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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:CASC1-C1orf53 (FusionGDB2 ID:HG55259TG388722)

Fusion Gene Summary for CASC1-C1orf53

check button Fusion gene summary
Fusion gene informationFusion gene name: CASC1-C1orf53
Fusion gene ID: hg55259tg388722
HgeneTgene
Gene symbol

CASC1

C1orf53

Gene ID

55259

388722

Gene namecancer susceptibility 1chromosome 1 open reading frame 53
SynonymsLAS1|PPP1R54-
Cytomap('CASC1')('C1orf53')

12p12.1

1q31.3

Type of geneprotein-codingprotein-coding
Descriptionprotein CASC1cancer susceptibility candidate 1cancer susceptibility candidate gene 1 proteinlung adenoma susceptibility 1-like proteinprotein phosphatase 1 regulatory subunit 54uncharacterized protein C1orf53
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000320267, ENST00000395987, 
ENST00000545133, ENST00000395990, 
ENST00000537577, ENST00000557684, 
ENST00000354189, 
Fusion gene scores* DoF score7 X 4 X 4=1122 X 1 X 2=4
# samples 82
** MAII scorelog2(8/112*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/4*10)=2.32192809488736
Context

PubMed: CASC1 [Title/Abstract] AND C1orf53 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCASC1(25348009)-C1orf53(197874925), # samples:1
Anticipated loss of major functional domain due to fusion event.CASC1-C1orf53 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CASC1-C1orf53 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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

check buttonFusion gene breakpoints across CASC1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across C1orf53 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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-10-0931CASC1chr12

25348009

-C1orf53chr1

197874925

+


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Fusion Gene ORF analysis for CASC1-C1orf53

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-3UTRENST00000320267ENST00000542800CASC1chr12

25348009

-C1orf53chr1

197874925

+
5CDS-3UTRENST00000395987ENST00000542800CASC1chr12

25348009

-C1orf53chr1

197874925

+
5CDS-3UTRENST00000545133ENST00000542800CASC1chr12

25348009

-C1orf53chr1

197874925

+
5UTR-3CDSENST00000395990ENST00000367393CASC1chr12

25348009

-C1orf53chr1

197874925

+
5UTR-3CDSENST00000537577ENST00000367393CASC1chr12

25348009

-C1orf53chr1

197874925

+
5UTR-3CDSENST00000557684ENST00000367393CASC1chr12

25348009

-C1orf53chr1

197874925

+
5UTR-3UTRENST00000395990ENST00000542800CASC1chr12

25348009

-C1orf53chr1

197874925

+
5UTR-3UTRENST00000537577ENST00000542800CASC1chr12

25348009

-C1orf53chr1

197874925

+
5UTR-3UTRENST00000557684ENST00000542800CASC1chr12

25348009

-C1orf53chr1

197874925

+
In-frameENST00000320267ENST00000367393CASC1chr12

25348009

-C1orf53chr1

197874925

+
In-frameENST00000395987ENST00000367393CASC1chr12

25348009

-C1orf53chr1

197874925

+
In-frameENST00000545133ENST00000367393CASC1chr12

25348009

-C1orf53chr1

197874925

+
intron-3CDSENST00000354189ENST00000367393CASC1chr12

25348009

-C1orf53chr1

197874925

+
intron-3UTRENST00000354189ENST00000542800CASC1chr12

25348009

-C1orf53chr1

197874925

+

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)
ENST00000395987CASC1chr1225348009-ENST00000367393C1orf53chr1197874925+390698526760
ENST00000320267CASC1chr1225348009-ENST00000367393C1orf53chr1197874925+4068510128360
ENST00000545133CASC1chr1225348009-ENST00000367393C1orf53chr1197874925+372516724960

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
ENST00000395987ENST00000367393CASC1chr1225348009-C1orf53chr1197874925+0.815022230.18497775
ENST00000320267ENST00000367393CASC1chr1225348009-C1orf53chr1197874925+0.7415380.25846198
ENST00000545133ENST00000367393CASC1chr1225348009-C1orf53chr1197874925+0.6820010.317999

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Fusion Genomic Features for CASC1-C1orf53


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)
CASC1chr1225348009-C1orf53chr1197874925+2.43E-050.9999757
CASC1chr1225348009-C1orf53chr1197874925+2.43E-050.9999757

