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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:C1QA-CD74 (FusionGDB2 ID:HG712TG972)

Fusion Gene Summary for C1QA-CD74

check button Fusion gene summary
Fusion gene informationFusion gene name: C1QA-CD74
Fusion gene ID: hg712tg972
HgeneTgene
Gene symbol

C1QA

CD74

Gene ID

712

972

Gene namecomplement C1q A chainCD74 molecule
Synonyms-DHLAG|HLADG|II|Ia-GAMMA|p33
Cytomap('C1QA')('CD74')

1p36.12

5q33.1

Type of geneprotein-codingprotein-coding
Descriptioncomplement C1q subcomponent subunit Acomplement C1q chain Acomplement component 1, q subcomponent, A chaincomplement component 1, q subcomponent, alpha polypeptidecomplement component C1q, A chainHLA class II histocompatibility antigen gamma chainCD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)CD74 molecule, major histocompatibility complex, class II invariant chainHLA-DR antigens-associated
Modification date2020031320200313
UniProtAcc

P02745

P04233

Ensembl transtripts involved in fusion geneENST00000374642, ENST00000402322, 
Fusion gene scores* DoF score8 X 9 X 5=36031 X 31 X 11=10571
# samples 839
** MAII scorelog2(8/360*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(39/10571*10)=-4.76049392566144
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: C1QA [Title/Abstract] AND CD74 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC1QA(22965442)-CD74(149792314), # 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
TgeneCD74

GO:0001516

prostaglandin biosynthetic process

12782713

TgeneCD74

GO:0001934

positive regulation of protein phosphorylation

24942581

TgeneCD74

GO:0002792

negative regulation of peptide secretion

19849849

TgeneCD74

GO:0033674

positive regulation of kinase activity

24942581

TgeneCD74

GO:0043066

negative regulation of apoptotic process

12782713

TgeneCD74

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

24942581

TgeneCD74

GO:0043410

positive regulation of MAPK cascade

24942581

TgeneCD74

GO:0043518

negative regulation of DNA damage response, signal transduction by p53 class mediator

17045821

TgeneCD74

GO:0045657

positive regulation of monocyte differentiation

24942581

TgeneCD74

GO:0045893

positive regulation of transcription, DNA-templated

24942581

TgeneCD74

GO:0046598

positive regulation of viral entry into host cell

24942581

TgeneCD74

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

17045821

TgeneCD74

GO:0070374

positive regulation of ERK1 and ERK2 cascade

17045821|24942581



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-91-6835-01AC1QAchr1

22965442

-CD74chr5

149792314

-


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Fusion Gene ORF analysis for C1QA-CD74

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-5UTRENST00000374642ENST00000009530C1QAchr1

22965442

-CD74chr5

149792314

-
5CDS-5UTRENST00000374642ENST00000353334C1QAchr1

22965442

-CD74chr5

149792314

-
5CDS-5UTRENST00000374642ENST00000377795C1QAchr1

22965442

-CD74chr5

149792314

-
5CDS-5UTRENST00000374642ENST00000524315C1QAchr1

22965442

-CD74chr5

149792314

-
5CDS-5UTRENST00000402322ENST00000009530C1QAchr1

22965442

-CD74chr5

149792314

-
5CDS-5UTRENST00000402322ENST00000353334C1QAchr1

22965442

-CD74chr5

149792314

-
5CDS-5UTRENST00000402322ENST00000377795C1QAchr1

22965442

-CD74chr5

149792314

-
5CDS-5UTRENST00000402322ENST00000524315C1QAchr1

22965442

-CD74chr5

149792314

-

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 C1QA-CD74


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 C1QA-CD74


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/:22965442/:149792314)
- 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
C1QA

P02745

CD74

P04233

FUNCTION: C1q associates with the proenzymes C1r and C1s to yield C1, the first component of the serum complement system. The collagen-like regions of C1q interact with the Ca(2+)-dependent C1r(2)C1s(2) proenzyme complex, and efficient activation of C1 takes place on interaction of the globular heads of C1q with the Fc regions of IgG or IgM antibody present in immune complexes.FUNCTION: Plays a critical role in MHC class II antigen processing by stabilizing peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to the endosomal/lysosomal system where the antigen processing and binding of antigenic peptides to MHC class II takes place. Serves as cell surface receptor for the cytokine MIF.; FUNCTION: [Class-II-associated invariant chain peptide]: Binds to the peptide-binding site of MHC class II alpha/beta heterodimers forming an alpha-beta-CLIP complex, thereby preventing the loading of antigenic peptides to the MHC class II complex until its release by HLA-DM in the endosome. {ECO:0000269|PubMed:1448172}.; FUNCTION: [Isoform p41]: Stabilizes the conformation of mature CTSL by binding to its active site and serving as a chaperone to help maintain a pool of mature enzyme in endocytic compartments and extracellular space of antigen-presenting cells (APCs). Has antiviral activity by stymieing the endosomal entry of Ebola virus and coronaviruses, including SARS-CoV-2 (PubMed:32855215). Disrupts cathepsin-mediated Ebola virus glycoprotein processing, which prevents viral fusion and entry. This antiviral activity is specific to p41 isoform (PubMed:32855215). {ECO:0000250|UniProtKB:P04441, ECO:0000269|PubMed:32855215}.

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 C1QA-CD74


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 C1QA-CD74


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 C1QA-CD74


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneC1QAP02745DB00002CetuximabBiotechApproved
HgeneC1QAP02745DB00110PalivizumabBiotechApproved|Investigational
HgeneC1QAP02745DB00112BevacizumabBiotechApproved|Investigational

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Related Diseases for C1QA-CD74


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneC1QAC0017661IGA Glomerulonephritis2CTD_human
HgeneC1QAC0015230Exanthema1CTD_human
HgeneC1QAC0017662Glomerulonephritis, Membranoproliferative1CTD_human
HgeneC1QAC0020951Immune Complex Diseases1CTD_human
HgeneC1QAC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneC1QAC0024141Lupus Erythematosus, Systemic1CTD_human
HgeneC1QAC0242380Libman-Sacks Disease1CTD_human
HgeneC1QAC0268742Membranoproliferative Glomerulonephritis, Type I1CTD_human
HgeneC1QAC0268743Membranoproliferative Glomerulonephritis, Type II1CTD_human
HgeneC1QAC0272242Complement deficiency disease1GENOMICS_ENGLAND
HgeneC1QAC1720821Membranoproliferative Glomerulonephritis, Type III1CTD_human
HgeneC1QAC3150902C1q DEFICIENCY1CTD_human;GENOMICS_ENGLAND
HgeneC1QAC3280742SYSTEMIC LUPUS ERYTHEMATOSUS 161ORPHANET
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0162557Liver Failure, Acute1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human