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NDRG3

gene
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Summary

NDRG3 (NDRG family member 3, HGNC:14462) is a protein-coding gene on chromosome 20q11.23, encoding Protein NDRG3 (Q9UGV2).

Predicted to be involved in decidualization and signal transduction. Located in cytoplasm.

Source: NCBI Gene 57446 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 56 total
  • MANE Select transcript: NM_032013

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14462
Approved symbolNDRG3
NameNDRG family member 3
Location20q11.23
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000101079
Ensembl biotypeprotein_coding
OMIM605273
Entrez57446

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 22 protein_coding

ENST00000349004, ENST00000359675, ENST00000373773, ENST00000373803, ENST00000422536, ENST00000855484, ENST00000855485, ENST00000855486, ENST00000855487, ENST00000855488, ENST00000930944, ENST00000930945, ENST00000930946, ENST00000930947, ENST00000930948, ENST00000956892, ENST00000956893, ENST00000956894, ENST00000956895, ENST00000956896, ENST00000956897, ENST00000956898

RefSeq mRNA: 2 — MANE Select: NM_032013 NM_022477, NM_032013

CCDS: CCDS13284, CCDS13285

Canonical transcript exons

ENST00000349004 — 16 exons

ExonStartEnd
ENSE000008004483668867936688784
ENSE000010368063674604536746090
ENSE000010368093668251836682578
ENSE000012002173668441336684475
ENSE000012002223668749236687612
ENSE000030499443666628936666392
ENSE000030974033665649736656532
ENSE000031162343666504636665097
ENSE000031183353666033736660384
ENSE000031277923666523636665301
ENSE000031348733668081636680902
ENSE000032250143665636036656411
ENSE000035185353672167936721783
ENSE000035419463670697236707007
ENSE000037855353667134136671397
ENSE000038487913665177136653701

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 99.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.0846 / max 453.0425, expressed in 1763 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
18713814.38841743
1871391.57981060
1871350.06753
1871330.01863
1871360.01463
1871340.00953
1871370.00623

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cerebellar vermisUBERON:000472099.38gold quality
ponsUBERON:000098899.10gold quality
lateral nuclear group of thalamusUBERON:000273698.41gold quality
cerebellumUBERON:000203798.22gold quality
cerebellar cortexUBERON:000212998.19gold quality
cerebellar hemisphereUBERON:000224598.17gold quality
middle temporal gyrusUBERON:000277198.15gold quality
superior vestibular nucleusUBERON:000722798.15gold quality
right hemisphere of cerebellumUBERON:001489097.93gold quality
parietal lobeUBERON:000187297.87gold quality
postcentral gyrusUBERON:000258197.77gold quality
Brodmann (1909) area 46UBERON:000648397.77gold quality
prefrontal cortexUBERON:000045197.76gold quality
superior frontal gyrusUBERON:000266197.67gold quality
occipital lobeUBERON:000202197.65gold quality
orbitofrontal cortexUBERON:000416797.65gold quality
frontal cortexUBERON:000187097.41gold quality
primary visual cortexUBERON:000243697.41gold quality
ventral tegmental areaUBERON:000269197.33gold quality
endothelial cellCL:000011597.28gold quality
dorsal plus ventral thalamusUBERON:000189797.26gold quality
lateral globus pallidusUBERON:000247697.10gold quality
Brodmann (1909) area 23UBERON:001355497.10gold quality
medulla oblongataUBERON:000189697.08gold quality
dorsolateral prefrontal cortexUBERON:000983497.08gold quality
substantia nigra pars compactaUBERON:000196597.06gold quality
entorhinal cortexUBERON:000272897.04gold quality
neocortexUBERON:000195096.93gold quality
Brodmann (1909) area 9UBERON:001354096.82gold quality
right frontal lobeUBERON:000281096.79gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting NDRG3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3120-5P100.0065.56965
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-656-3P100.0072.152788
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548AW99.9972.573559
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-1213699.9872.815713
HSA-MIR-314899.9775.066478
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-570-3P99.9672.414910
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-381-3P99.9371.872854
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-30099.9271.762856
HSA-MIR-61399.9171.501710
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-368699.9070.532432
HSA-MIR-129-5P99.8870.263273
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590

Literature-anchored findings (GeneRIF, showing 19)

