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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: 35294

FusionGeneSummary for SNX29_LITAF

check button Fusion gene summary
Fusion gene informationFusion gene name: SNX29_LITAF
Fusion gene ID: 35294
HgeneTgene
Gene symbol

SNX29

LITAF

Gene ID

92017

9516

Gene namesorting nexin 29lipopolysaccharide induced TNF factor
SynonymsA-388D4.1|RUNDC2APIG7|SIMPLE|TP53I7
Cytomap

16p13.13-p13.12

16p13.13

Type of geneprotein-codingprotein-coding
Descriptionsorting nexin-29RUN domain containing 2ARUN domain-containing protein 2Alipopolysaccharide-induced tumor necrosis factor-alpha factorLPS-induced TNF-alpha factorlipopolysaccharide-induced TNF-alpha factorp53-induced gene 7 proteinsmall integral membrane protein of lysosome/late endosometumor protein p53 inducible protein
Modification date2018051920180522
UniProtAcc

Q8TEQ0

Q99732

Ensembl transtripts involved in fusion geneENST00000566228, ENST00000323433, 
ENST00000306030, ENST00000568359, 
ENST00000571688, ENST00000413364, 
ENST00000339430, ENST00000381810, 
ENST00000570904, ENST00000571459, 
ENST00000572255, ENST00000576036, 
ENST00000574763, ENST00000571976, 
ENST00000574703, 
Fusion gene scores* DoF score12 X 11 X 9=11886 X 2 X 6=72
# samples 148
** MAII scorelog2(14/1188*10)=-3.0850361038558
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/72*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SNX29 [Title/Abstract] AND LITAF [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

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
TCGARVDLBCTCGA-FF-8043-01ASNX29chr16

12371893

+LITAFchr16

11650591

-
* 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-5UTRENST00000566228ENST00000571688SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000413364SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000339430SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000381810SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000570904SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000571459SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-intronENST00000566228ENST00000572255SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000576036SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000574763SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000571976SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000566228ENST00000574703SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000571688SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000413364SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000339430SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000381810SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000570904SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000571459SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-intronENST00000323433ENST00000572255SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000576036SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000574763SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000571976SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000323433ENST00000574703SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000571688SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000413364SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000339430SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000381810SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000570904SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000571459SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-intronENST00000306030ENST00000572255SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000576036SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000574763SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000571976SNX29chr16

12371893

+LITAFchr16

11650591

-
5CDS-5UTRENST00000306030ENST00000574703SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000571688SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000413364SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000339430SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000381810SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000570904SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000571459SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-intronENST00000568359ENST00000572255SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000576036SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000574763SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000571976SNX29chr16

12371893

+LITAFchr16

11650591

-
intron-5UTRENST00000568359ENST00000574703SNX29chr16

12371893

+LITAFchr16

11650591

-

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FusionProtFeatures for SNX29_LITAF


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SNX29

Q8TEQ0

LITAF

Q99732

Plays a role in endosomal protein trafficking and intargeting proteins for lysosomal degradation (PubMed:23166352).Plays a role in targeting endocytosed EGFR and ERGG3 for lysosomaldegradation, and thereby helps downregulate downstream signalingcascades (PubMed:23166352). Helps recruit the ESCRT complexcomponents TSG101, HGS and STAM to cytoplasmic membranes(PubMed:23166352). Probably plays a role in regulating proteindegradation via its interaction with NEDD4 (PubMed:15776429). Mayalso contribute to the regulation of gene expression in thenucleus (PubMed:10200294, PubMed:15793005). Binds DNA (in vitro)and may play a synergistic role with STAT6 in the nucleus inregulating the expression of various cytokines (PubMed:15793005).May regulate the expression of numerous cytokines, such as TNF,CCL2, CCL5, CXCL1, IL1A and IL10 (PubMed:10200294,PubMed:15793005). {ECO:0000269|PubMed:15793005,ECO:0000269|PubMed:23166352, ECO:0000303|PubMed:15776429,ECO:0000305|PubMed:10200294}.

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 SNX29_LITAF


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 SNX29_LITAF


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
SNX29AP2M1, EGFR, TRAF1LITAFELAVL1, NEDD4, TSG101, ITCH, ATXN1, STAT6, BAG3, HGS, CALCOCO2, STAM2, UBQLN1, REEP6, NEDD4L, WWP1, WWP2, TOM1, TAB2, R3HDM1, HPCAL4, CYHR1, BCS1L, UBB, PUM2, FGFR2, PTPRD, LRP10, APOB, REEP5, RASSF3, FGFR1, HECW2, CD320, PUM1, BMPR1A, CARS, RNF149, TTC33, ARL8A, ACOX1, SDCBP, TRIM25


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 SNX29_LITAF


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 SNX29_LITAF


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneLITAFC0270913Charcot-Marie-Tooth disease, Type 1C2CTD_human;ORPHANET;UNIPROT