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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:COMMD9-CD59 (FusionGDB2 ID:18560)

Fusion Gene Summary for COMMD9-CD59

check button Fusion gene summary
Fusion gene informationFusion gene name: COMMD9-CD59
Fusion gene ID: 18560
HgeneTgene
Gene symbol

COMMD9

CD59

Gene ID

29099

966

Gene nameCOMM domain containing 9CD59 molecule (CD59 blood group)
SynonymsC11orf55|HSPC166|LINC0061016.3A5|1F5|EJ16|EJ30|EL32|G344|HRF-20|HRF20|MAC-IP|MACIF|MEM43|MIC11|MIN1|MIN2|MIN3|MIRL|MSK21|p18-20
Cytomap

11p13

11p13

Type of geneprotein-codingprotein-coding
DescriptionCOMM domain-containing protein 9CD59 glycoprotein1F5 antigen20 kDa homologous restriction factorCD59 antigen p18-20 (antigen identified by monoclonal antibodies 16.3A5, EJ16, EJ30, EL32 and G344)CD59 blood group antigenCD59 molecule, complement regulatory proteinLy-6-like protein
Modification date2020031320200313
UniProtAcc

Q9P000

P13987

Ensembl transtripts involved in fusion geneENST00000263401, ENST00000452374, 
ENST00000532705, ENST00000533308, 
ENST00000534312, ENST00000395850, 
ENST00000533403, ENST00000351554, 
ENST00000415002, ENST00000445143, 
ENST00000426650, ENST00000437761, 
ENST00000527577, ENST00000528700, 
Fusion gene scores* DoF score6 X 4 X 4=9614 X 15 X 5=1050
# samples 517
** MAII scorelog2(5/96*10)=-0.941106310946431
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1050*10)=-2.62678267641578
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COMMD9 [Title/Abstract] AND CD59 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOMMD9(36300027)-CD59(33720060), # samples:3
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
TgeneCD59

GO:0030449

regulation of complement activation

25284781

TgeneCD59

GO:1903659

regulation of complement-dependent cytotoxicity

25284781


check buttonFusion gene breakpoints across COMMD9 (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 CD59 (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
ChimerDB4SKCMTCGA-FS-A1ZK-06ACOMMD9chr11

36300027

-CD59chr11

33720060

-
ChimerDB4SKCMTCGA-FS-A1ZK-06ACOMMD9chr11

36300027

-CD59chr11

33720060

-
ChimerDB4SKCMTCGA-FS-A1ZK-06ACOMMD9chr11

36300027

-CD59chr11

33720060

-


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Fusion Gene ORF analysis for COMMD9-CD59

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
In-frameENST00000263401ENST00000534312COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000395850COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000533403COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000351554COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000415002COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000445143COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000426650COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000437761COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000527577COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000263401ENST00000528700COMMD9chr11

36300027

-CD59chr11

33720060

-
In-frameENST00000452374ENST00000534312COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000395850COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000533403COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000351554COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000415002COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000445143COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000426650COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000437761COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000527577COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000452374ENST00000528700COMMD9chr11

36300027

-CD59chr11

33720060

-
In-frameENST00000532705ENST00000534312COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000395850COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000533403COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000351554COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000415002COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000445143COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000426650COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000437761COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000527577COMMD9chr11

36300027

-CD59chr11

33720060

-
5CDS-intronENST00000532705ENST00000528700COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-3CDSENST00000533308ENST00000534312COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000395850COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000533403COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000351554COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000415002COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000445143COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000426650COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000437761COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000527577COMMD9chr11

36300027

-CD59chr11

33720060

-
intron-intronENST00000533308ENST00000528700COMMD9chr11

36300027

-CD59chr11

33720060

-

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)
ENST00000263401COMMD9chr1136300027-ENST00000534312CD59chr1133720060-58833417457146
ENST00000452374COMMD9chr1136300027-ENST00000534312CD59chr1133720060-48222837351104
ENST00000532705COMMD9chr1136300027-ENST00000534312CD59chr1133720060-58332912452146

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
ENST00000263401ENST00000534312COMMD9chr1136300027-CD59chr1133720060-0.0083819910.991618
ENST00000452374ENST00000534312COMMD9chr1136300027-CD59chr1133720060-0.0644469860.935553
ENST00000532705ENST00000534312COMMD9chr1136300027-CD59chr1133720060-0.0087353240.99126464

