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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:CHIC2-LPHN3 (FusionGDB2 ID:HG26511TG23284)

Fusion Gene Summary for CHIC2-LPHN3

check button Fusion gene summary
Fusion gene informationFusion gene name: CHIC2-LPHN3
Fusion gene ID: hg26511tg23284
HgeneTgene
Gene symbol

CHIC2

LPHN3

Gene ID

26511

23284

Gene namecysteine rich hydrophobic domain 2adhesion G protein-coupled receptor L3
SynonymsBTLCIRL3|CL3|LEC3|LPHN3
Cytomap('CHIC2','CHIC2')('ADGRL3','LPHN3')

4q12

4q13.1

Type of geneprotein-codingprotein-coding
Descriptioncysteine-rich hydrophobic domain-containing protein 2BRX-like translocated in leukemiacystein-rich hydrophobic domain 2cysteine-rich hydrophobic domain 2 proteinadhesion G protein-coupled receptor L3CIRL-3calcium-independent alpha-latrotoxin receptor 3latrophilin homolog 3 (cow)latrophilin-3lectomedin 3
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000263921, ENST00000512964, 
Fusion gene scores* DoF score11 X 7 X 9=6935 X 5 X 5=125
# samples 126
** MAII scorelog2(12/693*10)=-2.5298209465287
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/125*10)=-1.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHIC2 [Title/Abstract] AND LPHN3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCHIC2(54880004)-ADGRL3(62248842), # samples:1
CHIC2(54880004)-LPHN3(62248842), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneLPHN3

GO:0098742

cell-cell adhesion via plasma-membrane adhesion molecules

26235030



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
ChimerDB4GBMTCGA-19-0957-02ACHIC2chr4

54880004

-ADGRL3chr4

62248842

+
ChimerDB4GBMTCGA-19-0957-02ACHIC2chr4

54880004

-LPHN3chr4

62248842

+


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Fusion Gene ORF analysis for CHIC2-LPHN3

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-5UTRENST00000263921ENST00000512091CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-5UTRENST00000263921ENST00000514591CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-5UTRENST00000512964ENST00000512091CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-5UTRENST00000512964ENST00000514591CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000504896CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000506700CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000506720CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000506746CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000507164CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000507625CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000508078CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000508693CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000508946CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000509896CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000511324CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000514157CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000514996CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000263921ENST00000545650CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000504896CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000506700CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000506720CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000506746CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000507164CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000507625CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000508078CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000508693CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000508946CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000509896CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000511324CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000514157CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000514996CHIC2chr4

54880004

-LPHN3chr4

62248842

+
5CDS-intronENST00000512964ENST00000545650CHIC2chr4

54880004

-LPHN3chr4

62248842

+

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 CHIC2-LPHN3


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)
CHIC2chr454880003-LPHN3chr462248841+7.88E-060.99999213
CHIC2chr454880003-LPHN3chr462248841+7.88E-060.99999213


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 CHIC2-LPHN3


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/:54880004/:62248842)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 CHIC2-LPHN3


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 CHIC2-LPHN3


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 CHIC2-LPHN3


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 CHIC2-LPHN3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0041671Attention Deficit Disorder1CTD_human
TgeneC1263846Attention deficit hyperactivity disorder1CTD_human
TgeneC1321905Minimal Brain Dysfunction1CTD_human