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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:NDRG1-VIM

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NDRG1-VIM
FusionPDB ID: 57983
FusionGDB2.0 ID: 57983
HgeneTgene
Gene symbol

NDRG1

VIM

Gene ID

10397

7431

Gene nameN-myc downstream regulated 1vimentin
SynonymsCAP43|CMT4D|DRG-1|DRG1|GC4|HMSNL|NDR1|NMSL|PROXY1|RIT42|RTP|TARG1|TDD5-
Cytomap

8q24.22

10p13

Type of geneprotein-codingprotein-coding
Descriptionprotein NDRG1N-myc downstream-regulated gene 1 proteindifferentiation-related gene 1 proteinnickel-specific induction protein Cap43protein regulated by oxygen-1reducing agents and tunicamycin-responsive proteinvimentinepididymis secretory sperm binding protein
Modification date2020032820200327
UniProtAcc

Q92597

VMAC

Ensembl transtripts involved in fusion geneENST idsENST00000323851, ENST00000354944, 
ENST00000414097, ENST00000518176, 
ENST00000522476, ENST00000537882, 
ENST00000521414, ENST00000518066, 
ENST00000485947, ENST00000224237, 
ENST00000544301, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score27 X 21 X 12=680442 X 25 X 11=11550
# samples 4041
** MAII scorelog2(40/6804*10)=-4.08831123588866
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(41/11550*10)=-4.81612513168534
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

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

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NDRG1(134256597)-VIM(17277844), # samples:1
Anticipated loss of major functional domain due to fusion event.NDRG1-VIM seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
NDRG1-VIM seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
NDRG1-VIM seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
NDRG1-VIM seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
NDRG1-VIM seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
NDRG1-VIM seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
NDRG1-VIM seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
NDRG1-VIM 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

check buttonFusion gene breakpoints across NDRG1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across VIM (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4Non-Cancer169NNDRG1chr8

134256597

-VIMchr10

17277844

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000537882NDRG1chr8134256597-ENST00000544301VIMchr1017277844+1408922274972232
ENST00000537882NDRG1chr8134256597-ENST00000224237VIMchr1017277844+1416922274972232

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
ENST00000537882ENST00000544301NDRG1chr8134256597-VIMchr1017277844+0.0044180490.9955819
ENST00000537882ENST00000224237NDRG1chr8134256597-VIMchr1017277844+0.0043561570.99564385

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>57983_57983_1_NDRG1-VIM_NDRG1_chr8_134256597_ENST00000537882_VIM_chr10_17277844_ENST00000224237_length(amino acids)=232AA_BP=216
MQEITQHFAVCHVDAPGQQDGAASFPAGYMYPSMDQLAEMLPGVLQQFGLKSIIGMGTGAGAYILTRFALNNPEMVEGLVLINVNPCAEG
WMDWAASKISGWTQALPDMVVSHLFGKEEMQSNVEVVHTYRQHIVNDMNPGNLHLFINAYNSRRDLEIERPMPGTHTVTLQCPALLVVGD

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

>57983_57983_2_NDRG1-VIM_NDRG1_chr8_134256597_ENST00000537882_VIM_chr10_17277844_ENST00000544301_length(amino acids)=232AA_BP=216
MQEITQHFAVCHVDAPGQQDGAASFPAGYMYPSMDQLAEMLPGVLQQFGLKSIIGMGTGAGAYILTRFALNNPEMVEGLVLINVNPCAEG
WMDWAASKISGWTQALPDMVVSHLFGKEEMQSNVEVVHTYRQHIVNDMNPGNLHLFINAYNSRRDLEIERPMPGTHTVTLQCPALLVVGD

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

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Fusion Protein Functional Features


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/chr8:134256597/chr10:17277844)
- 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

VIM

VMAC

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}.169

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneVIMchr8:134256597chr10:17277844ENST0000022423759408_466409.6666666666667467.0RegionNote=Tail
TgeneVIMchr8:134256597chr10:17277844ENST00000544301610408_466409.6666666666667467.0RegionNote=Tail

