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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: 19937

FusionGeneSummary for LNX1_IFT122

check button Fusion gene summary
Fusion gene informationFusion gene name: LNX1_IFT122
Fusion gene ID: 19937
HgeneTgene
Gene symbol

LNX1

IFT122

Gene ID

84708

55764

Gene nameligand of numb-protein X 1intraflagellar transport 122
SynonymsLNX|MPDZ|PDZRN2CED|CED1|SPG|WDR10|WDR10p|WDR140
Cytomap

4q12

3q21.3-q22.1

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase LNXPDZ domain-containing ring finger protein 2RING-type E3 ubiquitin transferase LNXligand of numb-protein X 1, E3 ubiquitin protein ligasemulti-PDZ-domain-containing protein, E3 ubiquitin-protein ligase LNXnumb-binding printraflagellar transport protein 122 homologWD repeat domain 10WD repeat-containing protein 10WD repeat-containing protein 140intraflagellar transport 122 homolog
Modification date2018052220180523
UniProtAcc

Q8TBB1

Q9HBG6

Ensembl transtripts involved in fusion geneENST00000306888, ENST00000263925, 
ENST00000504605, 
ENST00000347300, 
ENST00000296266, ENST00000507564, 
ENST00000431818, ENST00000504021, 
ENST00000349441, ENST00000348417, 
ENST00000440957, ENST00000513932, 
Fusion gene scores* DoF score5 X 3 X 4=604 X 4 X 2=32
# samples 54
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LNX1 [Title/Abstract] AND IFT122 [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
TCGARVLUSCTCGA-43-7657-01ALNX1chr4

54439790

-IFT122chr3

129168714

+
* 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-3CDSENST00000306888ENST00000347300LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-3CDSENST00000306888ENST00000296266LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-3CDSENST00000306888ENST00000507564LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000306888ENST00000431818LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000306888ENST00000504021LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000306888ENST00000349441LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000306888ENST00000348417LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000306888ENST00000440957LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-intronENST00000306888ENST00000513932LNX1chr4

54439790

-IFT122chr3

129168714

+
Frame-shiftENST00000263925ENST00000347300LNX1chr4

54439790

-IFT122chr3

129168714

+
Frame-shiftENST00000263925ENST00000296266LNX1chr4

54439790

-IFT122chr3

129168714

+
Frame-shiftENST00000263925ENST00000507564LNX1chr4

54439790

-IFT122chr3

129168714

+
5CDS-5UTRENST00000263925ENST00000431818LNX1chr4

54439790

-IFT122chr3

129168714

+
5CDS-5UTRENST00000263925ENST00000504021LNX1chr4

54439790

-IFT122chr3

129168714

+
5CDS-5UTRENST00000263925ENST00000349441LNX1chr4

54439790

-IFT122chr3

129168714

+
5CDS-5UTRENST00000263925ENST00000348417LNX1chr4

54439790

-IFT122chr3

129168714

+
5CDS-5UTRENST00000263925ENST00000440957LNX1chr4

54439790

-IFT122chr3

129168714

+
5CDS-intronENST00000263925ENST00000513932LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-3CDSENST00000504605ENST00000347300LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-3CDSENST00000504605ENST00000296266LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-3CDSENST00000504605ENST00000507564LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000504605ENST00000431818LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000504605ENST00000504021LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000504605ENST00000349441LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000504605ENST00000348417LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-5UTRENST00000504605ENST00000440957LNX1chr4

54439790

-IFT122chr3

129168714

+
intron-intronENST00000504605ENST00000513932LNX1chr4

54439790

-IFT122chr3

129168714

+

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FusionProtFeatures for LNX1_IFT122


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LNX1

Q8TBB1

IFT122

Q9HBG6

E3 ubiquitin-protein ligase that mediates ubiquitinationand subsequent proteasomal degradation of NUMB. E3 ubiquitinligases accept ubiquitin from an E2 ubiquitin-conjugating enzymein the form of a thioester and then directly transfers theubiquitin to targeted substrates. Mediates ubiquitination ofisoform p66 and isoform p72 of NUMB, but not that of isoform p71or isoform p65. {ECO:0000250|UniProtKB:O70263}. Isoform 2 provides an endocytic scaffold for IGSF5/JAM4.{ECO:0000250|UniProtKB:O70263}.

