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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:49247) |
Fusion Gene Summary for LPCAT1-SDHA |
Fusion gene summary |
Fusion gene information | Fusion gene name: LPCAT1-SDHA | Fusion gene ID: 49247 | 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, | ENST00000264932, ENST00000504309, ENST00000510361, ENST00000507522, | |
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 |
In-frame | ENST00000283415 | ENST00000264932 | LPCAT1 | chr5 | 1488506 | - | SDHA | chr5 | 251453 | + |
5CDS-intron | ENST00000283415 | ENST00000504309 | LPCAT1 | chr5 | 1488506 | - | SDHA | chr5 | 251453 | + |
5CDS-intron | ENST00000283415 | ENST00000510361 | LPCAT1 | chr5 | 1488506 | - | SDHA | chr5 | 251453 | + |
5CDS-intron | ENST00000283415 | ENST00000507522 | 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 | ENST00000510361 | LPCAT1 | chr5 | 1488506 | - | SDHA | chr5 | 251453 | + |
intron-intron | ENST00000503252 | ENST00000507522 | 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 |
Go to FGviewer for the breakpoints of 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. |
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. |
- 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 | - | 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 |
- 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 | - | 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 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. |
>In-frame_ENST00000283415_ENST00000264932_TCGA-55-8506-01A_LPCAT1_chr5_1488506_-_SDHA_chr5_251453_length(transcript)=1412nt_BP=800nt CGCGCCTGCGCGCCCGGCCCGCTCCAGCCGCCGCGCATCCTCGGCCCGCGCCCCGAGACCCGCGCCCAGCTAGCCCCGGCCCCGCTCGGC GCCCCAGGCAGCTCGGCTGCGCTCGCCGCGGGACGGCGCGGCCATGAGGCTGCGGGGATGCGGACCCCGGGCCGCCCCTGCCTCCAGCGC AGGGGCCAGCGACGCTCGGCTGCTGGCGCCCCCGGGGCGGAACCCCTTCGTGCACGAGCTGCGCCTCAGCGCCCTGCAGAAGGCCCAGGT GGCCCTCATGACACTGACGCTCTTCCCGGTCCGGCTCCTGGTTGCCGCTGCCATGATGCTGCTGGCCTGGCCCCTCGCACTTGTCGCATC CCTGGGCTCTGCGGAGAAGGAACCCGAGCAGCCCCCGGCCCTGTGGAGGAAGGTTGTGGACTTCCTGCTGAAGGCCATCATGCGCACCAT GTGGTTCGCCGGCGGCTTCCACCGGGTGGCCGTGAAGGGGCGGCAGGCGCTGCCCACCGAGGCGGCCATCCTCACGCTCGCGCCTCACTC GTCCTACTTCGACGCCATCCCTGTGACCATGACGATGTCCTCCATCGTGATGAAGGCAGAGAGCAGAGACATCCCGATCTGGGGAACTCT GATCCAGTATATACGGCCTGTGTTCGTGTCCCGGTCAGACCAGGATTCTCGCAGGAAAACAGTAGAAGAAATCAAGAGACGGGCGCAGTC CAACGGAAAGTGGCCACAGATAATGATTTTTCCAGAAGGAACTTGTACAAACAGGACCTGCCTAATTACCTTCAAACCTGGAATGGTCTG GAACACGGACCTGGTGGAGACCCTGGAGCTGCAGAACCTGATGCTGTGTGCGCTGCAGACCATCTACGGAGCAGAGGCACGGAAGGAGTC ACGGGGCGCGCATGCCAGGGAAGACTACAAGGTGCGGATTGATGAGTACGATTACTCCAAGCCCATCCAGGGGCAACAGAAGAAGCCCTT TGAGGAGCACTGGAGGAAGCACACCCTGTCCTATGTGGACGTTGGCACTGGGAAGGTCACTCTGGAATATAGACCCGTGATCGACAAAAC TTTGAACGAGGCTGACTGTGCCACCGTCCCGCCAGCCATTCGCTCCTACTGATGAGACAAGATGTGGTGATGACAGAATCAGCTTTTGTA ATTATGTATAATAGCTCATGCATGTGTCCATGTCATAACTGTCTTCATACGCTTCTGCACTCTGGGGAAGAAGGAGTACATTGAAGGGAG ATTGGCACCTAGTGGCTGGGAGCTTGCCAGGAACCCAGTGGCCAGGGAGCGTGGCACTTACCTTTGTCCCTTGCTTCATTCTTGTGAGAT >In-frame_ENST00000283415_ENST00000264932_TCGA-55-8506-01A_LPCAT1_chr5_1488506_-_SDHA_chr5_251453_length(amino acids)=341AA_start in transcript=106_stop in transcript=1131 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 |
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 |
Tgene | SDHA | C0023264 | Leigh Disease | 11 | CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT |
Tgene | SDHA | C1708353 | Hereditary Paraganglioma-Pheochromocytoma Syndrome | 8 | CLINGEN;GENOMICS_ENGLAND |
Tgene | SDHA | C1838951 | LEIGH SYNDROME DUE TO MITOCHONDRIAL COMPLEX I DEFICIENCY | 8 | CLINGEN |
Tgene | SDHA | C1850597 | Leigh Syndrome Due To Mitochondrial Complex II Deficiency | 8 | CLINGEN |
Tgene | SDHA | C1850598 | Leigh Syndrome due to Mitochondrial Complex III Deficiency | 8 | CLINGEN |
Tgene | SDHA | C1850599 | Leigh Syndrome due to Mitochondrial Complex IV Deficiency | 8 | CLINGEN |
Tgene | SDHA | C1850600 | Leigh Syndrome due to Mitochondrial Complex V Deficiency | 8 | CLINGEN |
Tgene | SDHA | C2931891 | Necrotizing encephalopathy, infantile subacute, of Leigh | 8 | CLINGEN |
Tgene | SDHA | C0238198 | Gastrointestinal Stromal Tumors | 4 | GENOMICS_ENGLAND;ORPHANET |
Tgene | SDHA | C1855008 | Mitochondrial Complex II Deficiency | 4 | CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT |
Tgene | SDHA | C3179349 | Gastrointestinal Stromal Sarcoma | 4 | ORPHANET |
Tgene | SDHA | C3150898 | CARDIOMYOPATHY, DILATED, 1GG | 2 | GENOMICS_ENGLAND;UNIPROT |
Tgene | SDHA | C3279992 | PARAGANGLIOMAS 5 | 2 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
Tgene | SDHA | C0029408 | Degenerative polyarthritis | 1 | CTD_human |
Tgene | SDHA | C0036341 | Schizophrenia | 1 | PSYGENET |
Tgene | SDHA | C0086743 | Osteoarthrosis Deformans | 1 | CTD_human |
Tgene | SDHA | C0340427 | Familial dilated cardiomyopathy | 1 | ORPHANET |