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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:BAIAP2L1-LLGL2 (FusionGDB2 ID:HG55971TG3993)

Fusion Gene Summary for BAIAP2L1-LLGL2

check button Fusion gene summary
Fusion gene informationFusion gene name: BAIAP2L1-LLGL2
Fusion gene ID: hg55971tg3993
HgeneTgene
Gene symbol

BAIAP2L1

LLGL2

Gene ID

55971

3993

Gene nameBAR/IMD domain containing adaptor protein 2 like 1LLGL scribble cell polarity complex component 2
SynonymsIRTKSHGL|Hugl-2|LGL2
Cytomap('BAIAP2L1')('LLGL2')

7q21.3-q22.1

17q25.1

Type of geneprotein-codingprotein-coding
Descriptionbrain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1BAI1 associated protein 2 like 1BAI1-associated protein 2-like protein 1insulin receptor tyrosine kinase substrateLLGL scribble cell polarity complex component 2LLGL2, scribble cell polarity complex componenthuman giant larvae homologlethal giant larvae homolog 2, scribble cell polarity complex componentlethal(2) giant larvae protein homolog 2
Modification date2020031320200320
UniProtAcc

Q9UHR4

Q6P1M3

Ensembl transtripts involved in fusion geneENST00000005260, ENST00000462558, 
Fusion gene scores* DoF score20 X 13 X 9=234010 X 11 X 6=660
# samples 2314
** MAII scorelog2(23/2340*10)=-3.34680276352639
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(14/660*10)=-2.23703919730085
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BAIAP2L1 [Title/Abstract] AND LLGL2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBAIAP2L1(98030113)-LLGL2(73564556), # samples:1
Anticipated loss of major functional domain due to fusion event.BAIAP2L1-LLGL2 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
HgeneBAIAP2L1

GO:0009617

response to bacterium

19366662

HgeneBAIAP2L1

GO:0030838

positive regulation of actin filament polymerization

21098279

TgeneLLGL2

GO:0032878

regulation of establishment or maintenance of cell polarity

12725730



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
ChimerDB4STADTCGA-BR-7958BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+


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Fusion Gene ORF analysis for BAIAP2L1-LLGL2

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-intronENST00000005260ENST00000375227BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
5CDS-intronENST00000005260ENST00000392550BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
5CDS-intronENST00000005260ENST00000577200BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
5CDS-intronENST00000005260ENST00000578363BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
5UTR-3CDSENST00000462558ENST00000167462BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
5UTR-intronENST00000462558ENST00000375227BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
5UTR-intronENST00000462558ENST00000392550BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
5UTR-intronENST00000462558ENST00000577200BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
5UTR-intronENST00000462558ENST00000578363BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+
Frame-shiftENST00000005260ENST00000167462BAIAP2L1chr7

98030113

-LLGL2chr17

73564556

+

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 BAIAP2L1-LLGL2


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)
BAIAP2L1chr798030113-LLGL2chr1773564556+3.52E-091
BAIAP2L1chr798030113-LLGL2chr1773564556+3.52E-091


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 BAIAP2L1-LLGL2


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/:98030113/:73564556)
- 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
BAIAP2L1

Q9UHR4

LLGL2

Q6P1M3

FUNCTION: May function as adapter protein. Involved in the formation of clusters of actin bundles. Plays a role in the reorganization of the actin cytoskeleton in response to bacterial infection. {ECO:0000269|PubMed:17430976, ECO:0000269|PubMed:19366662, ECO:0000269|PubMed:22921828}.FUNCTION: Part of a complex with GPSM2/LGN, PRKCI/aPKC and PARD6B/Par-6, which may ensure the correct organization and orientation of bipolar spindles for normal cell division. This complex plays roles in the initial phase of the establishment of epithelial cell polarity. {ECO:0000269|PubMed:15632202}.

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 BAIAP2L1-LLGL2


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 BAIAP2L1-LLGL2


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 BAIAP2L1-LLGL2


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 BAIAP2L1-LLGL2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBAIAP2L1C0003873Rheumatoid Arthritis1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0027627Neoplasm Metastasis1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human