ENPP4

gene
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Also known as NPP4KIAA0879AP3Aase

Summary

ENPP4 (ectonucleotide pyrophosphatase/phosphodiesterase 4, HGNC:3359) is a protein-coding gene on chromosome 6p21.1, encoding Bis(5’-adenosyl)-triphosphatase ENPP4 (Q9Y6X5). Hydrolyzes extracellular Ap3A into AMP and ADP, and Ap4A into AMP and ATP.

Enables bis(5’-adenosyl)-triphosphatase activity. Involved in positive regulation of blood coagulation and purine ribonucleoside catabolic process. Located in extracellular exosome and membrane.

Source: NCBI Gene 22875 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 73 total
  • MANE Select transcript: NM_014936

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3359
Approved symbolENPP4
Nameectonucleotide pyrophosphatase/phosphodiesterase 4
Location6p21.1
Locus typegene with protein product
StatusApproved
AliasesNPP4, KIAA0879, AP3Aase
Ensembl geneENSG00000001561
Ensembl biotypeprotein_coding
OMIM617000
Entrez22875

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000321037, ENST00000859799, ENST00000962953, ENST00000962954, ENST00000962955

RefSeq mRNA: 1 — MANE Select: NM_014936 NM_014936

CCDS: CCDS34468

Canonical transcript exons

ENST00000321037 — 4 exons

ExonStartEnd
ENSE000007546924614105246141222
ENSE000012420684613955146140409
ENSE000014551474612998946130189
ENSE000017542654614327646146688

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 95.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.7488 / max 358.5780, expressed in 1295 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
681244.87771090
681254.13431019
681233.6412938
681220.9556429
681270.8998391
681260.2402117

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bronchial epithelial cellCL:000232895.50gold quality
endothelial cellCL:000011594.89gold quality
corpus callosumUBERON:000233694.48gold quality
nasal cavity epitheliumUBERON:000538494.45gold quality
epithelium of bronchusUBERON:000203194.04gold quality
inferior vagus X ganglionUBERON:000536393.99gold quality
bronchusUBERON:000218593.51gold quality
subthalamic nucleusUBERON:000190693.47gold quality
ponsUBERON:000098893.00gold quality
diaphragmUBERON:000110392.99gold quality
C1 segment of cervical spinal cordUBERON:000646992.71gold quality
spinal cordUBERON:000224092.52gold quality
middle frontal gyrusUBERON:000270292.04gold quality
epithelium of nasopharynxUBERON:000195191.88gold quality
seminal vesicleUBERON:000099891.64gold quality
medial globus pallidusUBERON:000247791.27gold quality
nasal cavity mucosaUBERON:000182691.11gold quality
globus pallidusUBERON:000187591.06gold quality
medulla oblongataUBERON:000189690.82gold quality
superior vestibular nucleusUBERON:000722790.78gold quality
biceps brachiiUBERON:000150790.75gold quality
renal glomerulusUBERON:000007490.74gold quality
islet of LangerhansUBERON:000000690.70gold quality
olfactory segment of nasal mucosaUBERON:000538690.64gold quality
metanephric glomerulusUBERON:000473690.54gold quality
pigmented layer of retinaUBERON:000178290.46gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450289.83gold quality
lower lobe of lungUBERON:000894989.70gold quality
frontal poleUBERON:000279589.63gold quality
dorsal plus ventral thalamusUBERON:000189789.44gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes16.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

145 targeting ENPP4, 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-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-8485100.0077.574731
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3646100.0073.565283
HSA-MIR-98-3P100.0074.083907
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-569699.9872.364487
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-477599.9875.006394
HSA-MIR-548P99.9872.253784
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-548AN99.9770.912817
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-590-3P99.9674.346478
HSA-MIR-365899.9673.874379
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-9-3P99.9670.882068
HSA-MIR-391099.9571.132227

Literature-anchored findings (GeneRIF, showing 2)

  • NPP4 promotes hemostasis in vivo by augmenting ADP-mediated platelet aggregation at the site of vascular injury. (PMID:22995898)
  • The combined studies expand our understanding of NPP1 and NPP4 substrate specificity and range and provide a rational mechanism by which polymorphisms in NPP1 confer stroke resistance. (PMID:24338010)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioenpp4ENSDARG00000006877
mus_musculusEnpp4ENSMUSG00000023961
rattus_norvegicusEnpp4ENSRNOG00000010174
caenorhabditis_elegansWBGENE00007753
caenorhabditis_elegansWBGENE00007755
caenorhabditis_elegansWBGENE00015283

