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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: 35270

FusionGeneSummary for SNX1_SCG5

check button Fusion gene summary
Fusion gene informationFusion gene name: SNX1_SCG5
Fusion gene ID: 35270
HgeneTgene
Gene symbol

SNX1

SCG5

Gene ID

6642

6447

Gene namesorting nexin 1secretogranin V
SynonymsHsT17379|VPS57B2|P7B2|SGNE1|SgV
Cytomap

15q22.31

15q13.3

Type of geneprotein-codingprotein-coding
Descriptionsorting nexin-1sorting nexin 1Aneuroendocrine protein 7B2pituitary polypeptideprohormone convertase chaperonesecretogranin-5secretory granule endocrine protein Isecretory granule, neuroendocrine protein 1 (7B2 protein)
Modification date2018052720180519
UniProtAcc

Q13596

P05408

Ensembl transtripts involved in fusion geneENST00000560829, ENST00000353874, 
ENST00000261889, ENST00000559844, 
ENST00000561026, ENST00000559339, 
ENST00000413748, ENST00000300175, 
ENST00000494364, ENST00000497208, 
ENST00000498069, 
Fusion gene scores* DoF score3 X 3 X 3=273 X 1 X 3=9
# samples 33
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SNX1 [Title/Abstract] AND SCG5 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneSNX1

GO:0072673

lamellipodium morphogenesis

20604901


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
TCGARVSKCMTCGA-EB-A57M-01ASNX1chr15

64429131

+SCG5chr15

32971967

+
* 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
Frame-shiftENST00000560829ENST00000413748SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000560829ENST00000300175SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000560829ENST00000494364SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000560829ENST00000497208SNX1chr15

64429131

+SCG5chr15

32971967

+
5CDS-3UTRENST00000560829ENST00000498069SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000353874ENST00000413748SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000353874ENST00000300175SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000353874ENST00000494364SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000353874ENST00000497208SNX1chr15

64429131

+SCG5chr15

32971967

+
5CDS-3UTRENST00000353874ENST00000498069SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000261889ENST00000413748SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000261889ENST00000300175SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000261889ENST00000494364SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000261889ENST00000497208SNX1chr15

64429131

+SCG5chr15

32971967

+
5CDS-3UTRENST00000261889ENST00000498069SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000559844ENST00000413748SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000559844ENST00000300175SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000559844ENST00000494364SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000559844ENST00000497208SNX1chr15

64429131

+SCG5chr15

32971967

+
5CDS-3UTRENST00000559844ENST00000498069SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000561026ENST00000413748SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000561026ENST00000300175SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000561026ENST00000494364SNX1chr15

64429131

+SCG5chr15

32971967

+
Frame-shiftENST00000561026ENST00000497208SNX1chr15

64429131

+SCG5chr15

32971967

+
5CDS-3UTRENST00000561026ENST00000498069SNX1chr15

64429131

+SCG5chr15

32971967

+
intron-3CDSENST00000559339ENST00000413748SNX1chr15

64429131

+SCG5chr15

32971967

+
intron-3CDSENST00000559339ENST00000300175SNX1chr15

64429131

+SCG5chr15

32971967

+
intron-3CDSENST00000559339ENST00000494364SNX1chr15

64429131

+SCG5chr15

32971967

+
intron-3CDSENST00000559339ENST00000497208SNX1chr15

64429131

+SCG5chr15

32971967

+
intron-3UTRENST00000559339ENST00000498069SNX1chr15

64429131

+SCG5chr15

32971967

+

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FusionProtFeatures for SNX1_SCG5


