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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:CD46-IGKC (FusionGDB2 ID:HG4179TG3514)

Fusion Gene Summary for CD46-IGKC

check button Fusion gene summary
Fusion gene informationFusion gene name: CD46-IGKC
Fusion gene ID: hg4179tg3514
HgeneTgene
Gene symbol

CD46

IGKC

Gene ID

4179

3514

Gene nameCD46 molecule
SynonymsAHUS2|MCP|MIC10|TLX|TRA2.10
Cytomap('CD46')('IGKC')

1q32.2

Type of geneprotein-coding
Descriptionmembrane cofactor proteinCD46 antigen, complement regulatory proteinCD46 molecule, complement regulatory proteinantigen identified by monoclonal antibody TRA-2-10complement membrane cofactor proteinmeasles virus receptormembrane cofactor protein (CD
Modification date20200313
UniProtAcc.

P01834

Ensembl transtripts involved in fusion geneENST00000469535, ENST00000322875, 
ENST00000322918, ENST00000354848, 
ENST00000357714, ENST00000358170, 
ENST00000360212, ENST00000361067, 
ENST00000367041, ENST00000367042, 
ENST00000367047, ENST00000441839, 
ENST00000480003, 
Fusion gene scores* DoF score12 X 12 X 6=864160 X 66 X 20=211200
# samples 14149
** MAII scorelog2(14/864*10)=-2.6256044852185
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(149/211200*10)=-7.14715369378365
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CD46 [Title/Abstract] AND IGKC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCD46(207934740)-IGKC(89161073), # 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
HgeneCD46

GO:0008593

regulation of Notch signaling pathway

23086448

HgeneCD46

GO:0010629

negative regulation of gene expression

23086448

HgeneCD46

GO:0032613

interleukin-10 production

23086448

HgeneCD46

GO:0032733

positive regulation of interleukin-10 production

12540904

HgeneCD46

GO:0035581

sequestering of extracellular ligand from receptor

23086448

HgeneCD46

GO:0042102

positive regulation of T cell proliferation

12540904

HgeneCD46

GO:0043382

positive regulation of memory T cell differentiation

12540904

HgeneCD46

GO:0045591

positive regulation of regulatory T cell differentiation

12540904

HgeneCD46

GO:0071636

positive regulation of transforming growth factor beta production

12540904



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
ChimerDB4HNSCTCGA-CR-5250CD46chr1

207934740

+IGKCchr2

89161073

-


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Fusion Gene ORF analysis for CD46-IGKC

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
3UTR-intronENST00000469535ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000322875ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000322918ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000354848ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000357714ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000358170ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000360212ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000361067ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000367041ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000367042ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000367047ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000441839ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-
5CDS-intronENST00000480003ENST00000390237CD46chr1

207934740

+IGKCchr2

89161073

-

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 CD46-IGKC


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)


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Fusion Protein Features for CD46-IGKC


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/:207934740/:89161073)
- 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
.IGKC

P01834

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: Constant region of immunoglobulin light chains. Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:22158414, PubMed:20176268). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268). {ECO:0000303|PubMed:17576170, ECO:0000303|PubMed:20176268, ECO:0000303|PubMed:22158414}.

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 CD46-IGKC


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 CD46-IGKC


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 CD46-IGKC


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 CD46-IGKC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCD46C2752040HEMOLYTIC UREMIC SYNDROME, ATYPICAL, SUSCEPTIBILITY TO, 26GENOMICS_ENGLAND;UNIPROT
HgeneCD46C2931788Atypical Hemolytic Uremic Syndrome2CTD_human;GENOMICS_ENGLAND
HgeneCD46C0019061Hemolytic-Uremic Syndrome1GENOMICS_ENGLAND
HgeneCD46C0025007Measles1CTD_human
HgeneCD46C0162739HELLP Syndrome1ORPHANET
HgeneCD46C0272242Complement deficiency disease1GENOMICS_ENGLAND
HgeneCD46C3658266Prostatic Cancer, Castration-Resistant1CTD_human
HgeneCD46C3658267Prostatic Neoplasms, Castration-Resistant1CTD_human
HgeneCD46C4087273C3 glomerulopathy1GENOMICS_ENGLAND
TgeneC3279824Kappa-Chain Deficiency2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0013374Dysgammaglobulinemia1CTD_human
TgeneC0019209Hepatomegaly1CTD_human
TgeneC0027121Myositis1CTD_human
TgeneC0158353Infectious Myositis1CTD_human
TgeneC0231221Asymptomatic1GENOMICS_ENGLAND
TgeneC0544796Myositis, Proliferative1CTD_human
TgeneC0751356Idiopathic Inflammatory Myopathies1CTD_human
TgeneC0751357Myositis, Focal1CTD_human