NUDT10

gene
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Also known as DIPP3ahDIPP3alpha

Summary

NUDT10 (nudix hydrolase 10, HGNC:17621) is a protein-coding gene on chromosome Xp11.22, encoding Diphosphoinositol polyphosphate phosphohydrolase 3-alpha (Q8NFP7). Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate), suggesting that it may play a role in signal transduction.

This gene is a member of the nudix (nucleoside diphosphate linked moiety X)-type motif containing family. The encoded protein is a phosphohydrolase and may regulate the turnover of diphosphoinositol polyphosphates. The turnover of these high-energy diphosphoinositol polyphosphates represents a molecular switching activity with important regulatory consequences. Molecular switching by diphosphoinositol polyphosphates may contribute to the regulation of intracellular trafficking. In some populations putative prostate cancer susceptibility alleles have been identified for this gene. Alternatively spliced transcript variants, which differ only in the 5’ UTR, have been found for this gene.

Source: NCBI Gene 170685 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 15 total
  • Druggable target: yes
  • MANE Select transcript: NM_001304963

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17621
Approved symbolNUDT10
Namenudix hydrolase 10
LocationXp11.22
Locus typegene with protein product
StatusApproved
AliasesDIPP3a, hDIPP3alpha
Ensembl geneENSG00000122824
Ensembl biotypeprotein_coding
OMIM300527
Entrez170685

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000356450, ENST00000376006

RefSeq mRNA: 2 — MANE Select: NM_001304963 NM_001304963, NM_153183

CCDS: CCDS35278

Canonical transcript exons

ENST00000356450 — 2 exons

ExonStartEnd
ENSE000014691025133282251333459
ENSE000014691135133623951337525

Expression profiles

Bgee: expression breadth ubiquitous, 171 present calls, max score 91.20.

FANTOM5 (CAGE): breadth broad, TPM avg 3.1711 / max 124.0915, expressed in 646 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1963601.9093471
1963610.6126326
2096840.4040227
1963580.1722103
1963590.072927

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534391.20gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099187.39gold quality
ganglionic eminenceUBERON:000402387.37gold quality
right testisUBERON:000453487.05gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.91gold quality
testisUBERON:000047385.50gold quality
left testisUBERON:000453385.46gold quality
Brodmann (1909) area 9UBERON:001354084.76gold quality
prefrontal cortexUBERON:000045184.40gold quality
right ovaryUBERON:000211883.95gold quality
ventricular zoneUBERON:000305383.78gold quality
dorsolateral prefrontal cortexUBERON:000983483.05gold quality
left ovaryUBERON:000211982.90gold quality
anterior cingulate cortexUBERON:000983582.72gold quality
seminal vesicleUBERON:000099882.59gold quality
hypothalamusUBERON:000189882.33gold quality
neocortexUBERON:000195081.35gold quality
frontal cortexUBERON:000187081.17gold quality
ovaryUBERON:000099280.38gold quality
right frontal lobeUBERON:000281080.35gold quality
nucleus accumbensUBERON:000188280.01gold quality
cerebral cortexUBERON:000095679.37gold quality
amygdalaUBERON:000187679.07gold quality
pancreatic ductal cellCL:000207978.14silver quality
prostate glandUBERON:000236777.46gold quality
forebrainUBERON:000189076.52gold quality
brainUBERON:000095575.89gold quality
Brodmann (1909) area 46UBERON:000648375.51gold quality
caudate nucleusUBERON:000187375.50gold quality
myometriumUBERON:000129675.39gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting NUDT10, 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-4795-3P100.0074.624024
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-480399.9871.993117
HSA-MIR-60799.9773.625593
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-367199.9073.043897
HSA-LET-7A-2-3P99.8770.531921
HSA-MIR-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-LET-7G-3P99.8570.431929
HSA-MIR-576-5P99.8470.462582
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-7161-5P99.6868.921592
HSA-MIR-580-3P99.6769.231841
HSA-MIR-548U99.6567.781463
HSA-MIR-18A-3P99.5665.681092
HSA-MIR-4753-5P99.5468.511356
HSA-MIR-7159-5P99.5372.122472
HSA-MIR-443799.5265.291266
HSA-MIR-143-3P99.4969.051457
HSA-MIR-477099.4969.091451
HSA-MIR-448099.4266.02735
HSA-MIR-568399.3668.592083
HSA-MIR-608899.2968.451284
HSA-MIR-3160-5P99.2869.071938
HSA-MIR-397399.2069.191990
HSA-MIR-205499.2068.891699
HSA-MIR-607199.1667.771780

