NUDT9

gene
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Also known as MGC3037

Summary

NUDT9 (nudix hydrolase 9, HGNC:8056) is a protein-coding gene on chromosome 4q22.1, encoding ADP-ribose pyrophosphatase (Q9BW91). Hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5’-phosphate.

The protein encoded by this gene belongs to the Nudix hydrolase family. Nudix boxes are found in a family of diverse enzymes that catalyze the hydrolysis of nucleoside diphosphate derivatives. This enzyme is an ADP-ribose pyrophosphatase that catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. It requires divalent metal ions and an intact Nudix motif for enzymatic activity. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 53343 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 56 total
  • Druggable target: yes
  • MANE Select transcript: NM_024047

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8056
Approved symbolNUDT9
Namenudix hydrolase 9
Location4q22.1
Locus typegene with protein product
StatusApproved
AliasesMGC3037
Ensembl geneENSG00000170502
Ensembl biotypeprotein_coding
OMIM606022
Entrez53343

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 12 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000302174, ENST00000440591, ENST00000473942, ENST00000502933, ENST00000512216, ENST00000514227, ENST00000514345, ENST00000515371, ENST00000851358, ENST00000851359, ENST00000851360, ENST00000851361, ENST00000925580, ENST00000925581, ENST00000965707, ENST00000965708

RefSeq mRNA: 3 — MANE Select: NM_024047 NM_001248011, NM_024047, NM_198038

CCDS: CCDS3620, CCDS3621

Canonical transcript exons

ENST00000302174 — 8 exons

ExonStartEnd
ENSE000011354498742257387423012
ENSE000011757188745437187454455
ENSE000011757448744182987441915
ENSE000011757548743827787438372
ENSE000015568218745784387459455
ENSE000035607768744914287449253
ENSE000036196038743498187435220
ENSE000036534198745158987451735

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 96.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.0063 / max 215.3042, expressed in 1799 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
4873011.85631782
487352.66441360
487311.1949729
487330.6885425
487340.3297143
487320.272684

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
islet of LangerhansUBERON:000000696.88gold quality
body of pancreasUBERON:000115095.54gold quality
pancreasUBERON:000126495.15gold quality
middle temporal gyrusUBERON:000277195.08gold quality
duodenumUBERON:000211494.41gold quality
parotid glandUBERON:000183193.35gold quality
right adrenal glandUBERON:000123392.58gold quality
right adrenal gland cortexUBERON:003582792.53gold quality
rectumUBERON:000105292.51gold quality
jejunal mucosaUBERON:000039992.48gold quality
left adrenal glandUBERON:000123492.46gold quality
adrenal glandUBERON:000236992.19gold quality
choroid plexus epitheliumUBERON:000391192.07gold quality
renal glomerulusUBERON:000007492.02gold quality
left adrenal gland cortexUBERON:003582591.99gold quality
nephron tubuleUBERON:000123191.98gold quality
metanephric glomerulusUBERON:000473691.98gold quality
adrenal cortexUBERON:000123591.77gold quality
adrenal tissueUBERON:001830391.77gold quality
visceral pleuraUBERON:000240191.70gold quality
tendon of biceps brachiiUBERON:000818891.69gold quality
mucosa of transverse colonUBERON:000499191.56gold quality
esophagus squamous epitheliumUBERON:000692091.39gold quality
endocervixUBERON:000045891.36gold quality
body of uterusUBERON:000985391.32gold quality
kidney epitheliumUBERON:000481991.30gold quality
metanephrosUBERON:000008191.29gold quality
ectocervixUBERON:001224991.25gold quality
prefrontal cortexUBERON:000045191.22gold quality
tibiaUBERON:000097991.16gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-5061yes8.86
E-ANND-3yes7.98
E-GEOD-83139no3.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting NUDT9, 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-1252-5P100.0069.802774
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-6499-3P99.9066.381212
HSA-MIR-627-3P99.9071.423316
HSA-LET-7A-2-3P99.8770.531921
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-LET-7G-3P99.8570.431929
HSA-MIR-5010-3P99.8370.602357
HSA-MIR-442099.8270.081624
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-205299.7969.372031
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-494-3P99.7071.452795
HSA-MIR-1212499.6869.172700
HSA-MIR-4804-3P99.6567.78866
HSA-MIR-450299.6566.991021
HSA-MIR-510-3P99.5470.062965
HSA-MIR-7159-5P99.5372.122472
HSA-MIR-4762-3P99.4369.722363
HSA-MIR-513A-3P99.3970.633620
HSA-MIR-513C-3P99.3970.633620
HSA-MIR-4652-3P99.3370.022742
HSA-MIR-124499.3368.38832
HSA-MIR-892C-5P99.1670.562116

Literature-anchored findings (GeneRIF, showing 8)