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.
genomic feature

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 CASC1-C1orf53


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/chr12:25348009/chr1:197874925)
- 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
HgeneCASC1chr12:25348009chr1:197874925ENST00000320267-11520_881717.0Compositional biasNote=Glu-rich
HgeneCASC1chr12:25348009chr1:197874925ENST00000320267-1155_81717.0Compositional biasNote=Poly-Lys
HgeneCASC1chr12:25348009chr1:197874925ENST00000354189-11620_880691.0Compositional biasNote=Glu-rich
HgeneCASC1chr12:25348009chr1:197874925ENST00000354189-1165_80691.0Compositional biasNote=Poly-Lys
HgeneCASC1chr12:25348009chr1:197874925ENST00000395990-11720_880677.0Compositional biasNote=Glu-rich
HgeneCASC1chr12:25348009chr1:197874925ENST00000395990-1175_80677.0Compositional biasNote=Poly-Lys
HgeneCASC1chr12:25348009chr1:197874925ENST00000545133-11320_881658.0Compositional biasNote=Glu-rich
HgeneCASC1chr12:25348009chr1:197874925ENST00000545133-1135_81658.0Compositional biasNote=Poly-Lys


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Fusion Gene Sequence for CASC1-C1orf53


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.
>13124_13124_1_CASC1-C1orf53_CASC1_chr12_25348009_ENST00000320267_C1orf53_chr1_197874925_ENST00000367393_length(transcript)=406nt_BP=85nt
GTCGTCCGGGCAACCCGGGAGCGTTTGTCCACACAATTTCTGCTCCGACTCTGCGGACTACTGCAGTGGAGCTTGACTCTTAATGGCTGG
CCAGCTAAACTATGTGGATCCAGCTACTGGCTATGTGGTGCTCACACAGATTGCCCACTTGCAAAGAGGTGAATGTTGTGGCTCTGCGTG
CAGACATTGTCCATATGGTCAAGTCAATGTTAAAGATCCATCTAAAAAGAAGCAATTCAATTCATATTTTTATGTTTGACAAGAATTTCA
TCTCTGTTCCCTAACTGTGCTTGTATTTTTTAAAAAATAAAGCCCCAATTCAGAATTGCTGGATTATTAGTACTTGAACACTAGTTTAAT

>13124_13124_1_CASC1-C1orf53_CASC1_chr12_25348009_ENST00000320267_C1orf53_chr1_197874925_ENST00000367393_length(amino acids)=60AA_BP=

--------------------------------------------------------------
>13124_13124_2_CASC1-C1orf53_CASC1_chr12_25348009_ENST00000395987_C1orf53_chr1_197874925_ENST00000367393_length(transcript)=390nt_BP=69nt
GGGAGCGTTTGTCCACACAATTTCTGCTCCGACTCTGCGGACTACTGCAGTGGAGCTTGACTCTTAATGGCTGGCCAGCTAAACTATGTG
GATCCAGCTACTGGCTATGTGGTGCTCACACAGATTGCCCACTTGCAAAGAGGTGAATGTTGTGGCTCTGCGTGCAGACATTGTCCATAT
GGTCAAGTCAATGTTAAAGATCCATCTAAAAAGAAGCAATTCAATTCATATTTTTATGTTTGACAAGAATTTCATCTCTGTTCCCTAACT
GTGCTTGTATTTTTTAAAAAATAAAGCCCCAATTCAGAATTGCTGGATTATTAGTACTTGAACACTAGTTTAATCCTAAATACATATATT

>13124_13124_2_CASC1-C1orf53_CASC1_chr12_25348009_ENST00000395987_C1orf53_chr1_197874925_ENST00000367393_length(amino acids)=60AA_BP=

--------------------------------------------------------------
>13124_13124_3_CASC1-C1orf53_CASC1_chr12_25348009_ENST00000545133_C1orf53_chr1_197874925_ENST00000367393_length(transcript)=372nt_BP=51nt
AATTTCTGCTCCGACTCTGCGGACTACTGCAGTGGAGCTTGACTCTTAATGGCTGGCCAGCTAAACTATGTGGATCCAGCTACTGGCTAT
GTGGTGCTCACACAGATTGCCCACTTGCAAAGAGGTGAATGTTGTGGCTCTGCGTGCAGACATTGTCCATATGGTCAAGTCAATGTTAAA
GATCCATCTAAAAAGAAGCAATTCAATTCATATTTTTATGTTTGACAAGAATTTCATCTCTGTTCCCTAACTGTGCTTGTATTTTTTAAA
AAATAAAGCCCCAATTCAGAATTGCTGGATTATTAGTACTTGAACACTAGTTTAATCCTAAATACATATATTAAAAGAACATCAATAAAA

>13124_13124_3_CASC1-C1orf53_CASC1_chr12_25348009_ENST00000545133_C1orf53_chr1_197874925_ENST00000367393_length(amino acids)=60AA_BP=

--------------------------------------------------------------

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Fusion Gene PPI Analysis for CASC1-C1orf53


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 CASC1-C1orf53


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 CASC1-C1orf53


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCASC1C0024121Lung Neoplasms1CTD_human
HgeneCASC1C0242379Malignant neoplasm of lung1CTD_human