Paralogs (6): ENPP5 (ENSG00000112796), ENPP2 (ENSG00000136960), ENPP3 (ENSG00000154269), ENPP6 (ENSG00000164303), ENPP7 (ENSG00000182156), ENPP1 (ENSG00000197594)

Protein

Protein identifiers

Bis(5’-adenosyl)-triphosphatase ENPP4Q9Y6X5 (reviewed: Q9Y6X5)

Alternative names: AP3A hydrolase, Ectonucleotide pyrophosphatase/phosphodiesterase family member 4

All UniProt accessions (1): Q9Y6X5

UniProt curated annotations — full annotation on UniProt →

Function. Hydrolyzes extracellular Ap3A into AMP and ADP, and Ap4A into AMP and ATP. Ap3A and Ap4A are diadenosine polyphosphates thought to induce proliferation of vascular smooth muscle cells. Acts as a procoagulant, mediating platelet aggregation at the site of nascent thrombus via release of ADP from Ap3A and activation of ADP receptors.

Subcellular location. Cell membrane.

Tissue specificity. Expressed on the surface of vascular endothelia.

Cofactor. Binds 2 Zn(2+) ions per subunit.

Similarity. Belongs to the nucleotide pyrophosphatase/phosphodiesterase family.

RefSeq proteins (1): NP_055751* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002591Phosphodiest/P_TrfaseFamily
IPR017850Alkaline_phosphatase_core_sfHomologous_superfamily

Pfam: PF01663

Enzyme classification (BRENDA):

  • EC 3.6.1.17 — bis(5’-nucleosyl)-tetraphosphatase (asymmetrical) (BRENDA: 21 organisms, 54 substrates, 68 inhibitors, 70 Km, 50 kcat entries)

Substrate kinetics (BRENDA)

21 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
AP4A0.0041–1028
P1,P4-BIS(5’-ADENOSYL) TETRAPHOSPHATE0.0007–0.0548
DIADENOSINE 5’,5’’-P1,P4-TETRAPHOSPHATE0.005–0.4076
P1,P4-BIS(5’-GUANOSYL) TETRAPHOSPHATE0.001–1.034
5’,5’’-DIADENOSINE TETRAPHOSPHATE0.0006–0.0033
5’,5’-DIADENOSINE TETRAPHOSPHATE0.009–0.0122
DIADENOSINE 5’,5’-P1,P4-TETRAPHOSPHATE0.002–0.00252
P1,P4-BIS(5’-URIDYL) TETRAPHOSPHATE0.01–0.0112
P1,P4-BIS(5’-XANTHOSYL) TETRAPHOSPHATE0.016–0.0182
2-OXO-DATP0.38461
5’,5’-DIADENOSINE HEXAPHOSPHATE0.0151
8-OXO-DGTP0.09861
AP5A0.0981
AP6A0.041
DATP0.11431

Catalyzed reactions (Rhea), 1 shown:

  • P(1),P(3)-bis(5’-adenosyl) triphosphate + H2O = AMP + ADP + 2 H(+) (RHEA:13893)

UniProt features (64 total): helix 18, strand 16, binding site 10, glycosylation site 4, turn 4, sequence variant 3, topological domain 2, disulfide bond 2, signal peptide 1, chain 1, sequence conflict 1, transmembrane region 1, active site 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
4LR2X-RAY DIFFRACTION1.5
4LQYX-RAY DIFFRACTION1.54

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y6X5-F192.490.87

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): 70 (amp-threonine intermediate)

Ligand- & substrate-binding residues (10): 189; 189; 193; 237; 238; 336; 34; 70; 91; 154

Disulfide bonds (2): 254–287, 394–401

Glycosylation sites (4): 155, 166, 276, 386

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6798695Neutrophil degranulation

MSigDB gene sets: 210 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, LEE_NEURAL_CREST_STEM_CELL_DN, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_REGULATION_OF_WOUND_HEALING, GOBP_REGULATION_OF_COAGULATION, GOCC_SECRETORY_GRANULE, GOBP_POSITIVE_REGULATION_OF_COAGULATION, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_WOUND_HEALING, GOBP_REGULATION_OF_RESPONSE_TO_WOUNDING, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, AAAGACA_MIR511

GO Biological Process (4): blood coagulation (GO:0007596), positive regulation of blood coagulation (GO:0030194), purine ribonucleoside catabolic process (GO:0046130), hemostasis (GO:0007599)