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SNX1

Q13596

SCG5

P05408

Involved in several stages of intracellular trafficking.Interacts with membranes containing phosphatidylinositol 3-phosphate (PtdIns(3P)) or phosphatidylinositol 3,5-bisphosphate(PtdIns(3,5)P2) (PubMed:12198132). Acts in part as component ofthe retromer membrane-deforming SNX-BAR subcomplex. The SNX-BARretromer mediates retrograde transport of cargo proteins fromendosomes to the trans-Golgi network (TGN) and is involved inendosome-to-plasma membrane transport for cargo protein recycling.The SNX-BAR subcomplex functions to deform the donor membrane intoa tubular profile called endosome-to-TGN transport carrier (ETC)(Probable). Can sense membrane curvature and has in vitro vesicle-to-membrane remodeling activity (PubMed:19816406,PubMed:23085988). Involved in retrograde endosome-to-TGN transportof lysosomal enzyme receptors (IGF2R, M6PR and SORT1) andShiginella dysenteria toxin stxB. Plays a role in targetingligand-activated EGFR to the lysosomes for degradation afterendocytosis from the cell surface and release from the Golgi(PubMed:12198132, PubMed:15498486, PubMed:17550970,PubMed:17101778, PubMed:18088323, PubMed:21040701). Involvement inretromer-independent endocytic trafficking of P2RY1 and lysosomaldegradation of protease-activated receptor-1/F2R (PubMed:16407403,PubMed:20070609). Promotes KALRN- and RHOG-dependent but retromer-independent membrane remodeling such as lamellipodium formation;the function is dependent on GEF activity of KALRN(PubMed:20604901). Required for endocytosis of DRD5 upon agoniststimulation but not for basal receptor trafficking(PubMed:23152498). {ECO:0000269|PubMed:12198132,ECO:0000269|PubMed:15498486, ECO:0000269|PubMed:16407403,ECO:0000269|PubMed:17101778, ECO:0000269|PubMed:17550970,ECO:0000269|PubMed:18088323, ECO:0000269|PubMed:19816406,ECO:0000269|PubMed:20070609, ECO:0000269|PubMed:20604901,ECO:0000269|PubMed:21040701, ECO:0000269|PubMed:23085988,ECO:0000269|PubMed:23152498, ECO:0000303|PubMed:15498486}. Acts as a molecular chaperone for PCSK2/PC2, preventingits premature activation in the regulated secretory pathway. Bindsto inactive PCSK2 in the endoplasmic reticulum and facilitates itstransport from there to later compartments of the secretorypathway where it is proteolytically matured and activated. Alsorequired for cleavage of PCSK2 but does not appear to be involvedin its folding. Plays a role in regulating pituitary hormonesecretion. The C-terminal peptide inhibits PCSK2 in vitro.{ECO:0000269|PubMed:7913882}.

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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for SNX1_SCG5


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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for SNX1_SCG5


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
SNX1F2R, HGS, SNX1, SNX6, ACVR2B, ACVR1B, PDGFRB, SNX2, EGFR, INSR, LEPR, ATXN7, UFD1L, TK1, DNAJC13, APP, ARFIP2, REEP6, GSPT2, MAT2B, NASP, SHMT2, ATG7, ATP6V1C1, CTTN, GARS, UGDH, STAT1, RTN3, RABAC1, ARL6IP1, AGTRAP, RTN4, CMTM5, FUNDC1, SNX32, MOV10, NXF1, BIN3, ZNF397, TMOD1, DNM3, GNAT2, CCNL2, FAM90A1, GSPT1, LSM2, RUVBL2, SMYD2, WDFY1, SNX5, VPS26A, VPS26B, VPS29, VPS35, NTRK1, MED4, MCM2, CDH1, CCDC88A, C1orf87, CCDC102B, HCLS1, MLX, FXR2, TMEM87A, POTEB3, KLHL10, GPX7, SLC35F2, STAM, DLDSCG5UBQLN4, NR1H2, KHDRBS1, UBQLN1, CSH2


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 SNX1_SCG5


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SNX1_SCG5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSCG5C0009404Colorectal Neoplasms1CTD_human
TgeneSCG5C0025149Medulloblastoma1CTD_human