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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:SNX30-LPAR1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SNX30-LPAR1
FusionPDB ID: 84984
FusionGDB2.0 ID: 84984
HgeneTgene
Gene symbol

SNX30

LPAR1

Gene ID

401548

1902

Gene namesorting nexin family member 30lysophosphatidic acid receptor 1
SynonymsATG24AEDG2|GPR26|Gpcr26|LPA1|Mrec1.3|VZG1|edg-2|rec.1.3|vzg-1
Cytomap

9q32

9q31.3

Type of geneprotein-codingprotein-coding
Descriptionsorting nexin-30lysophosphatidic acid receptor 1LPA receptor 1LPA-1endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2lysophosphatidic acid receptor Edg-2ventricular zone gene 1
Modification date2020031320200313
UniProtAcc.

Q92633

Ensembl transtripts involved in fusion geneENST idsENST00000374232, ENST00000604751, 
ENST00000358883, ENST00000374430, 
ENST00000374431, ENST00000538760, 
ENST00000541779, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 9 X 11=118810 X 6 X 6=360
# samples 1511
** MAII scorelog2(15/1188*10)=-2.98550043030489
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/360*10)=-1.71049338280502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SNX30 [Title/Abstract] AND LPAR1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SNX30(115513437)-LPAR1(113638002), # samples:2
Anticipated loss of major functional domain due to fusion event.SNX30-LPAR1 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.
SNX30-LPAR1 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.
SNX30-LPAR1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SNX30-LPAR1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SNX30-LPAR1 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneLPAR1

GO:0007202

activation of phospholipase C activity

19306925


check buttonFusion gene breakpoints across SNX30 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across LPAR1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LGGTCGA-DU-5853-01ASNX30chr9

115513437

-LPAR1chr9

113638002

-
ChimerDB4LGGTCGA-DU-5853-01ASNX30chr9

115513437

+LPAR1chr9

113638002

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000374232SNX30chr9115513437+ENST00000541779LPAR1chr9113638002-27793203320111
ENST00000374232SNX30chr9115513437+ENST00000538760LPAR1chr9113638002-8673203320111

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000374232ENST00000541779SNX30chr9115513437+LPAR1chr9113638002-0.6719560.328044
ENST00000374232ENST00000538760SNX30chr9115513437+LPAR1chr9113638002-0.33118040.6688196

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Fusion Amino Acid Sequences


check button 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

>84984_84984_1_SNX30-LPAR1_SNX30_chr9_115513437_ENST00000374232_LPAR1_chr9_113638002_ENST00000538760_length(amino acids)=111AA_BP=
MIKAPCHRSCGPSAGPGWACCHHPRPPRCWSRPAGAACRAGSGAPWTAGPWGARPPWRAPLGTRRRRFLLLPAAASSPSTPGRAPLGRRL

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

>84984_84984_2_SNX30-LPAR1_SNX30_chr9_115513437_ENST00000374232_LPAR1_chr9_113638002_ENST00000541779_length(amino acids)=111AA_BP=
MIKAPCHRSCGPSAGPGWACCHHPRPPRCWSRPAGAACRAGSGAPWTAGPWGARPPWRAPLGTRRRRFLLLPAAASSPSTPGRAPLGRRL

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

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr9:115513437/chr9:113638002)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.LPAR1

Q92633

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Receptor for lysophosphatidic acid (LPA) (PubMed:9070858, PubMed:19306925, PubMed:25025571, PubMed:26091040). Plays a role in the reorganization of the actin cytoskeleton, cell migration, differentiation and proliferation, and thereby contributes to the responses to tissue damage and infectious agents. Activates downstream signaling cascades via the G(i)/G(o), G(12)/G(13), and G(q) families of heteromeric G proteins. Signaling inhibits adenylyl cyclase activity and decreases cellular cAMP levels (PubMed:26091040). Signaling triggers an increase of cytoplasmic Ca(2+) levels (PubMed:19656035, PubMed:19733258, PubMed:26091040). Activates RALA; this leads to the activation of phospholipase C (PLC) and the formation of inositol 1,4,5-trisphosphate (PubMed:19306925). Signaling mediates activation of down-stream MAP kinases (By similarity). Contributes to the regulation of cell shape. Promotes Rho-dependent reorganization of the actin cytoskeleton in neuronal cells and neurite retraction (PubMed:26091040). Promotes the activation of Rho and the formation of actin stress fibers (PubMed:26091040). Promotes formation of lamellipodia at the leading edge of migrating cells via activation of RAC1 (By similarity). Through its function as lysophosphatidic acid receptor, plays a role in chemotaxis and cell migration, including responses to injury and wounding (PubMed:18066075, PubMed:19656035, PubMed:19733258). Plays a role in triggering inflammation in response to bacterial lipopolysaccharide (LPS) via its interaction with CD14. Promotes cell proliferation in response to lysophosphatidic acid. Required for normal skeleton development. May play a role in osteoblast differentiation. Required for normal brain development. Required for normal proliferation, survival and maturation of newly formed neurons in the adult dentate gyrus. Plays a role in pain perception and in the initiation of neuropathic pain (By similarity). {ECO:0000250|UniProtKB:P61793, ECO:0000269|PubMed:18066075, ECO:0000269|PubMed:19306925, ECO:0000269|PubMed:19656035, ECO:0000269|PubMed:19733258, ECO:0000269|PubMed:25025571, ECO:0000269|PubMed:26091040, ECO:0000269|PubMed:9070858, ECO:0000305|PubMed:11093753, ECO:0000305|PubMed:9069262}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324281_294264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324316_364264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035281_294264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035316_364264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135281_294264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135316_364264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324295_315264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D7
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035295_315264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D7
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135295_315264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D7

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSNX30chr9:115513437chr9:113638002ENST00000374232+1989_21052.0438.0DomainPX
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324124_129264.3333333333333365.0RegionLysophosphatidic acid binding
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035124_129264.3333333333333365.0RegionLysophosphatidic acid binding
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135124_129264.3333333333333365.0RegionLysophosphatidic acid binding
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324108_121264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324145_163264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324185_204264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST00000358883241_50264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324226_255264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST000003588832476_83264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035108_121264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035145_163264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035185_204264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST00000374430351_50264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035226_255264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST000003744303576_83264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135108_121264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135145_163264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135185_204264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST00000374431351_50264.3333333333333365.0Topological domainNote=Extracellular
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135226_255264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST000003744313576_83264.3333333333333365.0Topological domainNote=Cytoplasmic
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324122_144264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D3
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324164_184264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D4
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324205_225264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D5
TgeneLPAR1chr9:115513437chr9:113638002ENST0000035888324256_280264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D6
TgeneLPAR1chr9:115513437chr9:113638002ENST000003588832451_75264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D1
TgeneLPAR1chr9:115513437chr9:113638002ENST000003588832484_107264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D2
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035122_144264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D3
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035164_184264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D4
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035205_225264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D5
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443035256_280264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D6
TgeneLPAR1chr9:115513437chr9:113638002ENST000003744303551_75264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D1
TgeneLPAR1chr9:115513437chr9:113638002ENST000003744303584_107264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D2
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135122_144264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D3
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135164_184264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D4
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135205_225264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D5
TgeneLPAR1chr9:115513437chr9:113638002ENST0000037443135256_280264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D6
TgeneLPAR1chr9:115513437chr9:113638002ENST000003744313551_75264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D1
TgeneLPAR1chr9:115513437chr9:113638002ENST000003744313584_107264.3333333333333365.0TransmembraneNote=Helical%3B Name%3D2


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SNX30
LPAR1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to SNX30-LPAR1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to SNX30-LPAR1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource