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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 19986

FusionGeneSummary for LPCAT1_SDHA

check button Fusion gene summary
Fusion gene informationFusion gene name: LPCAT1_SDHA
Fusion gene ID: 19986
HgeneTgene
Gene symbol

LPCAT1

SDHA

Gene ID

79888

6389

Gene namelysophosphatidylcholine acyltransferase 1succinate dehydrogenase complex flavoprotein subunit A
SynonymsAGPAT10|AGPAT9|AYTL2|LPCAT-1|PFAAP3|lpcat|lysoPAFATCMD1GG|FP|PGL5|SDH1|SDH2|SDHF
Cytomap

5p15.33

5p15.33

Type of geneprotein-codingprotein-coding
Descriptionlysophosphatidylcholine acyltransferase 11-acylglycerophosphocholine O-acyltransferase1-alkylglycerophosphocholine O-acetyltransferaseLPC acyltransferase 1acetyl-CoA:lyso-PAF acetyltransferaseacetyl-CoA:lyso-platelet-activating factor acetyltransferasuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrialflavoprotein subunit of complex IIsuccinate dehydrogenase complex, subunit A, flavoprotein (Fp)
Modification date2018051920180523
UniProtAcc

Q8NF37

P31040

Ensembl transtripts involved in fusion geneENST00000283415, ENST00000503252, 
ENST00000264932, ENST00000504309, 
ENST00000510361, ENST00000507522, 
Fusion gene scores* DoF score6 X 5 X 4=1204 X 5 X 4=80
# samples 75
** MAII scorelog2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/80*10)=-0.678071905112638
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]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, in-frame but not retained their domain.
Tumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneLPCAT1

GO:0036151

phosphatidylcholine acyl-chain remodeling

21498505

TgeneSDHA

GO:0006105

succinate metabolic process

7550341

TgeneSDHA

GO:0022904

respiratory electron transport chain

7550341

TgeneSDHA

GO:0055114

oxidation-reduction process

7550341


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLUADTCGA-55-8506-01ALPCAT1chr5

1488506

-SDHAchr5

251453

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
In-frameENST00000283415ENST00000264932LPCAT1chr5

1488506

-SDHAchr5

251453

+
5CDS-intronENST00000283415ENST00000504309LPCAT1chr5

1488506

-SDHAchr5

251453

+
5CDS-intronENST00000283415ENST00000510361LPCAT1chr5

1488506

-SDHAchr5

251453

+
5CDS-intronENST00000283415ENST00000507522LPCAT1chr5

1488506

-SDHAchr5

251453

+
intron-3CDSENST00000503252ENST00000264932LPCAT1chr5

1488506

-SDHAchr5

251453

+
intron-intronENST00000503252ENST00000504309LPCAT1chr5

1488506

-SDHAchr5

251453

+
intron-intronENST00000503252ENST00000510361LPCAT1chr5

1488506

-SDHAchr5

251453

+
intron-intronENST00000503252ENST00000507522LPCAT1chr5

1488506

-SDHAchr5

251453

+

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FusionProtFeatures for LPCAT1_SDHA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LPCAT1

Q8NF37

SDHA

P31040

Possesses both acyltransferase and acetyltransferaseactivities (PubMed:16864775, PubMed:21498505). Activity iscalcium-independent (By similarity). Mediates the conversion of 1-acyl-sn-glycero-3-phosphocholine (LPC) into phosphatidylcholine(PC) (PubMed:21498505). Displays a clear preference for saturatedfatty acyl-CoAs, and 1-myristoyl or 1-palmitoyl LPC as acyl donorsand acceptors, respectively (PubMed:16704971). May synthesizephosphatidylcholine in pulmonary surfactant, thereby playing apivotal role in respiratory physiology (PubMed:16864775). Involvedin the regulation of lipid droplet number and size(PubMed:25491198). {ECO:0000250|UniProtKB:Q3TFD2,ECO:0000269|PubMed:16864775, ECO:0000269|PubMed:21498505,ECO:0000269|PubMed:25491198}. Flavoprotein (FP) subunit of succinate dehydrogenase(SDH) that is involved in complex II of the mitochondrial electrontransport chain and is responsible for transferring electrons fromsuccinate to ubiquinone (coenzyme Q) (PubMed:24781757). Can act asa tumor suppressor (PubMed:20484225).{ECO:0000269|PubMed:20484225, ECO:0000305|PubMed:24781757}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLPCAT1chr5:1488506chr5:251453ENST00000283415-514135_140222535MotifNote=HXXXXD motif
HgeneLPCAT1chr5:1488506chr5:251453ENST00000283415-5141_57222535Topological domainCytoplasmic
HgeneLPCAT1chr5:1488506chr5:251453ENST00000283415-51458_78222535TransmembraneHelical%3B Signal-anchor for type II membrane protein

