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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:CLPB-CTNNA2 (FusionGDB2 ID:17306)

Fusion Gene Summary for CLPB-CTNNA2

check button Fusion gene summary
Fusion gene informationFusion gene name: CLPB-CTNNA2
Fusion gene ID: 17306
HgeneTgene
Gene symbol

CLPB

CTNNA2

Gene ID

81570

1496

Gene namecaseinolytic mitochondrial matrix peptidase chaperone subunit Bcatenin alpha 2
SynonymsANKCLB|HSP78|MEGCANN|MGCA7|SKD3CAP-R|CAPR|CDCBM9|CT114|CTNR
Cytomap

11q13.4

2p12

Type of geneprotein-codingprotein-coding
Descriptioncaseinolytic peptidase B protein homologClpB caseinolytic peptidase B homologClpB homolog, mitochondrial AAA ATPase chaperoninankyrin-repeat containing bacterial clp fusionsuppressor of potassium transport defect 3testicular secretory protein Li 11catenin alpha-2alpha-N-cateninalpha-catenin-related proteincadherin-associated protein, relatedcancer/testis antigen 114catenin (cadherin-associated protein), alpha 2
Modification date2020031320200313
UniProtAcc

Q9H078

P26232

Ensembl transtripts involved in fusion geneENST00000294053, ENST00000538039, 
ENST00000437826, ENST00000340729, 
ENST00000543042, ENST00000445069, 
ENST00000538021, ENST00000542555, 
ENST00000466387, ENST00000496558, 
ENST00000361291, ENST00000402739, 
ENST00000540488, ENST00000541047, 
ENST00000343114, ENST00000496251, 
ENST00000409266, 
Fusion gene scores* DoF score17 X 12 X 7=142826 X 24 X 10=6240
# samples 1828
** MAII scorelog2(18/1428*10)=-2.98792716769943
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/6240*10)=-4.47804729680464
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLPB [Title/Abstract] AND CTNNA2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLPB(72091325)-CTNNA2(80620336), # samples:1
Anticipated loss of major functional domain due to fusion event.CLPB-CTNNA2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CLPB-CTNNA2 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CLPB-CTNNA2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
HgeneCLPB

GO:0034605

cellular response to heat

2745427


check buttonFusion gene breakpoints across CLPB (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 CTNNA2 (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
ChimerDB4PCPGTCGA-WB-A81R-01ACLPBchr11

72091325

-CTNNA2chr2

80620336

+


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Fusion Gene ORF analysis for CLPB-CTNNA2

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-shiftENST00000294053ENST00000466387CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000294053ENST00000496558CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000294053ENST00000361291CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000294053ENST00000402739CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000294053ENST00000540488CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000294053ENST00000541047CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000294053ENST00000343114CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000294053ENST00000496251CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000294053ENST00000409266CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000538039ENST00000466387CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000538039ENST00000496558CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000538039ENST00000361291CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000538039ENST00000402739CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000538039ENST00000540488CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000538039ENST00000541047CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000538039ENST00000343114CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000538039ENST00000496251CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000538039ENST00000409266CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000437826ENST00000466387CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000437826ENST00000496558CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000437826ENST00000361291CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000437826ENST00000402739CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000437826ENST00000540488CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000437826ENST00000541047CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000437826ENST00000343114CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000437826ENST00000496251CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000437826ENST00000409266CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000340729ENST00000466387CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000340729ENST00000496558CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000340729ENST00000361291CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000340729ENST00000402739CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000340729ENST00000540488CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000340729ENST00000541047CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000340729ENST00000343114CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000340729ENST00000496251CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000340729ENST00000409266CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000543042ENST00000466387CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000543042ENST00000496558CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000543042ENST00000361291CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000543042ENST00000402739CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000543042ENST00000540488CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000543042ENST00000541047CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000543042ENST00000343114CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000543042ENST00000496251CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000543042ENST00000409266CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000445069ENST00000466387CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000445069ENST00000496558CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000445069ENST00000361291CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000445069ENST00000402739CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000445069ENST00000540488CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000445069ENST00000541047CLPBchr11

72091325

-CTNNA2chr2

80620336

+
Frame-shiftENST00000445069ENST00000343114CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000445069ENST00000496251CLPBchr11

72091325

-CTNNA2chr2

80620336

+
5CDS-intronENST00000445069ENST00000409266CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000538021ENST00000466387CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000538021ENST00000496558CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000538021ENST00000361291CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000538021ENST00000402739CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000538021ENST00000540488CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000538021ENST00000541047CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000538021ENST00000343114CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-intronENST00000538021ENST00000496251CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-intronENST00000538021ENST00000409266CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000542555ENST00000466387CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000542555ENST00000496558CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000542555ENST00000361291CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000542555ENST00000402739CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000542555ENST00000540488CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000542555ENST00000541047CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-3CDSENST00000542555ENST00000343114CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-intronENST00000542555ENST00000496251CLPBchr11

72091325

-CTNNA2chr2

80620336

+
intron-intronENST00000542555ENST00000409266CLPBchr11

72091325

-CTNNA2chr2

80620336

+

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 CLPB-CTNNA2


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)
CLPBchr1172091324-CTNNA2chr280620335+0.0007731670.9992268
CLPBchr1172091324-CTNNA2chr280620335+0.0007731670.9992268

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 CLPB-CTNNA2


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
CLPB

Q9H078

CTNNA2

P26232

FUNCTION: May function as a regulatory ATPase and be related to secretion/protein trafficking process. Involved in mitochondrial-mediated antiviral innate immunity, activates RIG-I-mediated signal transduction and production of IFNB1 and proinflammatory cytokine IL6 (PubMed:31522117). {ECO:0000269|PubMed:31522117}.FUNCTION: May function as a linker between cadherin adhesion receptors and the cytoskeleton to regulate cell-cell adhesion and differentiation in the nervous system (By similarity). Required for proper regulation of cortical neuronal migration and neurite growth (PubMed:30013181). It acts as negative regulator of Arp2/3 complex activity and Arp2/3-mediated actin polymerization (PubMed:30013181). It thereby suppresses excessive actin branching which would impair neurite growth and stability (PubMed:30013181). Regulates morphological plasticity of synapses and cerebellar and hippocampal lamination during development. Functions in the control of startle modulation (By similarity). {ECO:0000250|UniProtKB:Q61301, ECO:0000269|PubMed:30013181}.

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 CLPB-CTNNA2


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 CLPB-CTNNA2


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 CLPB-CTNNA2


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 CLPB-CTNNA2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLPBC42253933-methylglutaconic aciduria type 73CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCLPBC0014548Epilepsy, Generalized1GENOMICS_ENGLAND
HgeneCLPBC0036572Seizures1GENOMICS_ENGLAND
TgeneCTNNA2C0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneCTNNA2C0024623Malignant neoplasm of stomach1CTD_human
TgeneCTNNA2C0036341Schizophrenia1PSYGENET
TgeneCTNNA2C0038356Stomach Neoplasms1CTD_human
TgeneCTNNA2C0266463Lissencephaly1CTD_human
TgeneCTNNA2C0266483Pachygyria1CTD_human
TgeneCTNNA2C0557874Global developmental delay1GENOMICS_ENGLAND
TgeneCTNNA2C1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneCTNNA2C1879312Agyria1CTD_human
TgeneCTNNA2C3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneCTNNA2C4748540CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 91GENOMICS_ENGLAND