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Fusion Genomic Features for COMMD9-CD59


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 COMMD9-CD59


check button Go to

FGviewer for the breakpoints of chr11:36300027-chr11:33720060

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COMMD9

Q9P000

CD59

P13987

FUNCTION: May modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes (PubMed:21778237). May down-regulate activation of NF-kappa-B (PubMed:15799966). Modulates Na(+) transport in epithelial cells by regulation of apical cell surface expression of amiloride-sensitive sodium channel (ENaC) subunits (PubMed:23637203). {ECO:0000269|PubMed:15799966, ECO:0000269|PubMed:23637203, ECO:0000305|PubMed:21778237}.FUNCTION: Potent inhibitor of the complement membrane attack complex (MAC) action. Acts by binding to the C8 and/or C9 complements of the assembling MAC, thereby preventing incorporation of the multiple copies of C9 required for complete formation of the osmolytic pore. This inhibitor appears to be species-specific. Involved in signal transduction for T-cell activation complexed to a protein tyrosine kinase.; FUNCTION: The soluble form from urine retains its specific complement binding activity, but exhibits greatly reduced ability to inhibit MAC assembly on cell membranes.

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
TgeneCD59chr11:36300027chr11:33720060ENST000003515540526_1080129.0DomainNote=UPAR/Ly6
TgeneCD59chr11:36300027chr11:33720060ENST000003958500426_1080129.0DomainNote=UPAR/Ly6
TgeneCD59chr11:36300027chr11:33720060ENST000004150020326_1080129.0DomainNote=UPAR/Ly6
TgeneCD59chr11:36300027chr11:33720060ENST000004266500426_1080129.0DomainNote=UPAR/Ly6
TgeneCD59chr11:36300027chr11:33720060ENST000004377610426_1080129.0DomainNote=UPAR/Ly6
TgeneCD59chr11:36300027chr11:33720060ENST000004451430426_1080129.0DomainNote=UPAR/Ly6
TgeneCD59chr11:36300027chr11:33720060ENST000005275770526_1080129.0DomainNote=UPAR/Ly6
TgeneCD59chr11:36300027chr11:33720060ENST000005287000626_1080129.0DomainNote=UPAR/Ly6

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCOMMD9chr11:36300027chr11:33720060ENST00000263401-36122_196105.66666666666667199.0DomainCOMM
HgeneCOMMD9chr11:36300027chr11:33720060ENST00000452374-25122_19663.666666666666664157.0DomainCOMM


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Fusion Gene Sequence for COMMD9-CD59


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.
>In-frame_ENST00000263401_ENST00000534312_TCGA-FS-A1ZK-06A_COMMD9_chr11_36300027_-_CD59_chr11_33720060_length(transcript)=588nt_BP=334nt
CATGTGACTTCGGCAAGATGGCTGCCCTGACAGCGGAGCATTTTGCAGCACTCCAGAGCCTGCTCAAGGCCTCCTCGAAAGATGTTGTCA
GACAGCTGTGTCAAGAAAGCTTTTCCAGTTCAGCCCTTGGCTTGAAAAAACTCTTGGATGTTACATGTTCCAGCTTGTCTGTGACCCAGG
AGGAGGCAGAGGAACTGCTCCAGGCTCTGCACCGCCTCACTAGGCTGGTGGCATTCCGTGACCTGTCCTCTGCCGAGGCAATTCTGGCTC
TCTTTCCAGAAAATTTCCACCAAAACCTCAAAAACCTGCTGACAAAGATCATCCTAGAACATGTACACATTCCTGAAGGCGCTAAAAGAC
GAAAAGTTACAAGGACTGAAGACCAAGCAACCTGGAAAGAAGTCGGCCTCTCTCTCCTGAGGAGCTGCCTACCAGAGCTTGGGCAGCCAC
CTCCTTAGGTGTTAGTGCTTAGATAATGTGTCCCATTTGTTGTCATTTCAAAGATGGTTATTTTCTGTTCTGTATTTACCGCTGTTCTTG

>In-frame_ENST00000263401_ENST00000534312_TCGA-FS-A1ZK-06A_COMMD9_chr11_36300027_-_CD59_chr11_33720060_length(amino acids)=146AA_start in transcript=17_stop in transcript=457
MAALTAEHFAALQSLLKASSKDVVRQLCQESFSSSALGLKKLLDVTCSSLSVTQEEAEELLQALHRLTRLVAFRDLSSAEAILALFPENF