  • Hydrolyses ADP-ribose to AMP and ribose-5-phosphate (PMID:11825615)
  • analysis of the human NUDT9 gene and its potential alternative transcripts along with detailed studies of the enzymatic properties and cell biological behavior of human NUDT9 protein (PMID:12427752)
  • Data report the crystal structures of NUDT9 in the presence and in the absence of the reaction product ribose 5’-phosphate. (PMID:12948489)
  • parallel enzymic characterization of the specific ADP-ribose pyrophosphatase from human placenta and a recombinant NUDT9 protein expressed from a cDNA clone was carried out (PMID:16860484)
  • NUDT9 may be involved in the regulation of the menstrual cycle and may be related to the proliferation of glandular cells in the human endometrium (PMID:19574167)
  • ADP-ribose reactive NUDT9 NUDIX hydrolase isoforms modulate HIF-1alpha in cancer cells (PMID:30190133)
  • Analysis of ligand binding and resulting conformational changes in pyrophosphatase NUDT9. (PMID:34189846)
  • NUDT6 and NUDT9, two mitochondrial members of the NUDIX family, have distinct hydrolysis activities. (PMID:37343711)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerionudt9ENSDARG00000087927
mus_musculusNudt9ENSMUSG00000029310
rattus_norvegicusNudt9ENSRNOG00000002186
drosophila_melanogasterspd-2FBGN0027500
caenorhabditis_elegansWBGENE00003583

Protein

Protein identifiers

ADP-ribose pyrophosphataseQ9BW91 (reviewed: Q9BW91)

Alternative names: ADP-ribose diphosphatase, ADP-ribose phosphohydrolase, Adenosine diphosphoribose pyrophosphatase, Nucleoside diphosphate-linked moiety X motif 9

All UniProt accessions (4): Q9BW91, D6R8Z6, D6RAW2, H7C386

UniProt curated annotations — full annotation on UniProt →

Function. Hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5’-phosphate. Has also a weak phosphohydrolase activity against NADH and FAD (in vitro).

Subunit / interactions. Monomer. Interacts with GLOD4.

Subcellular location. Mitochondrion Mitochondrion. Cytoplasm.

Tissue specificity. Ubiquitously expressed but isoform 1 is the most predominant isoform.

Induction. Inhibited by fluoride and N-acetyl-p-benzoquinoneimine.

Similarity. Belongs to the Nudix hydrolase family. NudF subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BW91-11, NUDT9alphayes
Q9BW91-22, NUDT9beta

RefSeq proteins (3): NP_001234940, NP_076952, NP_932155 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000086NUDIX_hydrolase_domDomain
IPR015797NUDIX_hydrolase-like_dom_sfHomologous_superfamily
IPR039989NUDT9Family

Pfam: PF00293, PF25969

Catalyzed reactions (Rhea), 1 shown:

  • ADP-D-ribose + H2O = D-ribose 5-phosphate + AMP + 2 H(+) (RHEA:10412)

UniProt features (30 total): strand 9, helix 8, turn 4, sequence conflict 2, transit peptide 1, chain 1, domain 1, region of interest 1, short sequence motif 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
1Q33X-RAY DIFFRACTION1.81
1QVJX-RAY DIFFRACTION1.91

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BW91-F185.430.78

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 (1): 121

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2393930Phosphate bond hydrolysis by NUDT proteins

MSigDB gene sets: 159 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, SHEPARD_BMYB_MORPHOLINO_UP, GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS, TGCGCANK_UNKNOWN, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, WANG_RECURRENT_LIVER_CANCER_DN, MODULE_206, GOBP_ORGANOPHOSPHATE_CATABOLIC_PROCESS, KEGG_PURINE_METABOLISM, GOBP_NUCLEOSIDE_PHOSPHATE_CATABOLIC_PROCESS, chr4q22, GOBP_PURINE_CONTAINING_COMPOUND_METABOLIC_PROCESS

GO Biological Process (2): ADP catabolic process (GO:0046032), nucleobase-containing small molecule metabolic process (GO:0055086)

GO Molecular Function (4): ADP-sugar pyrophosphatase activity (GO:0019144), ADP-ribose diphosphatase activity (GO:0047631), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (8): cytoplasm (GO:0005737), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), cytosol (GO:0005829), nuclear body (GO:0016604), cell junction (GO:0030054), nuclear membrane (GO:0031965), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Purine catabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
pyrophosphatase activity2
cytoplasm2
purine ribonucleotide catabolic process1
purine ribonucleoside diphosphate catabolic process1
ADP metabolic process1
nucleobase-containing compound metabolic process1
small molecule metabolic process1
binding1
catalytic activity1
intracellular anatomical structure1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1
nucleoplasm1
intracellular membraneless organelle1
nucleus1
nuclear envelope1
organelle membrane1
extracellular vesicle1