Literature-anchored findings (GeneRIF, showing 3)

  • The NUDT10 gene, located on chromosome X, is preferentially expressed in the testis (PMID:12105228)
  • Cloning and characterisation of NUDT10 as a diadenosine polyphosphate-metabolising Nudix hydrolase. (PMID:12121577)
  • Clinical correlations and prognostic value of Nudix hydroxylase 10 in patients with gastric cancer. (PMID:34696672)

Cross-species orthologs

0 orthologs

Paralogs (4): NUDT4 (ENSG00000173598), NUDT4B (ENSG00000177144), NUDT11 (ENSG00000196368), NUDT3 (ENSG00000272325)

Protein

Protein identifiers

Diphosphoinositol polyphosphate phosphohydrolase 3-alphaQ8NFP7 (reviewed: Q8NFP7)

Alternative names: Diadenosine 5’,5’’’-P1,P6-hexaphosphate hydrolase 3-alpha, Diadenosine hexaphosphate hydrolase (AMP-forming), Nucleoside diphosphate-linked moiety X motif 10, hAps2

All UniProt accessions (1): Q8NFP7

UniProt curated annotations — full annotation on UniProt →

Function. Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate), suggesting that it may play a role in signal transduction. Also able to catalyze the hydrolysis of dinucleoside oligophosphates, with Ap6A and Ap5A being the preferred substrates. The major reaction products are ADP and p4a from Ap6A and ADP and ATP from Ap5A. Also able to hydrolyze 5-phosphoribose 1-diphosphate.

Subcellular location. Cytoplasm.

Tissue specificity. Mainly expressed in testis and, at lower level in brain. According to PubMed:12121577, it is widely expressed.

Cofactor. Binds 3 Mg(2+) or Mn(2+) ions per subunit. Mn(2+) may be the true cofactor in vivo.

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

RefSeq proteins (2): NP_001291892, NP_694853 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000086NUDIX_hydrolase_domDomain
IPR015797NUDIX_hydrolase-like_dom_sfHomologous_superfamily
IPR020084NUDIX_hydrolase_CSConserved_site
IPR047198DDP-like_NUDIXDomain

Pfam: PF00293

Enzyme classification (BRENDA):

  • EC 3.6.1.60 — diadenosine hexaphosphate hydrolase (AMP-forming) (BRENDA: 3 organisms, 19 substrates, 9 inhibitors, 9 Km, 9 kcat entries)

Substrate kinetics (BRENDA)

2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
P1,P5-BIS(5’-ADENOSYL)PENTAPHOSPHATE0.0077–0.056
P1,P6-BIS(5’-ADENOSYL)HEXAPHOSPHATE0.0059–0.613

Catalyzed reactions (Rhea), 2 shown:

  • P(1),P(6)-bis(5’-adenosyl) hexaphosphate + H2O = adenosine 5’-pentaphosphate + AMP + 2 H(+) (RHEA:32047)
  • P(1),P(5)-bis(5’-adenosyl) pentaphosphate + H2O = adenosine 5’-tetraphosphate + AMP + 2 H(+) (RHEA:32051)

UniProt features (30 total): binding site 10, strand 8, helix 4, sequence conflict 2, chain 1, domain 1, region of interest 1, short sequence motif 1, compositionally biased region 1, active site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3MCFX-RAY DIFFRACTION2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NFP7-F189.800.80

Functional residue map

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

Catalytic / active sites (1): 68 (proton acceptor)

Ligand- & substrate-binding residues (10): 65; 65; 69; 89–91; 115; 133; 9; 17–19; 38–40; 49