  • Cloning and expression of the gene; highly expressed in brain and testis (PMID:11936845)
  • NDRG3 is a tumor promoter, the overexpression of which may contribute to the malignant phenotype of tumors (PMID:18975380)
  • miR-122 plays an important role in HBV-related hepatocarcinogenesis by targeting NDRG3. (PMID:21725618)
  • summarizes the current research on NDRG3 and NDRG4,including the molecular structure, cellular and tissue distribution, biological function,and function in cancer. (PMID:23725756)
  • the aberrant expression of NDRG2 and NDRG3 may contribute to the malignant progression of prostate cancer (PMID:24222185)
  • We identified a lactate-dependent signaling pathway in hypoxia, mediated by the oxygen- and lactate-regulated protein NDRG family member 3 (NDRG3). (PMID:25936780)
  • above findings suggested that NDRG3 may be identified as a novel biomarker predicting the prognosis of laryngeal squamous cell carcinoma (PMID:27780595)
  • increased NDRG3 expression is associated with hepatocellular carcinoma and drug resistance. (PMID:28269758)
  • the expression of NDRG3 had significant impact on survival, with NDRG3 downregulated patients having the worst event-free survival rate among others. (PMID:28326836)
  • Hypoxic postconditioning attenuates apoptosis via inactivation of adenosine A2a receptor through NDRG3-Raf-ERK pathway. (PMID:28743501)
  • The IHC data demonstrated that the NDRG3 expression was significantly correlated with pathological grade (p= 0.038), N (p= 0.020) and TNM stage (p= 0.002) in non-small cell lung cancer. (PMID:29171988)
  • NDRG3 may have an anti-metastatic function in prostate cancer under a hypoxic microenvironment. (PMID:29760417)
  • The results revealed that compared with non-tumor tissues, hepatocellular carcinoma tissues showed significantly higher NDRG3 expression. (PMID:30413609)
  • high NDRG3 expression facilitates HCC metastasis via regulating the turnover of beta-catenin, as well as provides a potential therapeutic target for future therapeutic interventions (PMID:31072445)
  • Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein. (PMID:31935861)
  • High expression of NDRG3 correlates with poor prognosis in gastric cancer patients. (PMID:33562989)
  • The LINC01410/miR-122-5p/NDRG3 axis is involved in the proliferation and migration of osteosarcoma cells. (PMID:33583123)
  • Lactate promotes neuronal differentiation of SH-SY5Y cells by lactate-responsive gene sets through NDRG3-dependent and -independent manners. (PMID:37172727)
  • NDRG3 regulates imatinib resistance by promoting beta-catenin accumulation in the nucleus in chronic myelogenous leukemia. (PMID:37350410)

Cross-species orthologs

10 orthologs

OrganismSymbolGene ID
danio_reriondrg3bENSDARG00000010052
danio_reriondrg3aENSDARG00000013087
mus_musculusNdrg3ENSMUSG00000027634
rattus_norvegicusLOC120101770ENSRNOG00000036813
rattus_norvegicusENSRNOG00000078841
rattus_norvegicusENSRNOG00000085471
drosophila_melanogasterCG2082FBGN0027608
drosophila_melanogasterMESK2FBGN0043070
caenorhabditis_elegansY48G10A.3WBGENE00013020
caenorhabditis_elegansWBGENE00014213

Paralogs (3): NDRG4 (ENSG00000103034), NDRG1 (ENSG00000104419), NDRG2 (ENSG00000165795)

Protein

Protein identifiers

Protein NDRG3 — Q9UGV2 (reviewed: Q9UGV2)

Alternative names: N-myc downstream-regulated gene 3 protein

All UniProt accessions (4): Q9UGV2, F8WBF9, Q5TH29, Q5TH30

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Ubiquitous. Highly expressed in brain.

Similarity. Belongs to the NDRG family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9UGV2-11yes
Q9UGV2-22
Q9UGV2-33

RefSeq proteins (2): NP_071922, NP_114402* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004142NDRGFamily
IPR029058AB_hydrolase_foldHomologous_superfamily

Pfam: PF03096

UniProt features (49 total): modified residue 13, helix 12, strand 11, compositionally biased region 3, sequence conflict 3, turn 3, splice variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

6 structures.

PDBMethodResolution (Å)
6L4BX-RAY DIFFRACTION2.2
9KCLELECTRON MICROSCOPY2.9
9KCMELECTRON MICROSCOPY2.9
9KCRELECTRON MICROSCOPY3.2
6L4GX-RAY DIFFRACTION3.3
6L4HX-RAY DIFFRACTION3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UGV2-F181.310.63

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (13): 334, 335, 338, 341, 352, 355, 361, 374, 1, 322, 329, 331, 332

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 191 (showing top): GCM_PTPRD, GOBP_NEGATIVE_REGULATION_OF_CELL_GROWTH, GOBP_GROWTH, GOBP_MALE_GAMETE_GENERATION, YY1_Q6, PATIL_LIVER_CANCER, CATTTCA_MIR203, YY1_02, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, chr20q11, BIDUS_METASTASIS_UP, TTTNNANAGCYR_UNKNOWN, NFE2_01, GOBP_CELL_GROWTH, GCM_PTK2

