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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:MDH1-CTNNA1 (FusionGDB2 ID:52357)

Fusion Gene Summary for MDH1-CTNNA1

check button Fusion gene summary
Fusion gene informationFusion gene name: MDH1-CTNNA1
Fusion gene ID: 52357
HgeneTgene
Gene symbol

MDH1

CTNNA1

Gene ID

4190

1495

Gene namemalate dehydrogenase 1catenin alpha 1
SynonymsHEL-S-32|MDH-s|MDHA|MGC:1375|MOR2CAP102|MDPT2
Cytomap

2p15

5q31.2

Type of geneprotein-codingprotein-coding
Descriptionmalate dehydrogenase, cytoplasmicmalate dehydrogenase, peroxisomalcytosolic malate dehydrogenasediiodophenylpyruvate reductaseepididymis secretory protein Li 32malate dehydrogenase 1, NAD (soluble)soluble malate dehydrogenasecatenin alpha-1alpha-E-catenincatenin (cadherin-associated protein), alpha 1, 102kDaepididymis secretory sperm binding proteinrenal carcinoma antigen NY-REN-13
Modification date2020031320200313
UniProtAcc

P40925

P35221

Ensembl transtripts involved in fusion geneENST00000462944, ENST00000233114, 
ENST00000409476, ENST00000409908, 
ENST00000394423, ENST00000539945, 
ENST00000544381, 		ENST00000302763, 
ENST00000355078, ENST00000518825, 
ENST00000540387, ENST00000520400, 
Fusion gene scores* DoF score5 X 7 X 3=10516 X 20 X 7=2240
# samples 722
** MAII scorelog2(7/105*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/2240*10)=-3.34792330342031
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MDH1 [Title/Abstract] AND CTNNA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMDH1(63816146)-CTNNA1(138269887), # 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
TgeneCTNNA1

GO:0071681

cellular response to indole-3-methanol

10868478


check buttonFusion gene breakpoints across MDH1 (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 CTNNA1 (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
ChiTaRS5.0N/ACK003575MDH1chr2

63816146

+CTNNA1chr5

138269887

+


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Fusion Gene ORF analysis for MDH1-CTNNA1

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-3UTRENST00000462944ENST00000302763MDH1chr2

63816146

+CTNNA1chr5

138269887

+
3UTR-3UTRENST00000462944ENST00000355078MDH1chr2

63816146

+CTNNA1chr5

138269887

+
3UTR-3UTRENST00000462944ENST00000518825MDH1chr2

63816146

+CTNNA1chr5

138269887

+
3UTR-3UTRENST00000462944ENST00000540387MDH1chr2

63816146

+CTNNA1chr5

138269887

+
3UTR-intronENST00000462944ENST00000520400MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000233114ENST00000302763MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000233114ENST00000355078MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000233114ENST00000518825MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000233114ENST00000540387MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000409476ENST00000302763MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000409476ENST00000355078MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000409476ENST00000518825MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000409476ENST00000540387MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000409908ENST00000302763MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000409908ENST00000355078MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000409908ENST00000518825MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-3UTRENST00000409908ENST00000540387MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-intronENST00000233114ENST00000520400MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-intronENST00000409476ENST00000520400MDH1chr2

63816146

+CTNNA1chr5

138269887

+
5UTR-intronENST00000409908ENST00000520400MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000394423ENST00000302763MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000394423ENST00000355078MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000394423ENST00000518825MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000394423ENST00000540387MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000539945ENST00000302763MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000539945ENST00000355078MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000539945ENST00000518825MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000539945ENST00000540387MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000544381ENST00000302763MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000544381ENST00000355078MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000544381ENST00000518825MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-3UTRENST00000544381ENST00000540387MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-intronENST00000394423ENST00000520400MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-intronENST00000539945ENST00000520400MDH1chr2

63816146

+CTNNA1chr5

138269887

+
intron-intronENST00000544381ENST00000520400MDH1chr2

63816146

+CTNNA1chr5

138269887

+

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 MDH1-CTNNA1


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 MDH1-CTNNA1


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/:63816146/:138269887)
- 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
MDH1

P40925

CTNNA1

P35221

FUNCTION: Catalyzes the reduction of aromatic alpha-keto acids in the presence of NADH (PubMed:3052244). Plays essential roles in the malate-aspartate shuttle and the tricarboxylic acid cycle, important in mitochondrial NADH supply for oxidative phosphorylation (PubMed:31538237). {ECO:0000269|PubMed:3052244, ECO:0000269|PubMed:31538237}.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}.

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 MDH1-CTNNA1


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 MDH1-CTNNA1


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 MDH1-CTNNA1


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 MDH1-CTNNA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource