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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:LRRC8A-MEN1 (FusionGDB2 ID:50046)

Fusion Gene Summary for LRRC8A-MEN1

check button Fusion gene summary
Fusion gene informationFusion gene name: LRRC8A-MEN1
Fusion gene ID: 50046
HgeneTgene
Gene symbol

LRRC8A

MEN1

Gene ID

56262

4221

Gene nameleucine rich repeat containing 8 VRAC subunit Amenin 1
SynonymsAGM5|LRRC8|SWELL1MEAI|SCG2
Cytomap

9q34.11

11q13.1

Type of geneprotein-codingprotein-coding
Descriptionvolume-regulated anion channel subunit LRRC8Aleucine rich repeat containing 8 family member Aleucine-rich repeat-containing protein 8Aswelling protein 1menin
Modification date2020032920200320
UniProtAcc

Q8IWT6

O00255

Ensembl transtripts involved in fusion geneENST00000372599, ENST00000372600, 
ENST00000259324, ENST00000492784, 
ENST00000337652, ENST00000394376, 
ENST00000312049, ENST00000315422, 
ENST00000377313, ENST00000377316, 
ENST00000377321, ENST00000377326, 
ENST00000394374, ENST00000443283, 
ENST00000478548, 
Fusion gene scores* DoF score7 X 6 X 4=1684 X 4 X 4=64
# samples 74
** MAII scorelog2(7/168*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRRC8A [Title/Abstract] AND MEN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLRRC8A(131644529)-MEN1(64578377), # samples:4
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
TgeneMEN1

GO:0000122

negative regulation of transcription by RNA polymerase II

9989505|12837246|23784080

TgeneMEN1

GO:0000165

MAPK cascade

12226747

TgeneMEN1

GO:0001933

negative regulation of protein phosphorylation

12226747

TgeneMEN1

GO:0006974

cellular response to DNA damage stimulus

16690369

TgeneMEN1

GO:0008285

negative regulation of cell proliferation

15331604

TgeneMEN1

GO:0009411

response to UV

16690369

TgeneMEN1

GO:0010332

response to gamma radiation

12874027

TgeneMEN1

GO:0032092

positive regulation of protein binding

20484083

TgeneMEN1

GO:0043433

negative regulation of DNA-binding transcription factor activity

11526476|12226747

TgeneMEN1

GO:0045786

negative regulation of cell cycle

15331604

TgeneMEN1

GO:0045892

negative regulation of transcription, DNA-templated

12226747

TgeneMEN1

GO:0046329

negative regulation of JNK cascade

12226747


check buttonFusion gene breakpoints across LRRC8A (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 MEN1 (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
ChimerDB4UCECTCGA-E6-A8L9-01ALRRC8Achr9

131644529

-MEN1chr11

64578377

-
ChimerDB4UCECTCGA-E6-A8L9-01ALRRC8Achr9

131644529

+MEN1chr11

64578377

-
ChimerDB4UCECTCGA-E6-A8L9LRRC8Achr9

131644529

+MEN1chr11

64578377

-


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Fusion Gene ORF analysis for LRRC8A-MEN1

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
5UTR-5UTRENST00000372599ENST00000337652LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-5UTRENST00000372599ENST00000394376LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-5UTRENST00000372600ENST00000337652LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-5UTRENST00000372600ENST00000394376LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000312049LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000315422LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000377313LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000377316LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000377321LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000377326LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000394374LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000443283LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372599ENST00000478548LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000312049LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000315422LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000377313LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000377316LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000377321LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000377326LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000394374LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000443283LRRC8Achr9

131644529

+MEN1chr11

64578377

-
5UTR-intronENST00000372600ENST00000478548LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-5UTRENST00000259324ENST00000337652LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-5UTRENST00000259324ENST00000394376LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-5UTRENST00000492784ENST00000337652LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-5UTRENST00000492784ENST00000394376LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000312049LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000315422LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000377313LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000377316LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000377321LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000377326LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000394374LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000443283LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000259324ENST00000478548LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000312049LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000315422LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000377313LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000377316LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000377321LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000377326LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000394374LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000443283LRRC8Achr9

131644529

+MEN1chr11

64578377

-
intron-intronENST00000492784ENST00000478548LRRC8Achr9

131644529

+MEN1chr11

64578377

-

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 LRRC8A-MEN1


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 LRRC8A-MEN1


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/:131644529/:64578377)
- 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
LRRC8A