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNDRG1chr8:134256597chr10:17277844ENST00000323851-1416339_368297.0395.0RegionNote=3 X 10 AA tandem repeats of G-T-R-S-R-S-H-T-S-E
HgeneNDRG1chr8:134256597chr10:17277844ENST00000414097-1416339_368297.0395.0RegionNote=3 X 10 AA tandem repeats of G-T-R-S-R-S-H-T-S-E
HgeneNDRG1chr8:134256597chr10:17277844ENST00000522476-1214339_368231.0329.0RegionNote=3 X 10 AA tandem repeats of G-T-R-S-R-S-H-T-S-E
HgeneNDRG1chr8:134256597chr10:17277844ENST00000537882-1315339_368216.0314.0RegionNote=3 X 10 AA tandem repeats of G-T-R-S-R-S-H-T-S-E
HgeneNDRG1chr8:134256597chr10:17277844ENST00000323851-1416339_348297.0395.0RepeatNote=1
HgeneNDRG1chr8:134256597chr10:17277844ENST00000323851-1416349_358297.0395.0RepeatNote=2
HgeneNDRG1chr8:134256597chr10:17277844ENST00000323851-1416359_368297.0395.0RepeatNote=3
HgeneNDRG1chr8:134256597chr10:17277844ENST00000414097-1416339_348297.0395.0RepeatNote=1
HgeneNDRG1chr8:134256597chr10:17277844ENST00000414097-1416349_358297.0395.0RepeatNote=2
HgeneNDRG1chr8:134256597chr10:17277844ENST00000414097-1416359_368297.0395.0RepeatNote=3
HgeneNDRG1chr8:134256597chr10:17277844ENST00000522476-1214339_348231.0329.0RepeatNote=1
HgeneNDRG1chr8:134256597chr10:17277844ENST00000522476-1214349_358231.0329.0RepeatNote=2
HgeneNDRG1chr8:134256597chr10:17277844ENST00000522476-1214359_368231.0329.0RepeatNote=3
HgeneNDRG1chr8:134256597chr10:17277844ENST00000537882-1315339_348216.0314.0RepeatNote=1
HgeneNDRG1chr8:134256597chr10:17277844ENST00000537882-1315349_358216.0314.0RepeatNote=2
HgeneNDRG1chr8:134256597chr10:17277844ENST00000537882-1315359_368216.0314.0RepeatNote=3
TgeneVIMchr8:134256597chr10:17277844ENST0000022423759154_245409.6666666666667467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr8:134256597chr10:17277844ENST0000022423759303_407409.6666666666667467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr8:134256597chr10:17277844ENST000002242375996_131409.6666666666667467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr8:134256597chr10:17277844ENST00000544301610154_245409.6666666666667467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr8:134256597chr10:17277844ENST00000544301610303_407409.6666666666667467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr8:134256597chr10:17277844ENST0000054430161096_131409.6666666666667467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr8:134256597chr10:17277844ENST0000022423759103_411409.6666666666667467.0DomainIF rod
TgeneVIMchr8:134256597chr10:17277844ENST00000544301610103_411409.6666666666667467.0DomainIF rod
TgeneVIMchr8:134256597chr10:17277844ENST0000022423759326_329409.6666666666667467.0Motif[IL]-x-C-x-x-[DE] motif
TgeneVIMchr8:134256597chr10:17277844ENST00000544301610326_329409.6666666666667467.0Motif[IL]-x-C-x-x-[DE] motif
TgeneVIMchr8:134256597chr10:17277844ENST0000022423759132_153409.6666666666667467.0RegionNote=Linker 1
TgeneVIMchr8:134256597chr10:17277844ENST0000022423759246_268409.6666666666667467.0RegionNote=Linker 12
TgeneVIMchr8:134256597chr10:17277844ENST0000022423759269_407409.6666666666667467.0RegionNote=Coil 2
TgeneVIMchr8:134256597chr10:17277844ENST00000224237592_95409.6666666666667467.0RegionNote=Head
TgeneVIMchr8:134256597chr10:17277844ENST00000544301610132_153409.6666666666667467.0RegionNote=Linker 1
TgeneVIMchr8:134256597chr10:17277844ENST00000544301610246_268409.6666666666667467.0RegionNote=Linker 12
TgeneVIMchr8:134256597chr10:17277844ENST00000544301610269_407409.6666666666667467.0RegionNote=Coil 2
TgeneVIMchr8:134256597chr10:17277844ENST000005443016102_95409.6666666666667467.0RegionNote=Head


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors
NDRG1ARL4D, PHYHIP, S100B, HSP90AA1, HSPA5, VCP, CANX, PSMC3, PSMC2, PSMD2, XRCC6, RUVBL2, ILF3, SEC23A, COPB2, CLTC, AP2M1, AP1M2, MME, CTNNB1, ACTG1, KIF5B, PPP2R2A, TLE3, HSD17B4, CNDP2, DARS, DLST, ACSL3, FASN, MAOA, LDHA, PKM, RPN2, TARS, SHMT2, SLC25A6, ATP1A1, EEF2, EEF1G, EIF2S3, EIF3E, PABPC1, RPS3, RPS6, RPL24, RPL3, RPS16, RPS8, RPS20, RPS9, RPL4, RPS26, NCL, HNRNPF, HNRNPU, HNRNPH1, DDX1, DDX5, UPF1, EWSR1, CDH1, ANXA5, CLNS1A, IGBP1, SPAG9, MLH1, ACOT7, DDX39B, GSR, DPP3, EIF4H, FTO, KYNU, MVD, NAMPT, PEPD, PGD, BCL2L11, HSPA4, CUL2, TAF9, SGK1, SUZ12, EED, NDRG2, DHX15, G6PD, GART, HIP1R, CCDC22, CLIC4, NAA50, RTCB, SH2D4A, THUMPD1, TIMM13, TSG101, USP14, XPO1, NIF3L1, NTMT1, TARDBP, UFM1, TMEM17, ERBB3, FXYD1, PDE4DIP, S1PR2, FAM60A, CDK15, TRIM25, HNRNPL, MYC, SKP2, RABAC1, GSK3B, NR4A1, YAP1, RTN1, Apoa1, Apoa2, Rabac1, Arl6ip1, APOA1, APOA2, RAB4A, ZBTB38, EZR, TGOLN2, LAMP1, PPM1F, HRAS, NRAS, KRAS, RFFL, DYNC1I2, CUL4A, CTBP2, ORF3a, PRKCB, RAB5A, SH2D3C, M, Rnf183, HULC, ARF6, C11orf52, CAV1, LAMTOR1, LYN, MARCKS, OCLN, RAB11A, RAB2A, RAB35, RAB9A, RHOB, STX4, STX6, STX7, ZFPL1, HTRA4, NAA40, ST6GALNAC6, OR2A4, HOXC5, RPL35A, FXYD3, SRRT, PPP2R2B, NAA11, YWHAH, GOT1, STX17, WIF1, GOLGA2, ATP1B1, COL10A1, CERS3, OPTN, SSBP2, ATP1B3, C2orf73, NTNG1, FGF12, OSGEP, CCR1, TIMMDC1, CEP19, MBNL1, CRCP, PINK1, NRSN1, CCDC53, SSUH2, DNAJB6,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
NDRG1all structure
VIM


