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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:LYPD6B-ACVR1 (FusionGDB2 ID:50456)

Fusion Gene Summary for LYPD6B-ACVR1

check button Fusion gene summary
Fusion gene informationFusion gene name: LYPD6B-ACVR1
Fusion gene ID: 50456
HgeneTgene
Gene symbol

LYPD6B

ACVR1

Gene ID

130576

90

Gene nameLY6/PLAUR domain containing 6Bactivin A receptor type 1
SynonymsCT116|LYPD7ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI
Cytomap

2q23.2

2q24.1

Type of geneprotein-codingprotein-coding
Descriptionly6/PLAUR domain-containing protein 6Bcancer/testis antigen 116activin 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 R1
Modification date2020031320200320
UniProtAcc.

Q8NER5

Ensembl transtripts involved in fusion geneENST00000409642, ENST00000409876, 
ENST00000280115, ENST00000409029, 
ENST00000450639, ENST00000498249, 
ENST00000263640, ENST00000410057, 
ENST00000434821, ENST00000409283, 
ENST00000487456, 
Fusion gene scores* DoF score6 X 3 X 5=905 X 5 X 3=75
# samples 65
** MAII scorelog2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LYPD6B [Title/Abstract] AND ACVR1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLYPD6B(149895315)-ACVR1(158675071), # 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
TgeneACVR1

GO:0006468

protein phosphorylation

12065756|19506109

TgeneACVR1

GO:0007179

transforming growth factor beta receptor signaling pathway

8242742

TgeneACVR1

GO:0010862

positive regulation of pathway-restricted SMAD protein phosphorylation

19506109

TgeneACVR1

GO:0018107

peptidyl-threonine phosphorylation

19736306

TgeneACVR1

GO:0030509

BMP signaling pathway

18436533

TgeneACVR1

GO:0032924

activin receptor signaling pathway

19506109

TgeneACVR1

GO:0045893

positive regulation of transcription, DNA-templated

8242742

TgeneACVR1

GO:0045944

positive regulation of transcription by RNA polymerase II

19506109

TgeneACVR1

GO:0060389

pathway-restricted SMAD protein phosphorylation

19736306

TgeneACVR1

GO:2000017

positive regulation of determination of dorsal identity

19506109


check buttonFusion gene breakpoints across LYPD6B (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 ACVR1 (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
ChimerDB4Non-Cancer271NLYPD6Bchr2

149895315

+ACVR1chr2

158675071

-


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Fusion Gene ORF analysis for LYPD6B-ACVR1

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-5UTRENST00000409642ENST00000263640LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-5UTRENST00000409642ENST00000410057LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-5UTRENST00000409642ENST00000434821LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-5UTRENST00000409876ENST00000263640LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-5UTRENST00000409876ENST00000410057LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-5UTRENST00000409876ENST00000434821LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-intronENST00000409642ENST00000409283LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-intronENST00000409642ENST00000487456LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-intronENST00000409876ENST00000409283LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
5UTR-intronENST00000409876ENST00000487456LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000280115ENST00000263640LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000280115ENST00000410057LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000280115ENST00000434821LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000409029ENST00000263640LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000409029ENST00000410057LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000409029ENST00000434821LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000450639ENST00000263640LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000450639ENST00000410057LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000450639ENST00000434821LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000498249ENST00000263640LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000498249ENST00000410057LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-5UTRENST00000498249ENST00000434821LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-intronENST00000280115ENST00000409283LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-intronENST00000280115ENST00000487456LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-intronENST00000409029ENST00000409283LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-intronENST00000409029ENST00000487456LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-intronENST00000450639ENST00000409283LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-intronENST00000450639ENST00000487456LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-intronENST00000498249ENST00000409283LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-
intron-intronENST00000498249ENST00000487456LYPD6Bchr2

149895315

+ACVR1chr2

158675071

-

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 LYPD6B-ACVR1


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 LYPD6B-ACVR1


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/:149895315/:158675071)
- 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
.ACVR1

Q8NER5

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: Serine/threonine protein kinase which forms a receptor complex on ligand binding. The receptor complex consisting of 2 type II and 2 type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators, SMAD2 and SMAD3. Receptor for activin AB, activin B and NODAL. Plays a role in cell differentiation, growth arrest and apoptosis. {ECO:0000269|PubMed:12063393, ECO:0000269|PubMed:15531507}.

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 LYPD6B-ACVR1


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 LYPD6B-ACVR1


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 LYPD6B-ACVR1


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 LYPD6B-ACVR1


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