GO Molecular Function (4): metal ion binding (GO:0046872), bis(5’-adenosyl)-triphosphatase activity (GO:0047710), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (4): plasma membrane (GO:0005886), membrane (GO:0016020), extracellular exosome (GO:0070062), ficolin-1-rich granule membrane (GO:0101003)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Innate Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
hemostasis1
wound healing1
coagulation1
blood coagulation1
regulation of blood coagulation1
positive regulation of coagulation1
positive regulation of wound healing1
positive regulation of hemostasis1
purine nucleoside catabolic process1
ribonucleoside catabolic process1
purine ribonucleoside metabolic process1
regulation of body fluid levels1
cation binding1
pyrophosphatase activity1
binding1
catalytic activity1
membrane1
cell periphery1
cellular anatomical structure1
extracellular vesicle1
secretory granule membrane1
tertiary granule1
ficolin-1-rich granule1

Protein interactions and networks

STRING

794 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ENPP4ZNF883P0CG24581
ENPP4AK6Q9Y3D8450
ENPP4GDPD1Q8N9F7403
ENPP4GDPD3Q7L5L3383
ENPP4ENTPD7Q9NQZ7376
ENPP4ENTPD4Q9Y227347
ENPP4GNG13Q9P2W3342
ENPP4TUFT1Q9NNX1342
ENPP4OTORQ9NRC9337
ENPP4RARS2Q5T160337
ENPP4B3GLCTQ6Y288336
ENPP4FKBP7Q9Y680334
ENPP4NME8Q8N427333
ENPP4GAL3ST1Q99999330
ENPP4CLIC5Q9NZA1329
ENPP4ENTPD6O75354329

IntAct

40 interactions, top by confidence:

ABTypeScore
TMBIM6ENPP4psi-mi:“MI:0915”(physical association)0.560
TMEM147ENPP4psi-mi:“MI:0915”(physical association)0.560
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
IPPKTMEM223psi-mi:“MI:0914”(association)0.530
SOX2PDLIM1psi-mi:“MI:0914”(association)0.530
LPAR1TMEM120Bpsi-mi:“MI:0914”(association)0.530
ANKHFAM234Bpsi-mi:“MI:0914”(association)0.530
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
LGALS3PODXLpsi-mi:“MI:0914”(association)0.530
CLGNNPC1psi-mi:“MI:0914”(association)0.530
LGALS8SLC22A23psi-mi:“MI:0914”(association)0.350
LGALS9PODXLpsi-mi:“MI:0914”(association)0.350
LGALS3PODXLpsi-mi:“MI:0914”(association)0.350
IL17RCC2CD2Lpsi-mi:“MI:0914”(association)0.350
LMAN2LACP2psi-mi:“MI:0914”(association)0.350
ARHGAP18CLTBpsi-mi:“MI:0914”(association)0.350
CANXHLA-Apsi-mi:“MI:0914”(association)0.350
CLTACLTBpsi-mi:“MI:0914”(association)0.350
LAMP1DSTpsi-mi:“MI:0914”(association)0.350
RAB14TSPAN6psi-mi:“MI:0914”(association)0.350
STX12SCAMP1psi-mi:“MI:0914”(association)0.350
VAMP3SCAMP1psi-mi:“MI:0914”(association)0.350

BioGRID (49): ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Synthetic Lethality), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), ENPP4 (Affinity Capture-MS), TMEM147 (Two-hybrid)

ESM2 similar proteins: A0A2D0TC04, A2VDP5, B0BND0, F1N5C8, J3SBP3, J3SEZ3, O14638, O62806, O94323, P06802, P0DQQ4, P23188, P23377, P29119, P54793, P70699, P84039, P97675, Q0VA77, Q29444, Q32KH8, Q4FZV0, Q566N0, Q58D68, Q5BKW7, Q5FYA8, Q5R5M5, Q5RAC0, Q5RB45, Q6AX80, Q6DDP3, Q6DYE8, Q6P179, Q6P7A9, Q6UVY6, Q6UWR7, Q8BGN3, Q8BTJ4, Q8C129, Q8IVL8

Diamond homologs: A0A2D0TC04, A1A4K5, A2VDP5, J3SBP3, J3SEZ3, O14638, O94323, P06802, P0DQQ4, P15396, P22413, P84039, P97675, Q0VA77, Q13822, Q3TIW9, Q566N0, Q5EZ72, Q5R5M5, Q5RAC0, Q64610, Q6AX80, Q6DYE8, Q6UWV6, Q8BTJ4, Q924C3, Q9EQG7, Q9R1E6, Q9UJA9, Q9Y6X5, W8E7D1, P90754, A1YYW7, B0BND0, F1N5C8, P90755, Q58D68, Q5BKW7, Q5RB45, Q6DDP3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance65
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

412 predictions. Top by Δscore:

