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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:PRKAR1A-BCAS3 (FusionGDB2 ID:68651)

Fusion Gene Summary for PRKAR1A-BCAS3

check button Fusion gene summary
Fusion gene informationFusion gene name: PRKAR1A-BCAS3
Fusion gene ID: 68651
HgeneTgene
Gene symbol

PRKAR1A

BCAS3

Gene ID

5573

54828

Gene nameprotein kinase cAMP-dependent type I regulatory subunit alphaBCAS3 microtubule associated cell migration factor
SynonymsACRDYS1|ADOHR|CAR|CNC|CNC1|PKR1|PPNAD1|PRKAR1|TSE1GAOB1|MAAB
Cytomap

17q24.2

17q23.2

Type of geneprotein-codingprotein-coding
DescriptioncAMP-dependent protein kinase type I-alpha regulatory subunitCarney complex type 1cAMP-dependent protein kinase regulatory subunit RIalphacAMP-dependent protein kinase type I-alpha regulatory chainepididymis secretory sperm binding proteinprotein kinbreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1
Modification date2020032920200313
UniProtAcc.

Q9H6U6

Ensembl transtripts involved in fusion geneENST00000358598, ENST00000392711, 
ENST00000536854, ENST00000586397, 
ENST00000588188, ENST00000589228, 
ENST00000585812, ENST00000390652, 
ENST00000407086, ENST00000408905, 
ENST00000585744, ENST00000588462, 
ENST00000588874, ENST00000589222, 
Fusion gene scores* DoF score15 X 15 X 8=180045 X 32 X 19=27360
# samples 1853
** MAII scorelog2(18/1800*10)=-3.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(53/27360*10)=-5.6899320603227
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRKAR1A [Title/Abstract] AND BCAS3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRKAR1A(66511717)-BCAS3(59445688), # samples:2
Anticipated loss of major functional domain due to fusion event.PRKAR1A-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PRKAR1A-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
PRKAR1A-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PRKAR1A-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PRKAR1A-BCAS3 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
HgenePRKAR1A

GO:2000480

negative regulation of cAMP-dependent protein kinase activity

21812984

TgeneBCAS3

GO:0043085

positive regulation of catalytic activity

17505058

TgeneBCAS3

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

TgeneBCAS3

GO:0071391

cellular response to estrogen stimulus

17505058


check buttonFusion gene breakpoints across PRKAR1A (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 BCAS3 (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
ChimerDB4BRCATCGA-D8-A140-01APRKAR1Achr17

66511717

+BCAS3chr17

59445688

+


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Fusion Gene ORF analysis for PRKAR1A-BCAS3

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-3UTRENST00000358598ENST00000585812PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
5CDS-3UTRENST00000392711ENST00000585812PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
5CDS-3UTRENST00000536854ENST00000585812PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
5CDS-3UTRENST00000586397ENST00000585812PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
5CDS-3UTRENST00000588188ENST00000585812PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
5CDS-3UTRENST00000589228ENST00000585812PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000358598ENST00000390652PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000358598ENST00000407086PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000358598ENST00000408905PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000358598ENST00000585744PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000358598ENST00000588462PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000358598ENST00000588874PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000358598ENST00000589222PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000392711ENST00000390652PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000392711ENST00000407086PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000392711ENST00000408905PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000392711ENST00000585744PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000392711ENST00000588462PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000392711ENST00000588874PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000392711ENST00000589222PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000536854ENST00000390652PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000536854ENST00000407086PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000536854ENST00000408905PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000536854ENST00000585744PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000536854ENST00000588462PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000536854ENST00000588874PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000536854ENST00000589222PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000586397ENST00000390652PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000586397ENST00000407086PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000586397ENST00000408905PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000586397ENST00000585744PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000586397ENST00000588462PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000586397ENST00000588874PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000586397ENST00000589222PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000588188ENST00000390652PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000588188ENST00000407086PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000588188ENST00000408905PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000588188ENST00000585744PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000588188ENST00000588462PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000588188ENST00000588874PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000588188ENST00000589222PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000589228ENST00000390652PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000589228ENST00000407086PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000589228ENST00000408905PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000589228ENST00000585744PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000589228ENST00000588462PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000589228ENST00000588874PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+
Frame-shiftENST00000589228ENST00000589222PRKAR1Achr17

66511717

+BCAS3chr17

59445688

+

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 PRKAR1A-BCAS3


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)
PRKAR1Achr1766511717+BCAS3chr1759445687+1.17E-081
PRKAR1Achr1766511717+BCAS3chr1759445687+1.17E-081

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.
genomic feature of top 1%

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Fusion Protein Features for PRKAR1A-BCAS3


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/:66511717/:59445688)
- 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
.BCAS3

Q9H6U6

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: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.

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 PRKAR1A-BCAS3


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 PRKAR1A-BCAS3


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 PRKAR1A-BCAS3


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 PRKAR1A-BCAS3


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