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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:ACVR1-GNLY (FusionGDB2 ID:HG90TG10578)

Fusion Gene Summary for ACVR1-GNLY

check button Fusion gene summary
Fusion gene informationFusion gene name: ACVR1-GNLY
Fusion gene ID: hg90tg10578
HgeneTgene
Gene symbol

ACVR1

GNLY

Gene ID

90

10578

Gene nameactivin A receptor type 1granulysin
SynonymsACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRID2S69E|LAG-2|LAG2|NKG5|TLA519
Cytomap('ACVR1')('GNLY')

2q24.1

2p11.2

Type of geneprotein-codingprotein-coding
Descriptionactivin receptor type-1TGF-B superfamily receptor type Iactivin A receptor, type Iactivin A receptor, type II-like kinase 2activin receptor type Iactivin receptor-like kinase 2hydroxyalkyl-protein kinaseserine/threonine-protein kinase receptor R1granulysinT-cell activation protein 519T-lymphocyte activation gene 519lymphocyte-activation gene 2lymphokine LAG-2
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000434821, ENST00000263640, 
ENST00000409283, ENST00000410057, 
ENST00000487456, 
Fusion gene scores* DoF score4 X 5 X 4=804 X 3 X 4=48
# samples 76
** MAII scorelog2(7/80*10)=-0.192645077942396
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/48*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ACVR1 [Title/Abstract] AND GNLY [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointACVR1(158732308)-GNLY(85922443), # samples:2
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
HgeneACVR1

GO:0006468

protein phosphorylation

12065756|19506109

HgeneACVR1

GO:0007179

transforming growth factor beta receptor signaling pathway

8242742

HgeneACVR1

GO:0010862

positive regulation of pathway-restricted SMAD protein phosphorylation

19506109

HgeneACVR1

GO:0018107

peptidyl-threonine phosphorylation

19736306

HgeneACVR1

GO:0030509

BMP signaling pathway

18436533

HgeneACVR1

GO:0032924

activin receptor signaling pathway

19506109

HgeneACVR1

GO:0045893

positive regulation of transcription, DNA-templated

8242742

HgeneACVR1

GO:0045944

positive regulation of transcription by RNA polymerase II

19506109

HgeneACVR1

GO:0060389

pathway-restricted SMAD protein phosphorylation

19736306

HgeneACVR1

GO:2000017

positive regulation of determination of dorsal identity

19506109

TgeneGNLY

GO:0006968

cellular defense response

9756476

TgeneGNLY

GO:0031640

killing of cells of other organism

9756476

TgeneGNLY

GO:0042742

defense response to bacterium

9756476

TgeneGNLY

GO:0061844

antimicrobial humoral immune response mediated by antimicrobial peptide

9756476



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
ChimerDB4OVTCGA-30-1714-01AACVR1chr2

158732308

-GNLYchr2

85922443

+
ChimerDB4OVTCGA-30-1714ACVR1chr2

158732307

-GNLYchr2

85922442

+


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Fusion Gene ORF analysis for ACVR1-GNLY

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-3CDSENST00000434821ENST00000263863ACVR1chr2