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneLPCAT1chr5:1488506chr5:251453ENST00000283415-514392_403222535Calcium binding1
HgeneLPCAT1chr5:1488506chr5:251453ENST00000283415-514379_414222535DomainEF-hand 1
HgeneLPCAT1chr5:1488506chr5:251453ENST00000283415-514451_486222535DomainEF-hand 2
HgeneLPCAT1chr5:1488506chr5:251453ENST00000283415-514531_534222535MotifNote=Di-lysine motif
HgeneLPCAT1chr5:1488506chr5:251453ENST00000283415-51479_534222535Topological domainLumenal
TgeneSDHAchr5:1488506chr5:251453ENST00000264932+1115456_457554665Nucleotide bindingFAD
TgeneSDHAchr5:1488506chr5:251453ENST00000264932+111568_73554665Nucleotide bindingFAD
TgeneSDHAchr5:1488506chr5:251453ENST00000264932+111591_106554665Nucleotide bindingFAD


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FusionGeneSequence for LPCAT1_SDHA


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_LPCAT1_ENST00000283415_chr5_1488506_-_SDHA_ENST00000264932_chr5_251453_+_333aa
MRLRGCGPRAAPASSAGASDARLLAPPGRNPFVHELRLSALQKAQVALMTLTLFPVRLLVAAAMMLLAWPLALVASLGSAEKEPEQPPAL
WRKVVDFLLKAIMRTMWFAGGFHRVAVKGRQALPTEAAILTLAPHSSYFDAIPVTMTMSSIVMKAESRDIPIWGTLIQYIRPVFVSRSDQ
DSRRKTVEEIKRRAQSNGKWPQIMIFPEGTCTNRTCLITFKPGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKVRID


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_LPCAT1_ENST00000283415_chr5_1488506_-_SDHA_ENST00000264932_chr5_251453_+_999nt
ATGAGGCTGCGGGGATGCGGACCCCGGGCCGCCCCTGCCTCCAGCGCAGGGGCCAGCGACGCTCGGCTGCTGGCGCCCCCGGGGCGGAAC
CCCTTCGTGCACGAGCTGCGCCTCAGCGCCCTGCAGAAGGCCCAGGTGGCCCTCATGACACTGACGCTCTTCCCGGTCCGGCTCCTGGTT
GCCGCTGCCATGATGCTGCTGGCCTGGCCCCTCGCACTTGTCGCATCCCTGGGCTCTGCGGAGAAGGAACCCGAGCAGCCCCCGGCCCTG
TGGAGGAAGGTTGTGGACTTCCTGCTGAAGGCCATCATGCGCACCATGTGGTTCGCCGGCGGCTTCCACCGGGTGGCCGTGAAGGGGCGG
CAGGCGCTGCCCACCGAGGCGGCCATCCTCACGCTCGCGCCTCACTCGTCCTACTTCGACGCCATCCCTGTGACCATGACGATGTCCTCC
ATCGTGATGAAGGCAGAGAGCAGAGACATCCCGATCTGGGGAACTCTGATCCAGTATATACGGCCTGTGTTCGTGTCCCGGTCAGACCAG
GATTCTCGCAGGAAAACAGTAGAAGAAATCAAGAGACGGGCGCAGTCCAACGGAAAGTGGCCACAGATAATGATTTTTCCAGAAGGAACT
TGTACAAACAGGACCTGCCTAATTACCTTCAAACCTGGAATGGTCTGGAACACGGACCTGGTGGAGACCCTGGAGCTGCAGAACCTGATG
CTGTGTGCGCTGCAGACCATCTACGGAGCAGAGGCACGGAAGGAGTCACGGGGCGCGCATGCCAGGGAAGACTACAAGGTGCGGATTGAT
GAGTACGATTACTCCAAGCCCATCCAGGGGCAACAGAAGAAGCCCTTTGAGGAGCACTGGAGGAAGCACACCCTGTCCTATGTGGACGTT
GGCACTGGGAAGGTCACTCTGGAATATAGACCCGTGATCGACAAAACTTTGAACGAGGCTGACTGTGCCACCGTCCCGCCAGCCATTCGC