Protein interactions and networks

STRING

654 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NUDT9NUDT5Q9UKK9794
NUDT9NUDT14O95848721
NUDT9NUDT12Q9BQG2712
NUDT9NUDT2P50583680
NUDT9NUDT18Q6ZVK8670
NUDT9PARGQ86W56655
NUDT9NUDT22Q9BRQ3579
NUDT9PTK2BQ14289573
NUDT9NUDT16Q96DE0572
NUDT9TRPM6Q9BX84523
NUDT9ADPRSQ9NX46506
NUDT9MACROD1Q9BQ69479
NUDT9NUDT17P0C025475
NUDT9TRPM8Q7Z2W7464
NUDT9TRPM7Q96QT4463

IntAct

27 interactions, top by confidence:

ABTypeScore
SDHAF3NDUFAB1psi-mi:“MI:0914”(association)0.640
GET3GET1psi-mi:“MI:0914”(association)0.640
FBXO6MAN2B1psi-mi:“MI:0914”(association)0.640
SDF4ACAD11psi-mi:“MI:0914”(association)0.640
PBX3NUDT9psi-mi:“MI:0915”(physical association)0.560
NUDT9EPHA2psi-mi:“MI:0915”(physical association)0.370
APBA1KIF2Apsi-mi:“MI:0914”(association)0.350
SLC39A7AIPpsi-mi:“MI:0914”(association)0.350
LCN9C1QL1psi-mi:“MI:0914”(association)0.350
CCDC32AP2A2psi-mi:“MI:0914”(association)0.350
DPP6ATP5MC1psi-mi:“MI:0914”(association)0.350
SLC2A2CAPGpsi-mi:“MI:0914”(association)0.350
NUDT9WDR5Bpsi-mi:“MI:0914”(association)0.350
FAHD1VWA8psi-mi:“MI:0914”(association)0.350
NUDT9HARS2psi-mi:“MI:0914”(association)0.350
CALM1PLEKHG3psi-mi:“MI:0914”(association)0.350
DDX28UBA6psi-mi:“MI:0914”(association)0.350
FBXO6TMEM131Lpsi-mi:“MI:0914”(association)0.350
GAB2UBA6psi-mi:“MI:0914”(association)0.350
MOAP1TAF4psi-mi:“MI:0914”(association)0.350
MRPL49UBA6psi-mi:“MI:0914”(association)0.350
NUDT9POF1Bpsi-mi:“MI:0914”(association)0.350
SERPINA12COQ9psi-mi:“MI:0914”(association)0.350
PBX3NUDT9psi-mi:“MI:0915”(physical association)0.000
NUDT9MDM2psi-mi:“MI:0915”(physical association)0.000

BioGRID (51): NUDT9 (Affinity Capture-MS), DUT (Co-fractionation), IMPA1 (Co-fractionation), IMPA2 (Co-fractionation), MAN2A1 (Co-fractionation), NIT1 (Co-fractionation), NUDT9 (Co-fractionation), NUDT9 (Co-fractionation), PHPT1 (Co-fractionation), WDR5B (Affinity Capture-MS), NUDT9 (Affinity Capture-MS), NUDT9 (Affinity Capture-MS), TRIM11 (Affinity Capture-MS), NUDT9 (Synthetic Lethality), NUDT9 (Co-fractionation)

ESM2 similar proteins: A0A061AE05, A0A1D8PLI2, A6QXC6, A7KAL8, B9FK36, G2XR75, I1RZ92, M7U9B9, O42641, O74516, O74927, O81395, P09880, P15496, P24521, P41888, P45350, P51820, P53070, P78820, Q00955, Q05762, Q09297, Q09580, Q10258, Q10313, Q17693, Q29RH3, Q2QRX6, Q38970, Q45EK7, Q4R4P6, Q4R7L8, Q4WM52, Q5AWA2, Q5PQ50, Q5RD76, Q5XIG0, Q6C3P4, Q6NPD7

Diamond homologs: A0A0R4IMY7, A7T1N0, A8DYE2, E9PTA2, J9SQF3, O94759, Q2TV84, Q2WEA5, Q5XIG0, Q7TN37, Q7Z2W7, Q7Z4N2, Q8BVU5, Q8R455, Q8R4D5, Q8TD43, Q91YD4, Q9BW91, Q9ESQ5, Q9HCF6, Q9JJH7, Q9NZQ8, S5UH55, Q09297, Q8CIR4, Q923J1, Q925B3, Q96QT4, Q9BX84, Q93971

SIGNOR signaling

0 interactions.