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-1855167Synthesis of pyrophosphates in the cytosol

MSigDB gene sets: 64 (showing top): AP1_01, TGCGCANK_UNKNOWN, GOBP_INOSITOL_PHOSPHATE_METABOLIC_PROCESS, GOBP_POLYOL_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_CATABOLIC_PROCESS, TGANTCA_AP1_C, NRF2_Q4, GOBP_NUCLEOSIDE_PHOSPHATE_CATABOLIC_PROCESS, WHN_B, GOBP_PURINE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_PURINE_CONTAINING_COMPOUND_CATABOLIC_PROCESS

GO Biological Process (4): diphosphoinositol polyphosphate metabolic process (GO:0071543), diadenosine pentaphosphate catabolic process (GO:1901907), diadenosine hexaphosphate catabolic process (GO:1901909), adenosine 5’-(hexahydrogen pentaphosphate) catabolic process (GO:1901911)

GO Molecular Function (8): endopolyphosphatase activity (GO:0000298), diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486), bis(5’-adenosyl)-hexaphosphatase activity (GO:0034431), bis(5’-adenosyl)-pentaphosphatase activity (GO:0034432), metal ion binding (GO:0046872), protein binding (GO:0005515), pyrophosphatase activity (GO:0016462), hydrolase activity (GO:0016787)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Inositol phosphate metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
pyrophosphatase activity4
diadenosine polyphosphate catabolic process2
cellular anatomical structure2
inositol phosphate metabolic process1
purine ribonucleotide catabolic process1
cation binding1
binding1
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides1
catalytic activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

770 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NUDT10AIREO43918833
NUDT10TOR1AO14656774
NUDT10TNFRSF25P78507751
NUDT10MICBP79525666
NUDT10PTPN22Q9Y2R2629
NUDT10TNFRSF10AO00220626
NUDT10Q5Y7H0Q5Y7H0534
NUDT10HLA-BP01889503
NUDT10HLA-DRAP01903426
NUDT10RASSF1Q9NS23422
NUDT10TGP01266371
NUDT10TPOP07202371
NUDT10NUDT22Q9BRQ3367
NUDT10POMCP01189366
NUDT10NUDT17P0C025330

IntAct

28 interactions, top by confidence:

ABTypeScore
RNASEH2CRNASEH2Apsi-mi:“MI:0914”(association)0.640
NUDT10SNAPC5psi-mi:“MI:0915”(physical association)0.560
NUDT10TCF4psi-mi:“MI:0915”(physical association)0.560
MTUS2NUDT10psi-mi:“MI:0915”(physical association)0.560
SNAPC5NUDT10psi-mi:“MI:0915”(physical association)0.560
TCF4NUDT10psi-mi:“MI:0915”(physical association)0.560
NUDT10MTUS2psi-mi:“MI:0915”(physical association)0.560
NUDT10PDLIM7psi-mi:“MI:0915”(physical association)0.560
RELNUDT10psi-mi:“MI:0915”(physical association)0.560
HSF2BPNUDT10psi-mi:“MI:0915”(physical association)0.560
NUDT10TRIM8psi-mi:“MI:0915”(physical association)0.560
NUDT10NUDT4Bpsi-mi:“MI:0914”(association)0.500
NUDT10NUDT4Bpsi-mi:“MI:0915”(physical association)0.500
NUDT3NUDT10psi-mi:“MI:0914”(association)0.350
NUDT10TRIM8psi-mi:“MI:0915”(physical association)0.000
NUDT10PDLIM7psi-mi:“MI:0915”(physical association)0.000
NUDT10RELpsi-mi:“MI:0915”(physical association)0.000
NUDT10HSF2BPpsi-mi:“MI:0915”(physical association)0.000
ddhANUDT10psi-mi:“MI:0915”(physical association)0.000
RASSF1NUDT10psi-mi:“MI:0915”(physical association)0.000

