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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:LNX1-IFT122 (FusionGDB2 ID:45631)

Fusion Gene Summary for LNX1-IFT122

check button Fusion gene summary
Fusion gene informationFusion gene name: LNX1-IFT122
Fusion gene ID: 45631
HgeneTgene
Gene symbol

LNX1

IFT122

Gene ID

84708

55764

Gene nameligand of numb-protein X 1intraflagellar transport 122
SynonymsLNX|MPDZ|PDZRN2CED|CED1|FAP80|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 date2020032720200313
UniProtAcc

Q8TBB1

Q9HBG6

Ensembl transtripts involved in fusion geneENST00000306888, ENST00000263925, 
ENST00000504605, 		ENST00000347300, 
ENST00000296266, ENST00000507564, 
ENST00000431818, ENST00000504021, 
ENST00000349441, ENST00000348417, 
ENST00000440957, ENST00000513932, 
Fusion gene scores* DoF score12 X 7 X 7=5887 X 8 X 4=224
# samples 138
** MAII scorelog2(13/588*10)=-2.17730453180791
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/224*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LNX1 [Title/Abstract] AND IFT122 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLNX1(54439790)-IFT122(129168714), # samples:2
Anticipated loss of major functional domain due to fusion event.LNX1-IFT122 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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 buttonFusion gene breakpoints across LNX1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across IFT122 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LUSCTCGA-43-7657-01ALNX1chr4

54439790

-IFT122chr3

129168714

+
ChimerDB4LUSCTCGA-43-7657-01ALNX1chr4

54439790

-IFT122chr3

129168714

+


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Fusion Gene ORF analysis for LNX1-IFT122

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

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for LNX1-IFT122


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
LNX1chr454439789-IFT122chr3129168713+3.50E-050.99996495
LNX1chr454439789-IFT122chr3129168713+3.50E-050.99996495

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for LNX1-IFT122


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

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

Q8TBB1

IFT122

Q9HBG6

FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of NUMB. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Mediates ubiquitination of isoform p66 and isoform p72 of NUMB, but not that of isoform p71 or isoform p65. {ECO:0000250|UniProtKB:O70263}.; FUNCTION: Isoform 2 provides an endocytic scaffold for IGSF5/JAM4. {ECO:0000250|UniProtKB:O70263}.FUNCTION: As a component of the IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), it is required in ciliogenesis and ciliary protein trafficking (PubMed:27932497, PubMed:29220510). Involved in cilia formation during neuronal patterning. Acts as a negative regulator of Shh signaling. Required to recruit TULP3 to primary cilia (By similarity). {ECO:0000250|UniProtKB:Q6NWV3, ECO:0000269|PubMed:27932497, ECO:0000269|PubMed:29220510}.

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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Fusion Gene Sequence for LNX1-IFT122


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis 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


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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Related Drugs for LNX1-IFT122


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for LNX1-IFT122


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneIFT122C0432235CRANIOECTODERMAL DYSPLASIA 18CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneIFT122C0008780Ciliary Motility Disorders1CTD_human
TgeneIFT122C0009451Communicating Hydrocephalus1CTD_human
TgeneIFT122C0010278Craniosynostosis1CTD_human
TgeneIFT122C0011989Camurati-Engelmann Syndrome1GENOMICS_ENGLAND
TgeneIFT122C0013608Edema, Cardiac1CTD_human
TgeneIFT122C0015393Eye Abnormalities1CTD_human
TgeneIFT122C0020255Hydrocephalus1CTD_human
TgeneIFT122C0020256Congenital Hydrocephalus1CTD_human
TgeneIFT122C0022658Kidney Diseases1CTD_human
TgeneIFT122C0030044Acrocephaly1CTD_human
TgeneIFT122C0037932Curvature of spine1CTD_human
TgeneIFT122C0221356Brachycephaly1CTD_human
TgeneIFT122C0265534Scaphycephaly1CTD_human
TgeneIFT122C0265535Trigonocephaly1CTD_human
TgeneIFT122C0270720Hydrocephalus Ex-Vacuo1CTD_human
TgeneIFT122C0432198Short rib-polydactyly syndrome, Beemer type1ORPHANET
TgeneIFT122C0477432Post-Traumatic Hydrocephalus1CTD_human
TgeneIFT122C0549423Obstructive Hydrocephalus1CTD_human
TgeneIFT122C1531647Cerebral ventriculomegaly1CTD_human
TgeneIFT122C1833340Synostotic Posterior Plagiocephaly1CTD_human
TgeneIFT122C1860819Metopic synostosis1CTD_human
TgeneIFT122C2931150Synostotic Anterior Plagiocephaly1CTD_human
TgeneIFT122C2936718Fetal Cerebral Ventriculomegaly1CTD_human
TgeneIFT122C2936786Aqueductal Stenosis1CTD_human
TgeneIFT122C4551720Primary Ciliary Dyskinesia1CTD_human
TgeneIFT122C4551902Craniosynostosis, Type 11CTD_human