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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: 4117

FusionGeneSummary for BEND3_SNX3

check button Fusion gene summary
Fusion gene informationFusion gene name: BEND3_SNX3
Fusion gene ID: 4117
HgeneTgene
Gene symbol

BEND3

SNX3

Gene ID

57673

8724

Gene nameBEN domain containing 3sorting nexin 3
SynonymsKIAA1553Grd19|MCOPS8|SDP3
Cytomap

6q21

6q21

Type of geneprotein-codingprotein-coding
DescriptionBEN domain-containing protein 3sorting nexin-3sorting nexin 3A
Modification date2018051920180519
UniProtAcc

Q5T5X7

O60493

Ensembl transtripts involved in fusion geneENST00000369042, ENST00000429433, 
ENST00000230085, ENST00000426155, 
ENST00000349379, ENST00000368982, 
Fusion gene scores* DoF score2 X 2 X 2=84 X 3 X 3=36
# samples 24
** MAII scorelog2(2/8*10)=1.32192809488736log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: BEND3 [Title/Abstract] AND SNX3 [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
HgeneBEND3

GO:0000122

negative regulation of transcription by RNA polymerase II

21914818

HgeneBEND3

GO:0034773

histone H4-K20 trimethylation

26100909

HgeneBEND3

GO:0036124

histone H3-K9 trimethylation

26100909

HgeneBEND3

GO:0043967

histone H4 acetylation

26100909

HgeneBEND3

GO:0051260

protein homooligomerization

28977671

HgeneBEND3

GO:0098532

histone H3-K27 trimethylation

26100909

HgeneBEND3

GO:1903580

positive regulation of ATP metabolic process

28977671

TgeneSNX3

GO:0009617

response to bacterium

20482551

TgeneSNX3

GO:0010324

membrane invagination

18767904

TgeneSNX3

GO:0022615

protein to membrane docking

24344282

TgeneSNX3

GO:0042177

negative regulation of protein catabolic process

18767904

TgeneSNX3

GO:0046597

negative regulation of viral entry into host cell

18767904

TgeneSNX3

GO:0051224

negative regulation of protein transport

18767904

TgeneSNX3

GO:2000642

negative regulation of early endosome to late endosome transport

18767904


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
TCGALDESCATCGA-LN-A4A2-01ABEND3chr6

107436294

-SNX3chr6

108544249

-
* 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
5UTR-3CDSENST00000369042ENST00000230085BEND3chr6

107436294

-SNX3chr6

108544249

-
5UTR-intronENST00000369042ENST00000426155BEND3chr6

107436294

-SNX3chr6

108544249

-
5UTR-intronENST00000369042ENST00000349379BEND3chr6

107436294

-SNX3chr6

108544249

-
5UTR-intronENST00000369042ENST00000368982BEND3chr6

107436294

-SNX3chr6

108544249

-
intron-3CDSENST00000429433ENST00000230085BEND3chr6

107436294

-SNX3chr6

108544249

-
intron-intronENST00000429433ENST00000426155BEND3chr6

107436294

-SNX3chr6

108544249

-
intron-intronENST00000429433ENST00000349379BEND3chr6

107436294

-SNX3chr6

108544249

-
intron-intronENST00000429433ENST00000368982BEND3chr6

107436294

-SNX3chr6

108544249

-

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FusionProtFeatures for BEND3_SNX3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BEND3

Q5T5X7

SNX3

O60493

Transcriptional repressor which associates with the NoRC(nucleolar remodeling complex) complex and plays a key role inrepressing rDNA transcription. The sumoylated form modulates thestability of the NoRC complex component BAZ2A/TIP5 by controllingits USP21-mediated deubiquitination (PubMed:21914818,PubMed:26100909). Binds to unmethylated major satellite DNA and isinvolved in the recruitment of the Polycomb repressive complex 2(PRC2) to major satellites (By similarity). Stimulates the ERCC6Ltranslocase and ATPase activities (PubMed:28977671).{ECO:0000250|UniProtKB:Q6PAL0, ECO:0000269|PubMed:21914818,ECO:0000269|PubMed:26100909, ECO:0000269|PubMed:28977671}.

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 BEND3_SNX3


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 BEND3_SNX3


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
BEND3USP21, SMARCAD1, SIRT7, BARD1, TP53BP1, HDAC1, RIOK2, BEND3, FAM161A, MORN4, NTRK1, CFAP97, NFATC1, BAZ2A, SMARCA5, FOXP3, NFATC2, ZNF785, MAP7D2SNX3USP10, SCNN1A, ELAVL1, VPS35, NDUFA7, SBDS, PPM1G, NDUFA2, MRPL53, SRPRB, SUGP1, SSBP1, RBMS1, SEC23A, PPIA, IGBP1, PSMB1, AHCYL1, STX7, ZC3H11A, PLS3, BARD1, BRCA1, LIG4, PAXIP1, VCP, VCAM1, ITGA4, ARL6IP1, ARL6IP6, MBD5, SCNM1, SETD3, HSD17B6, SIRT4, SPRY2, TAS2R41, CYP1A1, RAB7A, AKR1A1, LOC101930400, AKR1C2, NME1-NME2, PIN1, PPIL3, RBM12, CAPG, CRIP1, DAZAP1, DYNLL1, GLOD4, GOT1, HEBP1, HGS, MTAP, PIR, SMEK1, TRIP6, UBE2L3, TAGLN, TAGLN2, TAGLN3, TMEM17, CTPS1, SSFA2, SMC1A, KCNAB2, GJB2, TFG, MPDZ, CTPS2, ANO3, MRPS5, TSC22D2, SNRNP27, MANSC1, SLC1A1, FGB, CAV3, USP47, FCGRT, MRAP2, SERPINB5


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 BEND3_SNX3


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 BEND3_SNX3


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