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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:CTNNA1-GEMIN6 (FusionGDB2 ID:HG1495TG79833)

Fusion Gene Summary for CTNNA1-GEMIN6

check button Fusion gene summary
Fusion gene informationFusion gene name: CTNNA1-GEMIN6
Fusion gene ID: hg1495tg79833
HgeneTgene
Gene symbol

CTNNA1

GEMIN6

Gene ID

1495

79833

Gene namecatenin alpha 1gem nuclear organelle associated protein 6
SynonymsCAP102|MDPT2-
Cytomap('CTNNA1')('GEMIN6')

5q31.2

2p22.1

Type of geneprotein-codingprotein-coding
Descriptioncatenin alpha-1alpha-E-catenincatenin (cadherin-associated protein), alpha 1, 102kDaepididymis secretory sperm binding proteinrenal carcinoma antigen NY-REN-13gem-associated protein 6SIP2gemin-6
Modification date2020031320200313
UniProtAcc

P35221

Q8WXD5

Ensembl transtripts involved in fusion geneENST00000302763, ENST00000355078, 
ENST00000518825, ENST00000520400, 
ENST00000540387, 
Fusion gene scores* DoF score25 X 19 X 12=57003 X 3 X 2=18
# samples 343
** MAII scorelog2(34/5700*10)=-4.06735526780176
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: CTNNA1 [Title/Abstract] AND GEMIN6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTNNA1(138053783)-GEMIN6(39005370), # 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
HgeneCTNNA1

GO:0071681

cellular response to indole-3-methanol

10868478

TgeneGEMIN6

GO:0000387

spliceosomal snRNP assembly

18984161



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
ChiTaRS5.0N/AFN051755CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+


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Fusion Gene ORF analysis for CTNNA1-GEMIN6

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
intron-5UTRENST00000302763ENST00000281950CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000302763ENST00000409011CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000302763ENST00000409566CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000355078ENST00000281950CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000355078ENST00000409011CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000355078ENST00000409566CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000518825ENST00000281950CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000518825ENST00000409011CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000518825ENST00000409566CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000520400ENST00000281950CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000520400ENST00000409011CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000520400ENST00000409566CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000540387ENST00000281950CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000540387ENST00000409011CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+
intron-5UTRENST00000540387ENST00000409566CTNNA1chr5

138053783

+GEMIN6chr2

39005370

+

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 CTNNA1-GEMIN6


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 CTNNA1-GEMIN6


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/:138053783/:39005370)
- 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
CTNNA1

P35221

GEMIN6

Q8WXD5

FUNCTION: Associates with the cytoplasmic domain of a variety of cadherins. The association of catenins to cadherins produces a complex which is linked to the actin filament network, and which seems to be of primary importance for cadherins cell-adhesion properties. Can associate with both E- and N-cadherins. Originally believed to be a stable component of E-cadherin/catenin adhesion complexes and to mediate the linkage of cadherins to the actin cytoskeleton at adherens junctions. In contrast, cortical actin was found to be much more dynamic than E-cadherin/catenin complexes and CTNNA1 was shown not to bind to F-actin when assembled in the complex suggesting a different linkage between actin and adherens junctions components. The homodimeric form may regulate actin filament assembly and inhibit actin branching by competing with the Arp2/3 complex for binding to actin filaments. Involved in the regulation of WWTR1/TAZ, YAP1 and TGFB1-dependent SMAD2 and SMAD3 nuclear accumulation (By similarity). May play a crucial role in cell differentiation. {ECO:0000250|UniProtKB:P26231, ECO:0000269|PubMed:25653389}.FUNCTION: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. {ECO:0000269|PubMed:11748230, ECO:0000269|PubMed:18984161}.

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 CTNNA1-GEMIN6


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 CTNNA1-GEMIN6


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 CTNNA1-GEMIN6


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 CTNNA1-GEMIN6


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCTNNA1C1708349Hereditary Diffuse Gastric Cancer3ORPHANET
HgeneCTNNA1C0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneCTNNA1C0026998Acute Myeloid Leukemia, M11CTD_human
HgeneCTNNA1C0238198Gastrointestinal Stromal Tumors1CTD_human
HgeneCTNNA1C1837029Macular Dystrophy, Butterfly-Shaped Pigmentary, 21CTD_human;UNIPROT
HgeneCTNNA1C1868569Patterned dystrophy of retinal pigment epithelium1CTD_human
HgeneCTNNA1C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
HgeneCTNNA1C2713368Hematopoetic Myelodysplasia1CTD_human
HgeneCTNNA1C3179349Gastrointestinal Stromal Sarcoma1CTD_human
HgeneCTNNA1C3463824MYELODYSPLASTIC SYNDROME1CTD_human
HgeneCTNNA1C4511237Butterfly-shaped pigmentary macular dystrophy1ORPHANET