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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:CCDC6-LIPI (FusionGDB2 ID:HG8030TG149998)

Fusion Gene Summary for CCDC6-LIPI

check button Fusion gene summary
Fusion gene informationFusion gene name: CCDC6-LIPI
Fusion gene ID: hg8030tg149998
HgeneTgene
Gene symbol

CCDC6

LIPI

Gene ID

8030

149998

Gene namecoiled-coil domain containing 6lipase I
SynonymsD10S170|H4|PTC|TPC|TST1CT17|LPDL|PLA1C|PRED5|mPA-PLA1 beta
Cytomap('CCDC6')('LIPI')

10q21.2

21q11.2

Type of geneprotein-codingprotein-coding
Descriptioncoiled-coil domain-containing protein 6papillary thyroid carcinoma-encoded proteinlipase member ILPD lipasecancer/testis antigen 17lipase, member Imembrane-associated phosphatidic acid-selective phospholipase A1-beta
Modification date2020032720200313
UniProtAcc

Q16204

.
Ensembl transtripts involved in fusion geneENST00000263102, 
Fusion gene scores* DoF score15 X 22 X 10=33003 X 3 X 2=18
# samples 383
** MAII scorelog2(38/3300*10)=-3.11839470080223
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CCDC6 [Title/Abstract] AND LIPI [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCCDC6(61612311)-LIPI(15481401), # samples:3
Anticipated loss of major functional domain due to fusion event.CCDC6-LIPI 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.
CCDC6-LIPI 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.
CCDC6-LIPI 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.
CCDC6-LIPI 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.
CCDC6-LIPI seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CCDC6-LIPI seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CCDC6-LIPI 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
TgeneLIPI

GO:0016042

lipid catabolic process

12963729


check buttonFusion gene breakpoints across CCDC6 (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 LIPI (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
ChimerDB4LUADTCGA-44-8117-01ACCDC6chr10

61612311

-LIPIchr21

15481401

-


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Fusion Gene ORF analysis for CCDC6-LIPI

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
Frame-shiftENST00000263102ENST00000344577CCDC6chr10

61612311

-LIPIchr21

15481401

-
In-frameENST00000263102ENST00000536861CCDC6chr10

61612311

-LIPIchr21

15481401

-

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)
ENST00000263102CCDC6chr1061612311-ENST00000536861LIPIchr2115481401-953685109705198

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
ENST00000263102ENST00000536861CCDC6chr1061612311-LIPIchr2115481401-0.0066615720.99333847

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Fusion Genomic Features for CCDC6-LIPI


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.
genomic feature

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Fusion Protein Features for CCDC6-LIPI


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/chr10:61612311/chr21:15481401)
- 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
CCDC6

Q16204

.
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
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-2917_20151475.0Compositional biasNote=Poly-Ser
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-2932_44151475.0Compositional biasNote=Poly-Gly
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29106_134151475.0RepeatNote=1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29253_332151475.0Coiled coilOntology_term=ECO:0000255
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-2953_237151475.0Coiled coilOntology_term=ECO:0000255
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29440_448151475.0Compositional biasNote=Poly-Pro
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29442_451151475.0MotifSH3-binding
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29106_235151475.0RegionNote=5 X 29 AA tandem repeats
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29135_163151475.0RepeatNote=2
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29164_192151475.0RepeatNote=3
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29193_206151475.0RepeatNote=4%3B approximate
HgeneCCDC6chr10:61612311chr21:15481401ENST00000263102-29207_235151475.0RepeatNote=5


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Fusion Gene Sequence for CCDC6-LIPI


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.
>13890_13890_1_CCDC6-LIPI_CCDC6_chr10_61612311_ENST00000263102_LIPI_chr21_15481401_ENST00000536861_length(transcript)=953nt_BP=685nt
AGTGCAATACTGCCCAAGCCCGGGCGGGGTCTCTGTTCTCTGGCAGAGGAGGTCCCTTGGCAGCGGGAAGCGCCCTCTCTTTCTCTCGCC
GCCGCTCCGAGTCTGCGCCCTGGTGCCAGGCGCTCAGCTCGGCGCTCCCCTGTGCTCGCCCGGCGCCCACTCATTCGCAGCCCGGCCTTC
GTCGCCGCCGCCTCCCTGCTGCTCCTCCTCCTTTCCCCAGCCCGCCGCGGCCATGGCGGACAGCGCCAGCGAGAGCGACACGGACGGGGC
GGGGGGCAACAGCAGCAGCTCGGCCGCCATGCAGTCGTCCTGCTCGTCGACCTCGGGCGGCGGCGGTGGCGGCGGGGGAGGCGGCGGCGG
TGGGAAGTCGGGGGGCATTGTCATCTCGCCGTTCCGCCTGGAGGAGCTCACCAACCGCCTGGCCTCGCTGCAGCAAGAGAACAAGGTGCT
GAAGATAGAGCTGGAGACCTACAAACTGAAGTGCAAGGCACTGCAGGAGGAGAACCGCGACCTGCGCAAAGCCAGCGTGACCATCCAAGC
CAGGGCTGAGCAGGAAGAAGAATTCATTAGTAACACTTTATTCAAGAAAATTCAGGCTTTGCAGAAGGAGAAAGAAACCCTTGCTGTAAA
TTATGAGAAAGAAGAAGAATTCCTCACTAATGAGCTCTCCAGAAAATTGATGCAGACCACCACTTTGCAGGTATAATATTGTACTTAAAG
ACAGAGAGGAAGTGTTTCTTAATCCAAACACATGTACACCAAAGAACACATAAGATGCCTTCTTCCATCAAATGCACTTGCTTGTGAATT
AATGGACTTGTAAATGAAACAATGCAATCAGTCTTTTATAATGCACTGTTCAATTTGAGATTCAAGTATTTCTATTTCTTGGAAAAAATT

>13890_13890_1_CCDC6-LIPI_CCDC6_chr10_61612311_ENST00000263102_LIPI_chr21_15481401_ENST00000536861_length(amino acids)=198AA_BP=
MVPGAQLGAPLCSPGAHSFAARPSSPPPPCCSSSFPQPAAAMADSASESDTDGAGGNSSSSAAMQSSCSSTSGGGGGGGGGGGGGKSGGI
VISPFRLEELTNRLASLQQENKVLKIELETYKLKCKALQEENRDLRKASVTIQARAEQEEEFISNTLFKKIQALQKEKETLAVNYEKEEE

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Fusion Gene PPI Analysis for CCDC6-LIPI


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 CCDC6-LIPI


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 CCDC6-LIPI


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCCDC6C0238463Papillary thyroid carcinoma2CTD_human;ORPHANET
HgeneCCDC6C3501843Nonmedullary Thyroid Carcinoma1CTD_human
HgeneCCDC6C3501844Familial Nonmedullary Thyroid Cancer1CTD_human
TgeneC0020480Hyperlipoproteinemia Type IV2GENOMICS_ENGLAND;UNIPROT