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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:MTA3-NDRG1 (FusionGDB2 ID:HG57504TG10397)

Fusion Gene Summary for MTA3-NDRG1

check button Fusion gene summary
Fusion gene informationFusion gene name: MTA3-NDRG1
Fusion gene ID: hg57504tg10397
HgeneTgene
Gene symbol

MTA3

NDRG1

Gene ID

57504

10397

Gene namemetastasis associated 1 family member 3N-myc downstream regulated 1
Synonyms-CAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5
Cytomap('MTA3')('NDRG1')

2p21

8q24.22

Type of geneprotein-codingprotein-coding
Descriptionmetastasis-associated protein MTA3metastasis associated gene family, member 3protein NDRG1N-myc downstream-regulated gene 1 proteindifferentiation-related gene 1 proteinnickel-specific induction protein Cap43protein regulated by oxygen-1reducing agents and tunicamycin-responsive protein
Modification date2020031320200328
UniProtAcc.

Q92597

Ensembl transtripts involved in fusion geneENST00000405094, ENST00000405592, 
ENST00000406652, ENST00000406911, 
ENST00000407270, ENST00000472767, 
Fusion gene scores* DoF score10 X 10 X 3=30024 X 17 X 10=4080
# samples 1126
** MAII scorelog2(11/300*10)=-1.44745897697122
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(26/4080*10)=-3.9719856238304
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MTA3 [Title/Abstract] AND NDRG1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMTA3(42916971)-NDRG1(134249418), # samples:2
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


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/AAA079109MTA3chr2

42916971

-NDRG1chr8

134249418

+
ChiTaRS5.0N/ABI492703MTA3chr2

42916971

-NDRG1chr8

134249418

+


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Fusion Gene ORF analysis for MTA3-NDRG1

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-intronENST00000405094ENST00000323851MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405094ENST00000354944MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405094ENST00000414097MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405094ENST00000518066MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405094ENST00000518176MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405094ENST00000521414MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405094ENST00000522476MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405094ENST00000537882MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405592ENST00000323851MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405592ENST00000354944MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405592ENST00000414097MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405592ENST00000518066MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405592ENST00000518176MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405592ENST00000521414MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405592ENST00000522476MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000405592ENST00000537882MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406652ENST00000323851MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406652ENST00000354944MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406652ENST00000414097MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406652ENST00000518066MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406652ENST00000518176MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406652ENST00000521414MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406652ENST00000522476MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406652ENST00000537882MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406911ENST00000323851MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406911ENST00000354944MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406911ENST00000414097MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406911ENST00000518066MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406911ENST00000518176MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406911ENST00000521414MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406911ENST00000522476MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000406911ENST00000537882MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000407270ENST00000323851MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000407270ENST00000354944MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000407270ENST00000414097MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000407270ENST00000518066MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000407270ENST00000518176MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000407270ENST00000521414MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000407270ENST00000522476MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000407270ENST00000537882MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000472767ENST00000323851MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000472767ENST00000354944MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000472767ENST00000414097MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000472767ENST00000518066MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000472767ENST00000518176MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000472767ENST00000521414MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000472767ENST00000522476MTA3chr2

42916971

-NDRG1chr8

134249418

+
intron-intronENST00000472767ENST00000537882MTA3chr2

42916971

-NDRG1chr8

134249418

+

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 MTA3-NDRG1


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 MTA3-NDRG1


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/:42916971/:134249418)
- 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
.NDRG1

Q92597

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Stress-responsive protein involved in hormone responses, cell growth, and differentiation. Acts as a tumor suppressor in many cell types. Necessary but not sufficient for p53/TP53-mediated caspase activation and apoptosis. Has a role in cell trafficking, notably of the Schwann cell, and is necessary for the maintenance and development of the peripheral nerve myelin sheath. Required for vesicular recycling of CDH1 and TF. May also function in lipid trafficking. Protects cells from spindle disruption damage. Functions in p53/TP53-dependent mitotic spindle checkpoint. Regulates microtubule dynamics and maintains euploidy. {ECO:0000269|PubMed:15247272, ECO:0000269|PubMed:15377670, ECO:0000269|PubMed:17786215, ECO:0000269|PubMed:9766676}.

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 MTA3-NDRG1


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 MTA3-NDRG1


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 MTA3-NDRG1


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 MTA3-NDRG1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0027627Neoplasm Metastasis2CTD_human
TgeneC1832334CHARCOT-MARIE-TOOTH DISEASE, TYPE 4D2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0004114Astrocytoma1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0017636Glioblastoma1CTD_human
TgeneC0022665Kidney Neoplasm1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0023903Liver neoplasms1CTD_human
TgeneC0025202melanoma1CTD_human
TgeneC0026640Mouth Neoplasms1CTD_human
TgeneC0029295Oropharyngeal Neoplasms1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0149925Small cell carcinoma of lung1CTD_human
TgeneC0153381Malignant neoplasm of mouth1CTD_human
TgeneC0205768Subependymal Giant Cell Astrocytoma1CTD_human
TgeneC0206658Smooth Muscle Tumor1CTD_human
TgeneC0206734Hemangioblastoma1CTD_human
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneC0280783Juvenile Pilocytic Astrocytoma1CTD_human
TgeneC0280785Diffuse Astrocytoma1CTD_human
TgeneC0334579Anaplastic astrocytoma1CTD_human
TgeneC0334580Protoplasmic astrocytoma1CTD_human
TgeneC0334581Gemistocytic astrocytoma1CTD_human
TgeneC0334582Fibrillary Astrocytoma1CTD_human
TgeneC0334583Pilocytic Astrocytoma1CTD_human
TgeneC0334588Giant Cell Glioblastoma1CTD_human
TgeneC0338070Childhood Cerebral Astrocytoma1CTD_human
TgeneC0345904Malignant neoplasm of liver1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC0547065Mixed oligoastrocytoma1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0740457Malignant neoplasm of kidney1CTD_human
TgeneC0750935Cerebral Astrocytoma1CTD_human
TgeneC0750936Intracranial Astrocytoma1CTD_human
TgeneC0751692Multiple Hemangioblastomas1CTD_human
TgeneC0887833Carcinoma, Pancreatic Ductal1CTD_human
TgeneC1168401Squamous cell carcinoma of the head and neck1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1621958Glioblastoma Multiforme1CTD_human
TgeneC1704230Grade I Astrocytoma1CTD_human
TgeneC2349952Oropharyngeal Carcinoma1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human