--------------------------------------------------------------
>In-frame_ENST00000452374_ENST00000534312_TCGA-FS-A1ZK-06A_COMMD9_chr11_36300027_-_CD59_chr11_33720060_length(transcript)=482nt_BP=228nt
GCTTCCCTGGGTGCCACGGTCATGTGACTTCGGCAAGATGGCTGCCCTGACAGCGGAGCATTTTGCAGCACTCCAGAGCCTGCTCAAGCT
GCTCCAGGCTCTGCACCGCCTCACTAGGCTGGTGGCATTCCGTGACCTGTCCTCTGCCGAGGCAATTCTGGCTCTCTTTCCAGAAAATTT
CCACCAAAACCTCAAAAACCTGCTGACAAAGATCATCCTAGAACATGTACACATTCCTGAAGGCGCTAAAAGACGAAAAGTTACAAGGAC
TGAAGACCAAGCAACCTGGAAAGAAGTCGGCCTCTCTCTCCTGAGGAGCTGCCTACCAGAGCTTGGGCAGCCACCTCCTTAGGTGTTAGT
GCTTAGATAATGTGTCCCATTTGTTGTCATTTCAAAGATGGTTATTTTCTGTTCTGTATTTACCGCTGTTCTTGTTGCTACCAGCATGTA

>In-frame_ENST00000452374_ENST00000534312_TCGA-FS-A1ZK-06A_COMMD9_chr11_36300027_-_CD59_chr11_33720060_length(amino acids)=104AA_start in transcript=37_stop in transcript=351
MAALTAEHFAALQSLLKLLQALHRLTRLVAFRDLSSAEAILALFPENFHQNLKNLLTKIILEHVHIPEGAKRRKVTRTEDQATWKEVGLS

--------------------------------------------------------------
>In-frame_ENST00000532705_ENST00000534312_TCGA-FS-A1ZK-06A_COMMD9_chr11_36300027_-_CD59_chr11_33720060_length(transcript)=583nt_BP=329nt
GACTTCGGCAAGATGGCTGCCCTGACAGCGGAGCATTTTGCAGCACTCCAGAGCCTGCTCAAGGCCTCCTCGAAAGATGTTGTCAGACAG
CTGTGTCAAGAAAGCTTTTCCAGTTCAGCCCTTGGCTTGAAAAAACTCTTGGATGTTACATGTTCCAGCTTGTCTGTGACCCAGGAGGAG
GCAGAGGAACTGCTCCAGGCTCTGCACCGCCTCACTAGGCTGGTGGCATTCCGTGACCTGTCCTCTGCCGAGGCAATTCTGGCTCTCTTT
CCAGAAAATTTCCACCAAAACCTCAAAAACCTGCTGACAAAGATCATCCTAGAACATGTACACATTCCTGAAGGCGCTAAAAGACGAAAA
GTTACAAGGACTGAAGACCAAGCAACCTGGAAAGAAGTCGGCCTCTCTCTCCTGAGGAGCTGCCTACCAGAGCTTGGGCAGCCACCTCCT
TAGGTGTTAGTGCTTAGATAATGTGTCCCATTTGTTGTCATTTCAAAGATGGTTATTTTCTGTTCTGTATTTACCGCTGTTCTTGTTGCT

>In-frame_ENST00000532705_ENST00000534312_TCGA-FS-A1ZK-06A_COMMD9_chr11_36300027_-_CD59_chr11_33720060_length(amino acids)=146AA_start in transcript=12_stop in transcript=452
MAALTAEHFAALQSLLKASSKDVVRQLCQESFSSSALGLKKLLDVTCSSLSVTQEEAEELLQALHRLTRLVAFRDLSSAEAILALFPENF

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

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Fusion Gene PPI Analysis for COMMD9-CD59


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 COMMD9-CD59


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 COMMD9-CD59


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCD59C2676767CD59 Deficiency4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCD59C0024790Paroxysmal nocturnal hemoglobinuria1GENOMICS_ENGLAND
TgeneCD59C0272242Complement deficiency disease1GENOMICS_ENGLAND
TgeneCD59C1148551X-Linked Dyskeratosis Congenita1GENOMICS_ENGLAND
TgeneCD59C4727002Chronic Hemolysis1GENOMICS_ENGLAND
TgeneCD59C4755276Primary CD59 deficiency1GENOMICS_ENGLAND