GO Biological Process (4): signal transduction (GO:0007165), spermatogenesis (GO:0007283), cell differentiation (GO:0030154), negative regulation of cell growth (GO:0030308)

GO Molecular Function (0):

GO Cellular Component (2): cytoplasm (GO:0005737), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
developmental process involved in reproduction1
male gamete generation1
cellular developmental process1
regulation of cell growth1
cell growth1
negative regulation of growth1
negative regulation of cellular process1
intracellular anatomical structure1
cellular anatomical structure1
extracellular vesicle1

Protein interactions and networks

STRING

698 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NDRG3STK38LQ9Y2H1922
NDRG3MYCNP04198798
NDRG3RAF1P04049615
NDRG3EGLN1Q9GZT9550
NDRG3CCNG1P51959545
NDRG3HDHD3Q9BSH5458
NDRG3NOCTQ9UK39445
NDRG3TAF4O00268419
NDRG3NPEPPSP55786398
NDRG3MAPRE1Q15691395
NDRG3KLK6Q92876389
NDRG3TRPC4APQ8TEL6388
NDRG3KLK1P06870388
NDRG3EDEM2Q9BV94387
NDRG3PPP2R2AP50409377

IntAct

25 interactions, top by confidence:

ABTypeScore
ATP1B1ATP1A1psi-mi:“MI:0914”(association)0.910
TUSC3RPN2psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
PICK1ILVBLpsi-mi:“MI:0914”(association)0.530
ATP1A3AGPAT2psi-mi:“MI:0914”(association)0.530
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
ATP1A3TMEM223psi-mi:“MI:0914”(association)0.350
FXYD3TNPO2psi-mi:“MI:0914”(association)0.350
ATP1B1TM9SF1psi-mi:“MI:0914”(association)0.350
TMC4MARCHF6psi-mi:“MI:0914”(association)0.350
FXYD1SPINK4psi-mi:“MI:0914”(association)0.350
TLCD5TOM1L1psi-mi:“MI:0914”(association)0.350
ATP1B3TMEM131Lpsi-mi:“MI:0914”(association)0.350
ATP1A3EI24psi-mi:“MI:0914”(association)0.350
DDX28UBA6psi-mi:“MI:0914”(association)0.350
LGALS3SDCBPpsi-mi:“MI:0914”(association)0.350
MRPL49UBA6psi-mi:“MI:0914”(association)0.350
OAS1UBA6psi-mi:“MI:0914”(association)0.350
VENTXUBA6psi-mi:“MI:0914”(association)0.350
KRASESYT2psi-mi:“MI:2364”(proximity)0.270
HRASESYT2psi-mi:“MI:2364”(proximity)0.270
NDRG3psi-mi:“MI:0915”(physical association)0.000

BioGRID (50): NDRG3 (Affinity Capture-MS), CSTF1 (Co-fractionation), NDRG3 (Co-fractionation), NPEPL1 (Co-fractionation), TARDBP (Co-fractionation), NDRG3 (Affinity Capture-MS), NDRG3 (Affinity Capture-MS), NDRG3 (Affinity Capture-MS), NDRG3 (Affinity Capture-RNA), RABAC1 (Affinity Capture-Western), NDRG3 (Proximity Label-MS), NDRG3 (Proximity Label-MS), NDRG3 (Proximity Label-MS), NDRG3 (Proximity Label-MS), NDRG3 (Proximity Label-MS)

ESM2 similar proteins: A2VE08, A7Y521, E1C6Q1, O15131, O35116, O35142, O35345, O55029, O60684, O70133, O88544, O94973, P17427, P18484, P26233, P35605, P35606, P52294, P52297, P70188, P83953, Q08211, Q0V7M0, Q0VCK5, Q13098, Q28141, Q3SZA0, Q4R5E6, Q503E9, Q56R16, Q5F418, Q5R648, Q5R664, Q5R874, Q5R909, Q5RBV0, Q5ZHN3, Q5ZML1, Q60960, Q68FK8

Diamond homologs: A0A126P745, A1A9R4, A1JMX1, A4VQH7, A4W922, A6T799, A7MB28, A7MFY0, A7ZKB4, A7ZYW4, A8GCT3, A8IAD8, A9W3H8, B0SW62, B1IV88, B1LIZ6, B1M5I5, B1X9D0, B1ZB18, B5XXN3, B5YU51, B6I985, B7KWT4, B7LFB9, B7M8Z4, B7MIF6, B7MTF2, B7N3G5, B7NLB7, B7UNZ2, B8H1Q3, B9JLT6, C4ZQD7, C5B0U6, C5CN82, C6EHJ8, C6UFC0, C6UPN1, C7CM33, C8TNB9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 33 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Ion transport by P-type ATPases654.2×1e-07
Ion homeostasis653.2×1e-07
Potential therapeutics for SARS629.8×1e-06
SARS-CoV Infections512.1×2e-04
Viral Infection Pathways56.7×2e-03
Infectious disease55.4×5e-03
Neutrophil degranulation55.0×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