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 significance45
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1757 predictions. Top by Δscore:

VariantEffectΔscore
4:87438258:ATT:Aacceptor_gain1.0000
4:87438275:A:AGacceptor_gain1.0000
4:87438276:G:GCacceptor_gain1.0000
4:87438276:GT:Gacceptor_gain1.0000
4:87438370:GAG:Gdonor_gain1.0000
4:87438371:AGG:Adonor_loss1.0000
4:87438372:GGTA:Gdonor_loss1.0000
4:87438373:G:GAdonor_loss1.0000
4:87438373:G:GGdonor_gain1.0000
4:87441818:T:Aacceptor_gain1.0000
4:87441825:CCA:Cacceptor_loss1.0000
4:87441827:A:ACacceptor_loss1.0000
4:87441827:A:AGacceptor_gain1.0000
4:87441828:G:GAacceptor_gain1.0000
4:87441828:GA:Gacceptor_gain1.0000
4:87441828:GAA:Gacceptor_gain1.0000
4:87441828:GAAA:Gacceptor_gain1.0000
4:87441828:GAAAT:Gacceptor_gain1.0000
4:87441912:CCAGG:Cdonor_loss1.0000
4:87441913:CAGGT:Cdonor_loss1.0000
4:87441914:AGG:Adonor_loss1.0000
4:87441915:GGTAA:Gdonor_loss1.0000
4:87441916:GTAAG:Gdonor_loss1.0000
4:87441917:T:Adonor_loss1.0000
4:87449140:A:AGacceptor_gain1.0000
4:87449141:G:GGacceptor_gain1.0000
4:87449251:GGG:Gdonor_gain1.0000
4:87449252:GGG:Gdonor_gain1.0000
4:87449253:GGTAA:Gdonor_loss1.0000
4:87449254:G:Adonor_loss1.0000

AlphaMissense

2312 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:87441878:T:AW165R0.999
4:87441878:T:CW165R0.999
4:87454416:T:AW279R0.999
4:87454416:T:CW279R0.999
4:87441889:T:AN168K0.998
4:87441889:T:GN168K0.998
4:87454399:G:CR273P0.998
4:87454403:C:AN274K0.998
4:87454403:C:GN274K0.998
4:87454413:G:CA278P0.998
4:87454418:G:CW279C0.998
4:87454418:G:TW279C0.998
4:87457899:T:AW311R0.998
4:87457899:T:CW311R0.998
4:87438328:A:CR133S0.997
4:87438328:A:TR133S0.997
4:87441863:G:TG160W0.997
4:87441864:G:AG160E0.997
4:87441881:G:CG166R0.997
4:87441882:G:AG166D0.997
4:87449210:T:AV200D0.997
4:87449223:G:CR204S0.997
4:87449223:G:TR204S0.997
4:87449239:T:AW210R0.997
4:87449239:T:CW210R0.997
4:87449242:G:CA211P0.997
4:87435201:T:AW110R0.996
4:87435201:T:CW110R0.996
4:87441863:G:AG160R0.996
4:87441863:G:CG160R0.996

dbSNP variants (sampled 300 via entrez): RS1000067760 (4:87447545 G>C), RS1000177029 (4:87433102 A>G), RS1000193807 (4:87430567 A>C), RS1000195347 (4:87423676 G>A), RS10002390 (4:87425517 C>T), RS1000287367 (4:87426869 C>G), RS1000310408 (4:87453681 G>A,C), RS1000392878 (4:87421492 T>C), RS1000484294 (4:87439117 G>T), RS1000582915 (4:87434882 G>A,C,T), RS1000653427 (4:87436692 T>A), RS1000707686 (4:87429931 A>G), RS1000750044 (4:87422607 A>C), RS1000863226 (4:87455344 A>C,G), RS10008963 (4:87457563 G>A)

Disease associations

OMIM: gene MIM:606022 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST005316_596Intelligence (MTAG)2.000000e-08
GCST006585_809Blood protein levels2.000000e-22

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004337intelligence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105984 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
manganese chloridedecreases reaction, increases activity, increases reaction1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
deguelinincreases expression1
bisphenol Bincreases expression1
pyrachlostrobinincreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
Acetaminophenincreases expression1
Dithiothreitoldecreases reaction, increases activity, increases reaction1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Fluoridesdecreases reaction, increases activity1
Hydrogen Peroxidedecreases reaction, increases activity, increases reaction1
Ivermectindecreases expression1
Magnesiumdecreases reaction, increases activity1
Manganesedecreases reaction, increases activity, increases reaction1
Quercetindecreases expression1
Magnesium Chloridedecreases reaction, increases activity1
Cyclosporinedecreases expression1
Acrylamideincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4008389BindingInhibition of NUDT9 (unknown origin) by malachite green reagent based assayIdentification of Triazolothiadiazoles as Potent Inhibitors of the dCTP Pyrophosphatase 1. — J Med Chem

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B5KKHAP1 NUDT9 (-) 2Cancer cell lineMale
CVCL_DX51HAP1 NUDT6 (-) NUDT9 (-)Cancer cell lineMale
CVCL_XR23HAP1 NUDT9 (-) 1Cancer cell lineMale

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.