Q8IWT6

MEN1

O00255

FUNCTION: Essential component of the volume-regulated anion channel (VRAC, also named VSOAC channel), an anion channel required to maintain a constant cell volume in response to extracellular or intracellular osmotic changes (PubMed:24725410, PubMed:29769723, PubMed:24790029, PubMed:26530471, PubMed:26824658, PubMed:28193731). The VRAC channel conducts iodide better than chloride and can also conduct organic osmolytes like taurine (PubMed:24725410, PubMed:30095067, PubMed:24790029, PubMed:26530471, PubMed:26824658, PubMed:28193731). Mediates efflux of amino acids, such as aspartate and glutamate, in response to osmotic stress (PubMed:28193731). LRRC8A and LRRC8D are required for the uptake of the drug cisplatin (PubMed:26530471). In complex with LRRC8C or LRRC8E, acts as a transporter of immunoreactive cyclic dinucleotide GMP-AMP (2'-3'-cGAMP), an immune messenger produced in response to DNA virus in the cytosol: mediates both import and export of 2'-3'-cGAMP, thereby promoting transfer of 2'-3'-cGAMP to bystander cells (PubMed:33171122). In contrast, complexes containing LRRC8D inhibit transport of 2'-3'-cGAMP (PubMed:33171122). Required for in vivo channel activity, together with at least one other family member (LRRC8B, LRRC8C, LRRC8D or LRRC8E); channel characteristics depend on the precise subunit composition (PubMed:24790029, PubMed:26824658, PubMed:28193731). Can form functional channels by itself (in vitro) (PubMed:26824658). Involved in B-cell development: required for the pro-B cell to pre-B cell transition (PubMed:14660746). Also required for T-cell development (By similarity). Required for myoblast differentiation: VRAC activity promotes membrane hyperpolarization and regulates insulin-stimulated glucose metabolism and oxygen consumption (By similarity). Also acts as a regulator of glucose-sensing in pancreatic beta cells: VRAC currents, generated in response to hypotonicity- or glucose-induced beta cell swelling, depolarize cells, thereby causing electrical excitation, leading to increase glucose sensitivity and insulin secretion (PubMed:29371604). Also plays a role in lysosome homeostasis by forming functional lysosomal VRAC channels in response to low cytoplasmic ionic strength condition: lysosomal VRAC channels are necessary for the formation of large lysosome-derived vacuoles, which store and then expel excess water to maintain cytosolic water homeostasis (PubMed:31270356, PubMed:33139539). {ECO:0000250|UniProtKB:Q80WG5, ECO:0000269|PubMed:14660746, ECO:0000269|PubMed:24725410, ECO:0000269|PubMed:24790029, ECO:0000269|PubMed:26530471, ECO:0000269|PubMed:26824658, ECO:0000269|PubMed:28193731, ECO:0000269|PubMed:29371604, ECO:0000269|PubMed:29769723, ECO:0000269|PubMed:30095067, ECO:0000269|PubMed:31270356, ECO:0000269|PubMed:33139539, ECO:0000269|PubMed:33171122}.FUNCTION: Essential component of a MLL/SET1 histone methyltransferase (HMT) complex, a complex that specifically methylates 'Lys-4' of histone H3 (H3K4). Functions as a transcriptional regulator. Binds to the TERT promoter and represses telomerase expression. Plays a role in TGFB1-mediated inhibition of cell-proliferation, possibly regulating SMAD3 transcriptional activity. Represses JUND-mediated transcriptional activation on AP1 sites, as well as that mediated by NFKB subunit RELA. Positively regulates HOXC8 and HOXC6 gene expression. May be involved in normal hematopoiesis through the activation of HOXA9 expression (By similarity). May be involved in DNA repair. {ECO:0000250|UniProtKB:O88559, ECO:0000269|PubMed:11274402, ECO:0000269|PubMed:11526476, ECO:0000269|PubMed:12837246, ECO:0000269|PubMed:12874027, ECO:0000269|PubMed:14992727, ECO:0000269|PubMed:22327296}.

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 LRRC8A-MEN1


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 LRRC8A-MEN1


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 LRRC8A-MEN1


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 LRRC8A-MEN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource