283415 | - | 5 | 14 | 58_78 | 222.33333333333334 | 535.0 | 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 | LPCAT1 | chr5:1488506 | chr5:251453 | ENST00000283415 | - | 5 | 14 | 392_403 | 222.33333333333334 | 535.0 | Calcium binding | 1 |
| Hgene | LPCAT1 | chr5:1488506 | chr5:251453 | ENST00000283415 | - | 5 | 14 | 379_414 | 222.33333333333334 | 535.0 | Domain | EF-hand 1 |
| Hgene | LPCAT1 | chr5:1488506 | chr5:251453 | ENST00000283415 | - | 5 | 14 | 451_486 | 222.33333333333334 | 535.0 | Domain | EF-hand 2 |
| Hgene | LPCAT1 | chr5:1488506 | chr5:251453 | ENST00000283415 | - | 5 | 14 | 531_534 | 222.33333333333334 | 535.0 | Motif | Di-lysine motif |
| Hgene | LPCAT1 | chr5:1488506 | chr5:251453 | ENST00000283415 | - | 5 | 14 | 79_534 | 222.33333333333334 | 535.0 | Topological domain | Lumenal |
| Tgene | SDHA | chr5:1488506 | chr5:251453 | ENST00000264932 | 11 | 15 | 456_457 | 554.3333333333334 | 665.0 | Nucleotide binding | FAD | |
| Tgene | SDHA | chr5:1488506 | chr5:251453 | ENST00000264932 | 11 | 15 | 68_73 | 554.3333333333334 | 665.0 | Nucleotide binding | FAD | |
| Tgene | SDHA | chr5:1488506 | chr5:251453 | ENST00000264932 | 11 | 15 | 91_106 | 554.3333333333334 | 665.0 | Nucleotide binding | FAD |
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Fusion Protein-Protein Interaction |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in |
| 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 |
| LPCAT1 | |
| SDHA |
| - 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 LPCAT1-SDHA |
| 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 LPCAT1-SDHA |
| 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 |
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