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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: 35326

FusionGeneSummary for SNX6_TCF3

check button Fusion gene summary
Fusion gene informationFusion gene name: SNX6_TCF3
Fusion gene ID: 35326
HgeneTgene
Gene symbol

SNX6

TCF3

Gene ID

58533

83439

Gene namesorting nexin 6transcription factor 7 like 1
SynonymsMSTP010|TFAF2TCF-3|TCF3
Cytomap

14q13.1

2p11.2

Type of geneprotein-codingprotein-coding
Descriptionsorting nexin-6TRAF4-associated factor 2tumor necrosis factor receptor-associated factor 4(TRAF4)-associated factor 2transcription factor 7-like 1HMG box transcription factor 3transcription factor 7-like 1 (T-cell specific, HMG-box)
Modification date2018052220180523
UniProtAcc

Q9UNH7

P15923

Ensembl transtripts involved in fusion geneENST00000396526, ENST00000396534, 
ENST00000362031, ENST00000355110, 
ENST00000344749, ENST00000262965, 
ENST00000453954, ENST00000395423, 
ENST00000588136, 
Fusion gene scores* DoF score6 X 6 X 4=1447 X 9 X 3=189
# samples 610
** MAII scorelog2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/189*10)=-0.918386234446348
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SNX6 [Title/Abstract] AND TCF3 [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
HgeneSNX6

GO:0030512

negative regulation of transforming growth factor beta receptor signaling pathway

11279102

HgeneSNX6

GO:0045892

negative regulation of transcription, DNA-templated

11279102|20830743


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
ChiTaRS3.1BC009346SNX6chr14

35038343

+TCF3chr19

1611021

-
* 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
intron-3UTRENST00000396526ENST00000344749SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-3UTRENST00000396526ENST00000262965SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000396526ENST00000453954SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000396526ENST00000395423SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000396526ENST00000588136SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-3UTRENST00000396534ENST00000344749SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-3UTRENST00000396534ENST00000262965SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000396534ENST00000453954SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000396534ENST00000395423SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000396534ENST00000588136SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-3UTRENST00000362031ENST00000344749SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-3UTRENST00000362031ENST00000262965SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000362031ENST00000453954SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000362031ENST00000395423SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000362031ENST00000588136SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-3UTRENST00000355110ENST00000344749SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-3UTRENST00000355110ENST00000262965SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000355110ENST00000453954SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000355110ENST00000395423SNX6chr14

35038343

+TCF3chr19

1611021

-
intron-intronENST00000355110ENST00000588136SNX6chr14

35038343

+TCF3chr19

1611021

-

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FusionProtFeatures for SNX6_TCF3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SNX6

Q9UNH7

TCF3

P15923

Involved in several stages of intracellular trafficking.Interacts with membranes phosphatidylinositol 3,4-bisphosphateand/or phosphatidylinositol 4,5-bisphosphate (Probable). Acts inpart as component of the retromer membrane-deforming SNX-BARsubcomplex (PubMed:19935774). The SNX-BAR retromer mediatesretrograde transport of cargo proteins from endosomes to thetrans-Golgi network (TGN) and is involved in endosome-to-plasmamembrane transport for cargo protein recycling. The SNX-BARsubcomplex functions to deform the donor membrane into a tubularprofile called endosome-to-TGN transport carrier (ETC) (Probable).Does not have in vitro vesicle-to-membrane remodeling activity(PubMed:23085988). Involved in retrograde endosome-to-TGNtransport of lysosomal enzyme receptor IGF2R (PubMed:17148574).May function as link between transport vesicles and dynactin(Probable). Negatively regulates retrograde transport of BACE1from the cell surface to the trans-Golgi network(PubMed:20354142). Involved in E-cadherin sorting and degradation;inhibits PIP5K1C isoform 3-mediated E-cadherin degradation(PubMed:24610942). In association with GIT1 involved in EGFRdegradation. Promotes lysosomal degradation of CDKN1B (Bysimilarity). May contribute to transcription regulation(Probable). {ECO:0000250|UniProtKB:Q6P8X1,ECO:0000269|PubMed:17148574, ECO:0000269|PubMed:19935774,ECO:0000269|PubMed:20354142, ECO:0000269|PubMed:23085988,ECO:0000269|PubMed:24610942, ECO:0000303|PubMed:19935774,ECO:0000303|PubMed:20830743, ECO:0000305}. Transcriptional regulator. Involved in the initiation ofneuronal differentiation. Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major rolesin determining tissue-specific cell fate during embryogenesis,like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappaimmunoglobulin gene enhancer. Binds to IEB1 and IEB2, which areshort DNA sequences in the insulin gene transcription controlregion. {ECO:0000250|UniProtKB:P15806}.

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 SNX6_TCF3


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 SNX6_TCF3


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


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 SNX6_TCF3


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 SNX6_TCF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneTCF3C0006413Burkitt Lymphoma2CTD_human
TgeneTCF3C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma1CTD_human
TgeneTCF3C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1CTD_human