BioGRID (20): NUDT10 (Two-hybrid), NUDT10 (Two-hybrid), NUDT10 (Two-hybrid), NUDT10 (Affinity Capture-MS), NUDT10 (Affinity Capture-MS), NUDT10 (Affinity Capture-MS), HSF2BP (Two-hybrid), REL (Two-hybrid), TRIM8 (Two-hybrid), PDLIM7 (Two-hybrid), NUDT10 (Affinity Capture-MS), NUDT10 (Affinity Capture-MS), NUDT4 (Affinity Capture-MS), NUDT10 (Affinity Capture-MS), HNRNPLL (Affinity Capture-MS)

ESM2 similar proteins: A0A024RBG1, A2VE79, A3KMI0, A7E320, B0R160, B6CHA3, F4JLK2, F6UA42, O22951, O45830, O59761, O95989, P0C027, P0C028, P32271, Q08C92, Q09790, Q566C7, Q58CW0, Q5RAF0, Q5RDX4, Q5U243, Q6NPD7, Q6P5D3, Q7TMI3, Q7TPK1, Q7YTB0, Q8BJM7, Q8CIG3, Q8L7W2, Q8NB78, Q8NFP7, Q8R2U6, Q8VDF2, Q8VHT6, Q91WU5, Q96G61, Q96PU4, Q96T88, Q99321

Diamond homologs: A0A024RBG1, A2VE79, O95989, P0C027, P0C028, P53370, P70563, P96590, Q09790, Q52K88, Q566C7, Q58CW0, Q5RAF0, Q8CH40, Q8NFP7, Q8R2U6, Q8VY81, Q93ZY7, Q96G61, Q99321, Q99MY2, Q9JI46, Q9LE73, Q9LHK1, Q9LQU5, Q9NZJ9, Q9ZU95, Q9RVK2, A1AA28, A4FUG7, A7ZKS4, A7ZZ89, B1IUD3, B1LI09, B1XA44, P0AEI6, P0AEI7, P0AEI8, P0AEI9, P0C025

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance9
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

386 predictions. Top by Δscore:

VariantEffectΔscore
X:51333460:G:GGdonor_gain0.9900
X:51336233:TTTTA:Tacceptor_loss0.9900
X:51336234:TTTA:Tacceptor_loss0.9900
X:51336237:A:AGacceptor_gain0.9800
X:51336238:G:GGacceptor_gain0.9800
X:51336238:GGT:Gacceptor_gain0.9800
X:51333447:A:Gdonor_gain0.9700
X:51333398:C:Gdonor_gain0.9600
X:51333458:TA:Tdonor_gain0.9600
X:51336227:TTTTC:Tacceptor_loss0.9600
X:51336228:TTTCT:Tacceptor_loss0.9600
X:51336229:TTCTT:Tacceptor_loss0.9600
X:51336230:TCTTT:Tacceptor_loss0.9600
X:51336231:CTTTT:Cacceptor_loss0.9600
X:51336232:TTTTT:Tacceptor_loss0.9600
X:51333455:CCCTA:Cdonor_gain0.9500
X:51333457:CTA:Cdonor_gain0.9500
X:51336225:ATTTT:Aacceptor_loss0.9500
X:51336226:TTTTT:Tacceptor_loss0.9500
X:51333071:G:GGdonor_gain0.9400
X:51333456:CCTA:Cdonor_gain0.9400
X:51333458:TAGTA:Tdonor_loss0.9300
X:51333459:AG:Adonor_loss0.9300
X:51333460:G:GAdonor_loss0.9300
X:51333461:TAT:Tdonor_loss0.9300
X:51333240:GAAC:Gdonor_gain0.9200
X:51333349:TCTCC:Tdonor_gain0.9200
X:51333420:G:GTdonor_gain0.9200
X:51332368:G:GGdonor_gain0.9100
X:51336238:GGTGA:Gacceptor_gain0.8900

