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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:LIFR-BCAS3 (FusionGDB2 ID:HG3977TG54828)

Fusion Gene Summary for LIFR-BCAS3

check button Fusion gene summary
Fusion gene informationFusion gene name: LIFR-BCAS3
Fusion gene ID: hg3977tg54828
HgeneTgene
Gene symbol

LIFR

BCAS3

Gene ID

3977

54828

Gene nameLIF receptor subunit alphaBCAS3 microtubule associated cell migration factor
SynonymsCD118|LIF-R|SJS2|STWS|SWSGAOB1|MAAB
Cytomap('LIFR')('BCAS3')

5p13.1

17q23.2

Type of geneprotein-codingprotein-coding
Descriptionleukemia inhibitory factor receptorCD118 antigenLIF receptorLIF receptor alphaleukemia inhibitory factor receptor alphabreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1
Modification date2020031320200313
UniProtAcc

P42702

Q9H6U6

Ensembl transtripts involved in fusion geneENST00000263409, ENST00000453190, 
ENST00000503088, 
Fusion gene scores* DoF score8 X 7 X 7=39245 X 32 X 19=27360
# samples 853
** MAII scorelog2(8/392*10)=-2.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(53/27360*10)=-5.6899320603227
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LIFR [Title/Abstract] AND BCAS3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLIFR(38496484)-BCAS3(59445688), # samples:3
Anticipated loss of major functional domain due to fusion event.LIFR-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
LIFR-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
LIFR-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
LIFR-BCAS3 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
HgeneLIFR

GO:0008284

positive regulation of cell proliferation

7957045|8999038

HgeneLIFR

GO:0019221

cytokine-mediated signaling pathway

7957045

HgeneLIFR

GO:0034097

response to cytokine

8999038

HgeneLIFR

GO:0048861

leukemia inhibitory factor signaling pathway

8999038|12643274

HgeneLIFR

GO:0070120

ciliary neurotrophic factor-mediated signaling pathway

12643274

TgeneBCAS3

GO:0043085

positive regulation of catalytic activity

17505058

TgeneBCAS3

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

TgeneBCAS3

GO:0071391

cellular response to estrogen stimulus

17505058



check button Fusion gene information
* 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-68-8250-01ALIFRchr5

38496484

-BCAS3chr17

59445688

+
ChimerDB4LUSCTCGA-68-8250LIFRchr5

38496484

-BCAS3chr17

59445688

+


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Fusion Gene ORF analysis for LIFR-BCAS3

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-3UTRENST00000263409ENST00000585812LIFRchr5

38496484

-BCAS3chr17

59445688

+
5CDS-3UTRENST00000453190ENST00000585812LIFRchr5

38496484

-BCAS3chr17

59445688

+
5UTR-3CDSENST00000503088ENST00000390652LIFRchr5

38496484

-BCAS3chr17

59445688

+
5UTR-3CDSENST00000503088ENST00000407086LIFRchr5

38496484

-BCAS3chr17

59445688

+
5UTR-3CDSENST00000503088ENST00000408905LIFRchr5

38496484

-BCAS3chr17

59445688

+
5UTR-3CDSENST00000503088ENST00000585744LIFRchr5

38496484

-BCAS3chr17

59445688

+
5UTR-3CDSENST00000503088ENST00000588462LIFRchr5

38496484

-BCAS3chr17

59445688

+
5UTR-3CDSENST00000503088ENST00000588874LIFRchr5

38496484

-BCAS3chr17

59445688

+
5UTR-3CDSENST00000503088ENST00000589222LIFRchr5

38496484

-BCAS3chr17

59445688

+
5UTR-3UTRENST00000503088ENST00000585812LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000263409ENST00000390652LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000263409ENST00000407086LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000263409ENST00000408905LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000263409ENST00000585744LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000263409ENST00000588462LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000263409ENST00000588874LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000263409ENST00000589222LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000453190ENST00000390652LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000453190ENST00000407086LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000453190ENST00000408905LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000453190ENST00000585744LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000453190ENST00000588462LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000453190ENST00000588874LIFRchr5

38496484

-BCAS3chr17

59445688

+
Frame-shiftENST00000453190ENST00000589222LIFRchr5

38496484

-BCAS3chr17

59445688

+

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 LIFR-BCAS3


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)
LIFRchr538496483-BCAS3chr1759445687+0.0004010190.99959904
LIFRchr538496483-BCAS3chr1759445687+0.0004010190.99959904
LIFRchr538496483-BCAS3chr1759445687+0.0004010190.99959904
LIFRchr538496483-BCAS3chr1759445687+0.0004010190.99959904


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.
genomic feature of top 1%

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Fusion Protein Features for LIFR-BCAS3


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:38496484/:59445688)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

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

P42702

BCAS3

Q9H6U6

FUNCTION: Signal-transducing molecule. May have a common pathway with IL6ST. The soluble form inhibits the biological activity of LIF by blocking its binding to receptors on target cells.FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.

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 LIFR-BCAS3


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 LIFR-BCAS3


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 LIFR-BCAS3


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 LIFR-BCAS3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLIFRC0796176STUVE-WIEDEMANN SYNDROME3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneLIFRC0032460Polycystic Ovary Syndrome1CTD_human
HgeneLIFRC0033578Prostatic Neoplasms1CTD_human
HgeneLIFRC0036341Schizophrenia1PSYGENET
HgeneLIFRC0349398Paranoid delusion1PSYGENET
HgeneLIFRC0376358Malignant neoplasm of prostate1CTD_human
HgeneLIFRC0432240Stuve-Wiedemann dysplasia1ORPHANET
HgeneLIFRC1136382Sclerocystic Ovaries1CTD_human
HgeneLIFRC1968949Cakut1GENOMICS_ENGLAND
HgeneLIFRC2239176Liver carcinoma1CTD_human