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to NDRG1-VIM


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to NDRG1-VIM


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNDRG1C0027627Neoplasm Metastasis2CTD_human
HgeneNDRG1C1832334CHARCOT-MARIE-TOOTH DISEASE, TYPE 4D2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneNDRG1C0004114Astrocytoma1CTD_human
HgeneNDRG1C0006142Malignant neoplasm of breast1CTD_human
HgeneNDRG1C0007131Non-Small Cell Lung Carcinoma1CTD_human
HgeneNDRG1C0007134Renal Cell Carcinoma1CTD_human
HgeneNDRG1C0017636Glioblastoma1CTD_human
HgeneNDRG1C0022665Kidney Neoplasm1CTD_human
HgeneNDRG1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneNDRG1C0023903Liver neoplasms1CTD_human
HgeneNDRG1C0025202melanoma1CTD_human
HgeneNDRG1C0026640Mouth Neoplasms1CTD_human
HgeneNDRG1C0029295Oropharyngeal Neoplasms1CTD_human
HgeneNDRG1C0033578Prostatic Neoplasms1CTD_human
HgeneNDRG1C0149925Small cell carcinoma of lung1CTD_human
HgeneNDRG1C0153381Malignant neoplasm of mouth1CTD_human
HgeneNDRG1C0205768Subependymal Giant Cell Astrocytoma1CTD_human
HgeneNDRG1C0206658Smooth Muscle Tumor1CTD_human
HgeneNDRG1C0206734Hemangioblastoma1CTD_human
HgeneNDRG1C0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
HgeneNDRG1C0280783Juvenile Pilocytic Astrocytoma1CTD_human
HgeneNDRG1C0280785Diffuse Astrocytoma1CTD_human
HgeneNDRG1C0334579Anaplastic astrocytoma1CTD_human
HgeneNDRG1C0334580Protoplasmic astrocytoma1CTD_human
HgeneNDRG1C0334581Gemistocytic astrocytoma1CTD_human
HgeneNDRG1C0334582Fibrillary Astrocytoma1CTD_human
HgeneNDRG1C0334583Pilocytic Astrocytoma1CTD_human
HgeneNDRG1C0334588Giant Cell Glioblastoma1CTD_human
HgeneNDRG1C0338070Childhood Cerebral Astrocytoma1CTD_human
HgeneNDRG1C0345904Malignant neoplasm of liver1CTD_human
HgeneNDRG1C0376358Malignant neoplasm of prostate1CTD_human
HgeneNDRG1C0547065Mixed oligoastrocytoma1CTD_human
HgeneNDRG1C0678222Breast Carcinoma1CTD_human
HgeneNDRG1C0740457Malignant neoplasm of kidney1CTD_human
HgeneNDRG1C0750935Cerebral Astrocytoma1CTD_human
HgeneNDRG1C0750936Intracranial Astrocytoma1CTD_human
HgeneNDRG1C0751692Multiple Hemangioblastomas1CTD_human
HgeneNDRG1C0887833Carcinoma, Pancreatic Ductal1CTD_human
HgeneNDRG1C1168401Squamous cell carcinoma of the head and neck1CTD_human
HgeneNDRG1C1257931Mammary Neoplasms, Human1CTD_human
HgeneNDRG1C1266042Chromophobe Renal Cell Carcinoma1CTD_human
HgeneNDRG1C1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
HgeneNDRG1C1266044Collecting Duct Carcinoma of the Kidney1CTD_human
HgeneNDRG1C1306837Papillary Renal Cell Carcinoma1CTD_human
HgeneNDRG1C1458155Mammary Neoplasms1CTD_human
HgeneNDRG1C1621958Glioblastoma Multiforme1CTD_human
HgeneNDRG1C1704230Grade I Astrocytoma1CTD_human
HgeneNDRG1C2349952Oropharyngeal Carcinoma1CTD_human
HgeneNDRG1C4704874Mammary Carcinoma, Human1CTD_human