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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:FAM20A-PRKAR1A (FusionGDB2 ID:28884)

Fusion Gene Summary for FAM20A-PRKAR1A

check button Fusion gene summary
Fusion gene informationFusion gene name: FAM20A-PRKAR1A
Fusion gene ID: 28884
HgeneTgene
Gene symbol

FAM20A

PRKAR1A

Gene ID

54757

5573

Gene nameFAM20A golgi associated secretory pathway pseudokinaseprotein kinase cAMP-dependent type I regulatory subunit alpha
SynonymsAI1G|AIGFS|FP2747ACRDYS1|ADOHR|CAR|CNC|CNC1|PKR1|PPNAD1|PRKAR1|TSE1
Cytomap

17q24.2

17q24.2

Type of geneprotein-codingprotein-coding
Descriptionpseudokinase FAM20Afamily with sequence similarity 20, member Aprotein FAM20AcAMP-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 kin
Modification date2020031320200329
UniProtAcc

Q96MK3

P10644

Ensembl transtripts involved in fusion geneENST00000226094, ENST00000592554, 
ENST00000358598, ENST00000392711, 
ENST00000536854, ENST00000586397, 
ENST00000589228, ENST00000588188, 
Fusion gene scores* DoF score4 X 5 X 2=4013 X 16 X 6=1248
# samples 717
** MAII scorelog2(7/40*10)=0.807354922057604
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(17/1248*10)=-2.87601128272455
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FAM20A [Title/Abstract] AND PRKAR1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFAM20A(66526418)-PRKAR1A(66526542), # samples:1
FAM20A(66526418)-PRKAR1A(66526463), # samples:1
FAM20A(66526418)-PRKAR1A(66526471), # samples:1
FAM20A(66528783)-PRKAR1A(66528066), # samples:1
PRKAR1A(66527977)-FAM20A(66528006), # 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
HgeneFAM20A

GO:0001934

positive regulation of protein phosphorylation

25789606

TgenePRKAR1A

GO:2000480

negative regulation of cAMP-dependent protein kinase activity

21812984


check buttonFusion gene breakpoints across FAM20A (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 PRKAR1A (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
ChiTaRS5.0N/AAW608309FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
ChiTaRS5.0N/ABE770868FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
ChiTaRS5.0N/ABE770917FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
ChiTaRS5.0N/ACN478669FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+


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Fusion Gene ORF analysis for FAM20A-PRKAR1A

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
intron-3CDSENST00000226094ENST00000358598FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000226094ENST00000358598FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000226094ENST00000358598FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000226094ENST00000392711FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000226094ENST00000392711FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000226094ENST00000392711FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000226094ENST00000536854FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000226094ENST00000536854FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000226094ENST00000536854FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000226094ENST00000586397FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000226094ENST00000586397FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000226094ENST00000586397FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000226094ENST00000589228FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000226094ENST00000589228FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000226094ENST00000589228FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000592554ENST00000358598FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000592554ENST00000358598FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000592554ENST00000358598FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000592554ENST00000392711FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000592554ENST00000392711FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000592554ENST00000392711FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000592554ENST00000536854FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000592554ENST00000536854FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000592554ENST00000536854FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000592554ENST00000586397FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000592554ENST00000586397FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000592554ENST00000586397FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3CDSENST00000592554ENST00000589228FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-3CDSENST00000592554ENST00000589228FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-3CDSENST00000592554ENST00000589228FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-3UTRENST00000226094ENST00000358598FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-3UTRENST00000226094ENST00000392711FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-3UTRENST00000226094ENST00000536854FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-3UTRENST00000226094ENST00000589228FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-3UTRENST00000592554ENST00000358598FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-3UTRENST00000592554ENST00000392711FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-3UTRENST00000592554ENST00000536854FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-3UTRENST00000592554ENST00000589228FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-intronENST00000226094ENST00000586397FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-intronENST00000226094ENST00000588188FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-intronENST00000226094ENST00000588188FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-intronENST00000226094ENST00000588188FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-intronENST00000226094ENST00000588188FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-intronENST00000592554ENST00000586397FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+
intron-intronENST00000592554ENST00000588188FAM20Achr17

66526418

-PRKAR1Achr17

66526542

-
intron-intronENST00000592554ENST00000588188FAM20Achr17

66526418

-PRKAR1Achr17

66526463

-
intron-intronENST00000592554ENST00000588188FAM20Achr17

66526418

-PRKAR1Achr17

66526471

-
intron-intronENST00000592554ENST00000588188FAM20Achr17

66528783

-PRKAR1Achr17

66528066

+

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 FAM20A-PRKAR1A


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 FAM20A-PRKAR1A


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/:66526418/:66526542)
- 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
FAM20A

Q96MK3

PRKAR1A

P10644

FUNCTION: Pseudokinase that acts as an allosteric activator of the Golgi serine/threonine protein kinase FAM20C and is involved in biomineralization of teeth. Forms a complex with FAM20C and increases the ability of FAM20C to phosphorylate the proteins that form the 'matrix' that guides the deposition of the enamel minerals. {ECO:0000269|PubMed:25789606}.FUNCTION: Regulatory subunit of the cAMP-dependent protein kinases involved in cAMP signaling in cells. {ECO:0000269|PubMed:16491121, ECO:0000269|PubMed:20215566, ECO:0000269|PubMed:26405036}.

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 FAM20A-PRKAR1A


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 FAM20A-PRKAR1A


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 FAM20A-PRKAR1A


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 FAM20A-PRKAR1A


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