56 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2263 predictions. Top by Δscore:

VariantEffectΔscore
20:36653697:TGGTA:Tacceptor_gain1.0000
20:36653702:C:CCacceptor_gain1.0000
20:36656493:TTAC:Tdonor_loss1.0000
20:36656494:TA:Tdonor_loss1.0000
20:36656495:A:Cdonor_loss1.0000
20:36665234:A:ACdonor_gain1.0000
20:36665235:C:CCdonor_gain1.0000
20:36666284:TATA:Tdonor_loss1.0000
20:36666285:ATAC:Adonor_gain1.0000
20:36666286:TACCC:Tdonor_loss1.0000
20:36666287:A:ACdonor_gain1.0000
20:36666287:A:ATdonor_loss1.0000
20:36666287:AC:Adonor_gain1.0000
20:36666288:C:Adonor_loss1.0000
20:36666288:C:CCdonor_gain1.0000
20:36666288:CC:Cdonor_gain1.0000
20:36666291:A:ACdonor_gain1.0000
20:36666389:CTTC:Cacceptor_gain1.0000
20:36666390:TTC:Tacceptor_gain1.0000
20:36666390:TTCC:Tacceptor_loss1.0000
20:36666391:TC:Tacceptor_gain1.0000
20:36666392:CC:Cacceptor_gain1.0000
20:36666393:C:CAacceptor_loss1.0000
20:36666393:C:CCacceptor_gain1.0000
20:36666399:C:CTacceptor_gain1.0000
20:36666402:T:TCacceptor_gain1.0000
20:36671336:CTTA:Cdonor_loss1.0000
20:36671337:TTA:Tdonor_loss1.0000
20:36671338:TA:Tdonor_loss1.0000
20:36671339:ACCTG:Adonor_gain1.0000

AlphaMissense

2474 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:36665075:C:AG261W1.000
20:36656372:C:GG312R0.999
20:36656372:C:TG312R0.999
20:36656384:A:GY308H0.999
20:36656510:G:CP294R0.999
20:36656510:G:TP294H0.999
20:36660341:A:GL285P0.999
20:36660365:A:GL277P0.999
20:36665074:C:AG261V0.999
20:36665074:C:TG261E0.999
20:36665075:C:GG261R0.999
20:36665075:C:TG261R0.999
20:36665083:A:GL258P0.999
20:36680874:A:GL158P0.999
20:36682543:C:TG140E0.999
20:36682555:C:TG136E0.999
20:36687531:G:TA94D0.999
20:36688684:A:GL65P0.999
20:36688687:C:TG64D0.999
20:36688688:C:GG64R0.999
20:36688693:T:AD62V0.999
20:36688702:G:TT59K0.999
20:36688708:A:TI57K0.999
20:36688747:A:TV44D0.999
20:36656371:C:TG312E0.998
20:36656384:A:CY308D0.998
20:36656385:C:AK307N0.998
20:36656385:C:GK307N0.998
20:36656401:A:GL302P0.998
20:36660337:C:AK286N0.998

dbSNP variants (sampled 300 via entrez): RS1000052300 (20:36699353 A>G), RS1000059160 (20:36747158 G>A), RS1000077093 (20:36654132 A>G), RS1000096508 (20:36697854 T>C), RS1000107424 (20:36739963 A>G), RS1000109914 (20:36693736 G>A,C), RS1000124106 (20:36723048 C>G), RS1000182212 (20:36726608 G>A), RS1000224080 (20:36661090 G>C), RS1000265738 (20:36698992 A>G), RS1000292291 (20:36719715 G>A), RS1000352807 (20:36713443 G>C), RS1000390567 (20:36704388 C>G,T), RS1000401425 (20:36712979 T>C), RS1000466644 (20:36660660 A>C)

Disease associations

OMIM: gene MIM:605273 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

49 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
Cyclosporinedecreases expression3
Cadmium Chlorideincreases abundance, increases expression, decreases expression3
sodium arseniteincreases abundance, decreases expression, affects cotreatment2
Cisplatinaffects cotreatment, increases expression, decreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
methylmercuric chloridedecreases expression1
bisphenol Aaffects cotreatment, decreases methylation1
beta-lapachonedecreases expression1
sulforaphanedecreases expression1
cobaltous chloridedecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
coumarinincreases phosphorylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
nutlin 3affects cotreatment, increases secretion1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangincreases expression, affects cotreatment1
Bortezomibdecreases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Fulvestrantdecreases methylation, affects cotreatment1
Vorinostatincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Air Pollutants, Occupationalaffects expression1
Arsenicdecreases expression, increases abundance, affects cotreatment1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

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