* Fusion transcript sequences (Full-length transcript).
>In-frame_LPCAT1_ENST00000283415_chr5_1488506_-_SDHA_ENST00000264932_chr5_251453_+_1412nt
CGCGCCTGCGCGCCCGGCCCGCTCCAGCCGCCGCGCATCCTCGGCCCGCGCCCCGAGACCCGCGCCCAGCTAGCCCCGGCCCCGCTCGGC
GCCCCAGGCAGCTCGGCTGCGCTCGCCGCGGGACGGCGCGGCCATGAGGCTGCGGGGATGCGGACCCCGGGCCGCCCCTGCCTCCAGCGC
AGGGGCCAGCGACGCTCGGCTGCTGGCGCCCCCGGGGCGGAACCCCTTCGTGCACGAGCTGCGCCTCAGCGCCCTGCAGAAGGCCCAGGT
GGCCCTCATGACACTGACGCTCTTCCCGGTCCGGCTCCTGGTTGCCGCTGCCATGATGCTGCTGGCCTGGCCCCTCGCACTTGTCGCATC
CCTGGGCTCTGCGGAGAAGGAACCCGAGCAGCCCCCGGCCCTGTGGAGGAAGGTTGTGGACTTCCTGCTGAAGGCCATCATGCGCACCAT
GTGGTTCGCCGGCGGCTTCCACCGGGTGGCCGTGAAGGGGCGGCAGGCGCTGCCCACCGAGGCGGCCATCCTCACGCTCGCGCCTCACTC
GTCCTACTTCGACGCCATCCCTGTGACCATGACGATGTCCTCCATCGTGATGAAGGCAGAGAGCAGAGACATCCCGATCTGGGGAACTCT
GATCCAGTATATACGGCCTGTGTTCGTGTCCCGGTCAGACCAGGATTCTCGCAGGAAAACAGTAGAAGAAATCAAGAGACGGGCGCAGTC
CAACGGAAAGTGGCCACAGATAATGATTTTTCCAGAAGGAACTTGTACAAACAGGACCTGCCTAATTACCTTCAAACCTGGAATGGTCTG
GAACACGGACCTGGTGGAGACCCTGGAGCTGCAGAACCTGATGCTGTGTGCGCTGCAGACCATCTACGGAGCAGAGGCACGGAAGGAGTC
ACGGGGCGCGCATGCCAGGGAAGACTACAAGGTGCGGATTGATGAGTACGATTACTCCAAGCCCATCCAGGGGCAACAGAAGAAGCCCTT
TGAGGAGCACTGGAGGAAGCACACCCTGTCCTATGTGGACGTTGGCACTGGGAAGGTCACTCTGGAATATAGACCCGTGATCGACAAAAC
TTTGAACGAGGCTGACTGTGCCACCGTCCCGCCAGCCATTCGCTCCTACTGATGAGACAAGATGTGGTGATGACAGAATCAGCTTTTGTA
ATTATGTATAATAGCTCATGCATGTGTCCATGTCATAACTGTCTTCATACGCTTCTGCACTCTGGGGAAGAAGGAGTACATTGAAGGGAG
ATTGGCACCTAGTGGCTGGGAGCTTGCCAGGAACCCAGTGGCCAGGGAGCGTGGCACTTACCTTTGTCCCTTGCTTCATTCTTGTGAGAT


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FusionGenePPI for LPCAT1_SDHA