AlphaMissense

1059 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:51333309:G:CR115T1.000
X:51333309:G:TR115M1.000
X:51333310:G:CR115S1.000
X:51333310:G:TR115S1.000
X:51333031:C:GC22W0.999
X:51333037:C:GC24W0.999
X:51333066:T:CL34P0.999
X:51333069:T:CL35S0.999
X:51333098:T:AW45R0.999
X:51333098:T:CW45R0.999
X:51333108:C:AP48Q0.999
X:51333173:G:CA70P0.999
X:51333177:G:AG71E0.999
X:51333320:T:AW119R0.999
X:51333320:T:CW119R0.999
X:51333322:G:CW119C0.999
X:51333322:G:TW119C0.999
X:51333029:T:CC22R0.998
X:51333035:T:CC24R0.998
X:51333036:G:AC24Y0.998
X:51333105:T:AV47E0.998
X:51333111:G:AG49D0.998
X:51333114:G:AG50E0.998
X:51333150:C:AA62E0.998
X:51333156:G:CR64P0.998
X:51333160:G:CE65D0.998
X:51333160:G:TE65D0.998
X:51333169:A:CE68D0.998
X:51333169:A:TE68D0.998
X:51333177:G:TG71V0.998

dbSNP variants (sampled 300 via entrez): RS1000477164 (X:51334979 C>T), RS1000787477 (X:51335537 G>T), RS1004900296 (X:51337309 C>G), RS1005398968 (X:51336592 G>A), RS1009150108 (X:51335571 T>C), RS1009183664 (X:51336030 G>A), RS1011946518 (X:51334909 G>A,T), RS1013383330 (X:51336712 C>G), RS1013623642 (X:51337382 T>C), RS1015026087 (X:51336658 C>G,T), RS1015198299 (X:51336160 T>C), RS1018917657 (X:51335190 C>T), RS1018991002 (X:51335590 G>C), RS1023388654 (X:51336770 T>C,G), RS1023459049 (X:51337408 C>T)

Disease associations

OMIM: gene MIM:300527 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST000152_12Prostate cancer2.000000e-09
GCST000153_1Prostate cancer4.000000e-13
GCST90000050_87Age at first birth1.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009101age at first birth measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4295904 (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
Benzo(a)pyreneaffects methylation, increases expression2
kojic aciddecreases expression1
P(1),P(5)-di(adenosine-5’-)pentaphosphateincreases metabolic processing, increases reaction, increases chemical synthesis1
diguanosine tetraphosphateincreases metabolic processing1
adenosine 5’-tetraphosphateincreases chemical synthesis, increases metabolic processing1
diadenosine tetraphosphateincreases metabolic processing1
manganese chlorideincreases metabolic processing, increases reaction1
4-aminophenylarsenoxideaffects binding, decreases reaction1
adenosine 5’-pentaphosphateincreases chemical synthesis, increases metabolic processing1
diadenosine 5’,5’’’’-P1,P6-hexaphosphateincreases chemical synthesis, increases metabolic processing1
CGP 52608affects binding, increases reaction1
nutlin 3affects cotreatment, increases expression1
abrinedecreases expression1
Sunitinibdecreases expression1
Arsenic Trioxideaffects binding, decreases reaction1
Adenosine Monophosphateincreases chemical synthesis, increases metabolic processing1
Clozapineincreases expression1
Dactinomycinaffects cotreatment, increases expression1
Diethylhexyl Phthalatedecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Silicon Dioxideincreases expression1
8-Bromo Cyclic Adenosine Monophosphatedecreases expression1

ChEMBL screening assays

4 unique, capped per target: 2 admet, 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4259508ADMETSubstrate activity at N-terminal His-tagged DIPP3-alpha (unknown origin) expressed in Escherichia coli assessed as enzyme-mediated test compound metabolism after 20 mins in presence of Mg2+ by malachite green dye based assayA synthetic diphosphoinositol phosphate analogue of inositol trisphosphate. — Medchemcomm
CHEMBL4259517BindingStabilization of N-terminal His-tagged DIPP3-alpha (unknown origin) expressed in Escherichia coli assessed as increase in melting temperature at 0.1 mM by SYPRO orange dye based DSF methodA synthetic diphosphoinositol phosphate analogue of inositol trisphosphate. — Medchemcomm

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E2ENHAP1 NUDT10 (-) 1Cancer cell lineMale
CVCL_E2EPHAP1 NUDT10 (-) 2Cancer 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.