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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: 12893

FusionGeneSummary for FAM96A_SNX1

check button Fusion gene summary
Fusion gene informationFusion gene name: FAM96A_SNX1
Fusion gene ID: 12893
HgeneTgene
Gene symbol

FAM96A

SNX1

Gene ID

6642

Gene namesorting nexin 1
SynonymsHsT17379|VPS5
Cytomap

15q22.31

Type of geneprotein-coding
Descriptionsorting nexin-1sorting nexin 1A
Modification date20180527
UniProtAcc

Q9H5X1

Q13596

Ensembl transtripts involved in fusion geneENST00000300030, ENST00000558779, 
ENST00000380290, ENST00000557835, 
ENST00000559950, 		ENST00000560829, 
ENST00000353874, ENST00000261889, 
ENST00000559844, ENST00000561026, 
ENST00000559339, 
Fusion gene scores* DoF score7 X 6 X 3=1266 X 4 X 4=96
# samples 77
** MAII scorelog2(7/126*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/96*10)=-0.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FAM96A [Title/Abstract] AND SNX1 [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
TgeneSNX1

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
TCGARVBRCATCGA-AN-A0AM-01AFAM96Achr15

64380886

-SNX1chr15

64404772

+
* 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
5CDS-5UTRENST00000300030ENST00000560829FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000300030ENST00000353874FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000300030ENST00000261889FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000300030ENST00000559844FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000300030ENST00000561026FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-intronENST00000300030ENST00000559339FAM96Achr15

64380886

-SNX1chr15

64404772

+
intron-5UTRENST00000558779ENST00000560829FAM96Achr15

64380886

-SNX1chr15

64404772

+
intron-5UTRENST00000558779ENST00000353874FAM96Achr15

64380886

-SNX1chr15

64404772

+
intron-5UTRENST00000558779ENST00000261889FAM96Achr15

64380886

-SNX1chr15

64404772

+
intron-5UTRENST00000558779ENST00000559844FAM96Achr15

64380886

-SNX1chr15

64404772

+
intron-5UTRENST00000558779ENST00000561026FAM96Achr15

64380886

-SNX1chr15

64404772

+
intron-intronENST00000558779ENST00000559339FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000380290ENST00000560829FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000380290ENST00000353874FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000380290ENST00000261889FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000380290ENST00000559844FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000380290ENST00000561026FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-intronENST00000380290ENST00000559339FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000557835ENST00000560829FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000557835ENST00000353874FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000557835ENST00000261889FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000557835ENST00000559844FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000557835ENST00000561026FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-intronENST00000557835ENST00000559339FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000559950ENST00000560829FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000559950ENST00000353874FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000559950ENST00000261889FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000559950ENST00000559844FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-5UTRENST00000559950ENST00000561026FAM96Achr15

64380886

-SNX1chr15

64404772

+
5CDS-intronENST00000559950ENST00000559339FAM96Achr15

64380886

-SNX1chr15

64404772

+

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FusionProtFeatures for FAM96A_SNX1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
FAM96A

Q9H5X1

SNX1

Q13596

May play a role in chromosome segregation throughestablishment of sister chromatid cohesion. {ECO:0000250}. 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}.

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 FAM96A_SNX1


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 FAM96A_SNX1


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
FAM96ACIAO1, IREB2, PRPS2, MYH11, TDRD3, DNAJB6, POLE, MLF2, NARFL, TOP3B, AGTRAPSNX1F2R, 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, DLD


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 FAM96A_SNX1


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 FAM96A_SNX1


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