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
LPCAT1SAP25, PCK1, ELAVL1, AUP1, LAMTOR3, ILF3, FAF2, ECT2, MDC1, HIPK4, ILK, BBS2, MSTO1, SLC27A2, DOCK7, DIP2A, NTRK1, TMEM216, NF2, BTRC, GSK3B, MTR, TRIM25, TESSDHAUBC, ICT1, CSNK2B, ARRB2, SIRT7, CUL3, CUL4A, CUL5, CUL2, CUL1, COPS5, COPS6, DCUN1D1, CAND1, NEDD8, SDHB, SUCLA2, SUCLG1, SUCLG2, UQCRFS1, UQCRB, SYNE2, MTERF3, RAVER1, TIMM50, LRRC8A, MDH1, SAMM50, DHODH, TOMM70A, TAP1, TMEM14B, HIGD1A, NDUFS2, OXCT1, MRPL1, MRPS9, ZC3H4, NDUFS3, CYB5R3, NDUFS6, NDUFS8, NDUFV2, EIF4A1, XRCC6, MARC1, IMPAD1, ACAT1, GCN1L1, PSMD1, PROCR, SLC2A14, SLC27A2, SQSTM1, PDHA1, ATP5F1, NDUFV1, FN1, ITGA4, FBXO6, NXF1, APOA1BP, ATP1B1, CPNE1, CPNE3, CYC1, DLD, DNAJA3, HSPA9, HSPB1, MDH2, MTCH1, NDUFA2, PPIB, RAB14, ACLY, CS, GLOD4, SDHC, UQCRQ, NTRK1, HSPB2, CEP128, RPGRIP1L, TMEM67, SDHAF2, CRY1, CRY2, UBXN10, OTUB1, NFATC2, DUSP4, DUSP9, C6orf57, PDZRN3, PDSS2, PDSS1, PDP1, ACN9, SIRT3, ACAD9, WBP2, SEC22B, YWHAB, PPIA, MYL12A, HSD17B10, BANF1, CKB, ANXA5, SFXN1, LDHA, RPL30, HNRNPH3, EEF2, ATP1A1, HIST1H2AD, CCT2, EIF4A3, CCT8, RPL26, EEF1G, CDK1, SLC25A5, CHCHD2, RPN2, ATP5H, PPIAL4B, RPL12, LDHAL6A, LDHB, PDIA3, SLC25A3, ARL6IP5, PMVK, HMGB3, RAB10, CKAP4, HSP90B1, MAP4K1, SERPINH1, PSMC2, TMED10, PDIA6, RAB21, EEF1B2, CHCHD3, RUVBL2, TMED9, GANAB, UQCRC1, TMEM109, YWHAQ, YWHAZ, TFAM, YWHAG, SHMT2, PGAM1, YWHAE, PRDX3, MCM3, CCT7, TPI1, PPP2R1A, CANX, EMC2, LMNB2, EIF2S1, APEX1, ELAVL1, LMNA, NDFIP2, ATP6V0D1, DNAJB11, HLA-B, HLA-A, IDH3A, HNRNPA1, JUP, MAT2A, PSMC5, SERBP1, PSMC1, UQCRC2, PRPH, NAMPT, DARS, FARSA, ASNS, LMNB1, RPN1, TKT, SSRP1, DSP, MCM5, HSD17B4, DDX1, PCSK1, CPT1A, DGKG, MCM6, HSPA4, KPNB1, PSMD2, AARS2, TPR, SMC3, COPA, FASN, HDLBP, EPRS, HIST1H2AE, HIST1H2AB, HIST1H2BD, HIST1H2BG, HIST1H2BF, HIST1H2BE, HIST1H2BI, HIST1H2BC


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for LPCAT1_SDHA


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneSDHAP31040DB09270UbidecarenoneSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrialsmall moleculeapproved|investigational|nutraceutical

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RelatedDiseases for LPCAT1_SDHA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSDHAC0023264Leigh Disease3CTD_human;ORPHANET;UNIPROT
TgeneSDHAC1855008Mitochondrial Complex II Deficiency2CTD_human;ORPHANET;UNIPROT
TgeneSDHAC0029408Degenerative polyarthritis1CTD_human
TgeneSDHAC0036341Schizophrenia1PSYGENET
TgeneSDHAC3279992PARAGANGLIOMAS 51UNIPROT