158732308

-GNLYchr2

85922443

+
5UTR-3CDSENST00000434821ENST00000263863ACVR1chr2

158732307

-GNLYchr2

85922442

+
5UTR-3CDSENST00000434821ENST00000524600ACVR1chr2

158732308

-GNLYchr2

85922443

+
5UTR-3CDSENST00000434821ENST00000524600ACVR1chr2

158732307

-GNLYchr2

85922442

+
5UTR-3UTRENST00000434821ENST00000409696ACVR1chr2

158732308

-GNLYchr2

85922443

+
5UTR-3UTRENST00000434821ENST00000409696ACVR1chr2

158732307

-GNLYchr2

85922442

+
5UTR-3UTRENST00000434821ENST00000533041ACVR1chr2

158732308

-GNLYchr2

85922443

+
5UTR-3UTRENST00000434821ENST00000533041ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3CDSENST00000263640ENST00000263863ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3CDSENST00000263640ENST00000263863ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3CDSENST00000263640ENST00000524600ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3CDSENST00000263640ENST00000524600ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3CDSENST00000409283ENST00000263863ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3CDSENST00000409283ENST00000263863ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3CDSENST00000409283ENST00000524600ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3CDSENST00000409283ENST00000524600ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3CDSENST00000410057ENST00000263863ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3CDSENST00000410057ENST00000263863ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3CDSENST00000410057ENST00000524600ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3CDSENST00000410057ENST00000524600ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3CDSENST00000487456ENST00000263863ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3CDSENST00000487456ENST00000263863ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3CDSENST00000487456ENST00000524600ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3CDSENST00000487456ENST00000524600ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3UTRENST00000263640ENST00000409696ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3UTRENST00000263640ENST00000409696ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3UTRENST00000263640ENST00000533041ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3UTRENST00000263640ENST00000533041ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3UTRENST00000409283ENST00000409696ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3UTRENST00000409283ENST00000409696ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3UTRENST00000409283ENST00000533041ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3UTRENST00000409283ENST00000533041ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3UTRENST00000410057ENST00000409696ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3UTRENST00000410057ENST00000409696ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3UTRENST00000410057ENST00000533041ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3UTRENST00000410057ENST00000533041ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3UTRENST00000487456ENST00000409696ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3UTRENST00000487456ENST00000409696ACVR1chr2

158732307

-GNLYchr2

85922442

+
intron-3UTRENST00000487456ENST00000533041ACVR1chr2

158732308

-GNLYchr2

85922443

+
intron-3UTRENST00000487456ENST00000533041ACVR1chr2

158732307

-GNLYchr2

85922442

+

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 ACVR1-GNLY


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)
ACVR1chr2158732307-GNLYchr285922442+0.0013236270.99867636
ACVR1chr2158732307-GNLYchr285922442+0.0013236270.99867636
ACVR1chr2158732307-GNLYchr285922442+0.0013236270.99867636
ACVR1chr2158732307-GNLYchr285922442+0.0013236270.99867636


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 ACVR1-GNLY


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/:158732308/:85922443)
- 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 ACVR1-GNLY


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 ACVR1-GNLY


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 ACVR1-GNLY


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 ACVR1-GNLY


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneACVR1C0016037Fibrodysplasia Ossificans Progressiva5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneACVR1C0017638Glioma3CGI;CTD_human
HgeneACVR1C0259783mixed gliomas3CTD_human
HgeneACVR1C0555198Malignant Glioma3CTD_human
HgeneACVR1C0004114Astrocytoma1CTD_human
HgeneACVR1C0006142Malignant neoplasm of breast1CTD_human
HgeneACVR1C0085576Iron-Refractory Iron Deficiency Anemia1GENOMICS_ENGLAND
HgeneACVR1C0205768Subependymal Giant Cell Astrocytoma1CTD_human
HgeneACVR1C0242488Acute Lung Injury1CTD_human
HgeneACVR1C0280783Juvenile Pilocytic Astrocytoma1CTD_human
HgeneACVR1C0280785Diffuse Astrocytoma1CTD_human
HgeneACVR1C0334579Anaplastic astrocytoma1CTD_human
HgeneACVR1C0334580Protoplasmic astrocytoma1CTD_human
HgeneACVR1C0334581Gemistocytic astrocytoma1CTD_human
HgeneACVR1C0334582Fibrillary Astrocytoma1CTD_human
HgeneACVR1C0334583Pilocytic Astrocytoma1CTD_human
HgeneACVR1C0338070Childhood Cerebral Astrocytoma1CTD_human
HgeneACVR1C0547065Mixed oligoastrocytoma1CTD_human
HgeneACVR1C0678222Breast Carcinoma1CTD_human
HgeneACVR1C0750935Cerebral Astrocytoma1CTD_human
HgeneACVR1C0750936Intracranial Astrocytoma1CTD_human
HgeneACVR1C1257931Mammary Neoplasms, Human1CTD_human
HgeneACVR1C1458155Mammary Neoplasms1CTD_human
HgeneACVR1C1704230Grade I Astrocytoma1CTD_human
HgeneACVR1C4704874Mammary Carcinoma, Human1CTD_human