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 LNX1_IFT122


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 LNX1_IFT122


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
LNX1MAGEA11, DCTD, LDOC1, CUTC, CALCOCO2, SRSF1, NADK, ENOX1, RBMX, RPIA, TRAF2, KHDRBS3, CCDC85B, PAFAH1B3, KLHL12, TRIP13, TIFA, CEP72, RABAC1, PCBD1, KRTAP4-12, NAGK, KCTD13, MAGEB18, AIMP2, APIP, KCTD17, DDX17, FHL3, TRIM23, NECAB2, SAT1, TSC22D4, ZBTB43, AKIRIN2, KXD1, KRT15, DVL3, EHMT2, PAICS, RAD54B, FBP1, ZBTB8A, NUMB, RHOC, CD8A, SRC, AMMECR1L, AURKB, AURKC, FAM212B, CAMK2N2, DAPK1, DEPTOR, EBF4, EPHB3, KIAA1598, MRPS24, MUSTN1, NKD2, PLEKHG5, PPID, RASL11B, SCLT1, SNCB, ZADH2, WWP1, SAPCD1, TMEM14C, WAC, STX5, PAK6, PBK, TYK2, KCNA4, PRKCA, SDK1, INSC, NRCAM, ABCB1, KALRN, CLDN17, GPR142, EXOC8, DOCK9, LRRC3B, GRIN1, ARHGAP6, LNX2, SSTR3, ADRA1D, SLC6A15, LGR6, TYRO3, CITED1, CGN, PTGIR, SLC6A5, HUNK, GIPR, ARVCF, CTNND2, PKP4, GAS2L2, CLDN1, TSC2, GJD4, TNFRSF18, CLDN2, ILF3, CTSO, VRK2, WNT8A, STRN, ARHGEF16, PQBP1, CDC42EP4, ORMDL3, BPIFA1, ABR, JOSD1, NUP37, BCR, HTR2B, PKDREJ, PDZRN3, PDZRN4, CXADR, ABCA1, SNW1, COIL, UBE2D2, APP, HSP90AA1, NACAP1, PRPH, IL3RA, ULK2, SUV39H1, SUV39H2, IGSF5, SPHKAP, CTBP1, ACAT2, ALDOC, BLVRA, CA8, CDA, CIRBP, CLK2, DAB1, GDI1, GRB2, HSBP1, PKM, PPIA, MAPK9, PTS, RAD51D, RBMY1A1, DPF2, SNRPF, TPM4, VCP, EIF4H, NCK2, SSNA1, RFPL3, NEK6, RUVBL2, MTUS2, ISCU, DNPEP, OSBP2, NME7, OSGIN1, ZNF593, MEMO1, ZNF581, PRR13, ROPN1, ZCCHC10, FBXL12, FAM118A, TRMT12, GOLPH3L, POMGNT1, ZFP64, NXT2, TRIM39, LGALS14, AGTRAP, TRIM54, HOMEZ, LSM2, PBLD, ROBO3, AIDA, MTMR9, HMBOX1, SNRNP25, CCDC102B, THAP7, APOL4, TSSK3, KRTAP9-2, ATRIP, DCUN1D5, LNX1, KRTAP4-2, MVB12B, ATPAF2, ACY3, CCDC114, CCDC101, C1QTNF1, MRFAP1L1, CIB3, METTL21A, FAM9B, KCTD6, TBCEL, FAM124A, ALKBH3, CPNE2, LCLAT1, NUDT14, CATSPERD, KCTD1, RUFY4, STAC2, NOTCH2NL, JAK3, PTPN11, SH2D2A, SOCS6, LRFN4, NXF2BIFT122C11orf74, IFT140, WDR35, SDF4, WDR19, IFT43, PIH1D1, GFOD1, NTRK1, DNAJC7, TULP3, TULP2, CRYL1, DEF8, PDDC1, ARHGEF16, IARS2, TTC21B, PFKP, CDC7, NDUFAF3, CCDC40, NEK7


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 LNX1_IFT122


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 LNX1_IFT122


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneIFT122C0008780Ciliary Motility Disorders1CTD_human
TgeneIFT122C0010278Craniosynostosis1CTD_human
TgeneIFT122C0013608Edema, Cardiac1CTD_human
TgeneIFT122C0015393Eye Abnormalities1CTD_human
TgeneIFT122C0020255Hydrocephalus1CTD_human
TgeneIFT122C0022658Kidney Diseases1CTD_human
TgeneIFT122C0037932Curvature of spine1CTD_human
TgeneIFT122C0432235Cranioectodermal Dysplasia1CTD_human;ORPHANET;UNIPROT