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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:IFT122-PITPNB (FusionGDB2 ID:38242)

Fusion Gene Summary for IFT122-PITPNB

check button Fusion gene summary
Fusion gene informationFusion gene name: IFT122-PITPNB
Fusion gene ID: 38242
HgeneTgene
Gene symbol

IFT122

PITPNB

Gene ID

55764

23760

Gene nameintraflagellar transport 122phosphatidylinositol transfer protein beta
SynonymsCED|CED1|FAP80|SPG|WDR10|WDR10p|WDR140PI-TP-beta|PtdInsTP|VIB1B
Cytomap

3q21.3-q22.1

22q12.1

Type of geneprotein-codingprotein-coding
Descriptionintraflagellar transport protein 122 homologWD repeat domain 10WD repeat-containing protein 10WD repeat-containing protein 140intraflagellar transport 122 homologphosphatidylinositol transfer protein beta isoformPtdIns transfer protein betaphosphotidylinositol transfer protein, beta
Modification date2020031320200313
UniProtAcc

Q9HBG6

.
Ensembl transtripts involved in fusion geneENST00000347300, ENST00000296266, 
ENST00000507564, ENST00000431818, 
ENST00000504021, ENST00000349441, 
ENST00000348417, ENST00000440957, 
ENST00000513932, 		ENST00000335272, 
ENST00000320996, ENST00000455418, 
Fusion gene scores* DoF score5 X 5 X 4=1007 X 8 X 7=392
# samples 510
** MAII scorelog2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/392*10)=-1.97085365434048
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointIFT122(129183624)-PITPNB(28250927), # samples:3
Anticipated loss of major functional domain due to fusion event.IFT122-PITPNB seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
IFT122-PITPNB seems lost the major protein functional domain in Tgene partner, which is a cell metabolism 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
TgenePITPNB

GO:0015914

phospholipid transport

16274224


check buttonFusion gene breakpoints across IFT122 (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 PITPNB (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
ChimerDB4PRADTCGA-G9-A9S4-01AIFT122chr3

129183624

+PITPNBchr22

28250927

-
ChimerDB4PRADTCGA-G9-A9S4IFT122chr3

129183624

+PITPNBchr22

28250927

-
ChimerDB4PRADTCGA-G9-A9S4-01AIFT122chr3

129183624

-PITPNBchr22

28250927

-


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Fusion Gene ORF analysis for IFT122-PITPNB

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
Frame-shiftENST00000347300ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000347300ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000347300ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-
Frame-shiftENST00000296266ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000296266ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000296266ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-
Frame-shiftENST00000507564ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000507564ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000507564ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-
Frame-shiftENST00000431818ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000431818ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000431818ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-
Frame-shiftENST00000504021ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000504021ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000504021ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-
Frame-shiftENST00000349441ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000349441ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000349441ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-
Frame-shiftENST00000348417ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000348417ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000348417ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-
Frame-shiftENST00000440957ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000440957ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
5CDS-intronENST00000440957ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-
intron-3CDSENST00000513932ENST00000335272IFT122chr3

129183624

+PITPNBchr22

28250927

-
intron-intronENST00000513932ENST00000320996IFT122chr3

129183624

+PITPNBchr22

28250927

-
intron-intronENST00000513932ENST00000455418IFT122chr3

129183624

+PITPNBchr22

28250927

-

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 IFT122-PITPNB


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)

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 IFT122-PITPNB


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
IFT122

Q9HBG6

.
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}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 IFT122-PITPNB


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 IFT122-PITPNB


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 IFT122-PITPNB


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 IFT122-PITPNB


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneIFT122C0432235CRANIOECTODERMAL DYSPLASIA 18CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneIFT122C0008780Ciliary Motility Disorders1CTD_human
HgeneIFT122C0009451Communicating Hydrocephalus1CTD_human
HgeneIFT122C0010278Craniosynostosis1CTD_human
HgeneIFT122C0011989Camurati-Engelmann Syndrome1GENOMICS_ENGLAND
HgeneIFT122C0013608Edema, Cardiac1CTD_human
HgeneIFT122C0015393Eye Abnormalities1CTD_human
HgeneIFT122C0020255Hydrocephalus1CTD_human
HgeneIFT122C0020256Congenital Hydrocephalus1CTD_human
HgeneIFT122C0022658Kidney Diseases1CTD_human
HgeneIFT122C0030044Acrocephaly1CTD_human
HgeneIFT122C0037932Curvature of spine1CTD_human
HgeneIFT122C0221356Brachycephaly1CTD_human
HgeneIFT122C0265534Scaphycephaly1CTD_human
HgeneIFT122C0265535Trigonocephaly1CTD_human
HgeneIFT122C0270720Hydrocephalus Ex-Vacuo1CTD_human
HgeneIFT122C0432198Short rib-polydactyly syndrome, Beemer type1ORPHANET
HgeneIFT122C0477432Post-Traumatic Hydrocephalus1CTD_human
HgeneIFT122C0549423Obstructive Hydrocephalus1CTD_human
HgeneIFT122C1531647Cerebral ventriculomegaly1CTD_human
HgeneIFT122C1833340Synostotic Posterior Plagiocephaly1CTD_human
HgeneIFT122C1860819Metopic synostosis1CTD_human
HgeneIFT122C2931150Synostotic Anterior Plagiocephaly1CTD_human
HgeneIFT122C2936718Fetal Cerebral Ventriculomegaly1CTD_human
HgeneIFT122C2936786Aqueductal Stenosis1CTD_human
HgeneIFT122C4551720Primary Ciliary Dyskinesia1CTD_human
HgeneIFT122C4551902Craniosynostosis, Type 11CTD_human