VariantEffectΔscore
6:46130185:GGCTG:Gdonor_gain1.0000
6:46130186:GCTG:Gdonor_gain1.0000
6:46130186:GCTGG:Gdonor_gain1.0000
6:46130188:TGGTG:Tdonor_loss1.0000
6:46130190:G:GGdonor_gain1.0000
6:46130191:T:Adonor_loss1.0000
6:46130194:G:GGdonor_gain1.0000
6:46141050:A:AGacceptor_gain1.0000
6:46141051:G:GGacceptor_gain1.0000
6:46141051:GAT:Gacceptor_gain1.0000
6:46141051:GATA:Gacceptor_gain1.0000
6:46141218:AAAAT:Adonor_gain1.0000
6:46141219:AAAT:Adonor_gain1.0000
6:46141220:AAT:Adonor_gain1.0000
6:46141220:AATGT:Adonor_loss1.0000
6:46141221:AT:Adonor_gain1.0000
6:46141221:ATGTA:Adonor_loss1.0000
6:46141222:TG:Tdonor_loss1.0000
6:46141223:G:GGdonor_gain1.0000
6:46141223:GT:Gdonor_loss1.0000
6:46141224:T:Adonor_loss1.0000
6:46143275:GTA:Gacceptor_gain1.0000
6:46130188:TG:Tdonor_gain0.9900
6:46130189:GG:Gdonor_gain0.9900
6:46140406:ATAA:Adonor_gain0.9900
6:46140407:TAA:Tdonor_gain0.9900
6:46140410:G:GGdonor_gain0.9900
6:46141048:TCA:Tacceptor_loss0.9900
6:46141050:AGATA:Aacceptor_loss0.9900
6:46143274:A:AGacceptor_gain0.9900

AlphaMissense

3035 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:46140289:A:CS236R0.998
6:46140291:T:AS236R0.998
6:46140291:T:GS236R0.998
6:46139989:T:AW136R0.997
6:46139989:T:CW136R0.997
6:46139809:A:CS76R0.996
6:46139811:T:AS76R0.996
6:46139811:T:GS76R0.996
6:46140290:G:TS236I0.995
6:46143330:C:AA351D0.995
6:46139941:T:AW120R0.994
6:46139941:T:CW120R0.994
6:46140293:A:TD237V0.994
6:46140298:G:TG239W0.992
6:46139991:G:CW136C0.990
6:46139991:G:TW136C0.990
6:46140292:G:CD237H0.990
6:46140293:A:CD237A0.990
6:46143329:G:CA351P0.990
6:46139677:T:CS32P0.989
6:46139684:A:TD34V0.989
6:46139822:G:AG80D0.989
6:46139851:G:CA90P0.989
6:46139943:G:CW120C0.989
6:46139943:G:TW120C0.989
6:46140296:A:CH238P0.989
6:46139685:T:AD34E0.988
6:46139685:T:GD34E0.988
6:46140294:T:AD237E0.988
6:46140294:T:GD237E0.988

dbSNP variants (sampled 300 via entrez): RS1000520317 (6:46130321 C>T), RS1000645723 (6:46137007 G>A), RS1000758999 (6:46144195 A>G), RS1000883558 (6:46134270 C>G), RS1000891218 (6:46146302 A>G), RS1000991439 (6:46139128 C>G,T), RS1001036594 (6:46130114 C>A,T), RS1001323970 (6:46134064 C>A,T), RS1001434155 (6:46140756 T>C), RS1001488559 (6:46132832 A>T), RS1002089049 (6:46144353 TTCTC>T), RS1002309904 (6:46129182 T>C), RS1002374727 (6:46138006 A>G), RS1002440929 (6:46135220 A>G), RS1002458792 (6:46131559 G>C)

Disease associations

OMIM: gene MIM:617000 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST004484_8Plasma trimethylamine N-oxide levels4.000000e-07
GCST007001_4Cerebrospinal AB1-42 levels in normal cognition7.000000e-07
GCST90002396_325Mean reticulocyte volume7.000000e-11
GCST90002397_147Mean spheric corpuscular volume6.000000e-11
GCST90002401_525Platelet distribution width8.000000e-10

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0005691plasma trimethylamine N-oxide measurement
EFO:0004670beta-amyloid 1-42 measurement
EFO:0010701mean reticulocyte volume
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression4
methylmercuric chloridedecreases expression3
trichostatin Aaffects cotreatment, decreases expression, increases expression3
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression2
Estradiolaffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Smokedecreases expression2
TAK-243decreases sumoylation1
triphenyl phosphateaffects expression1
bisphenol Aincreases methylation1
butyraldehydeincreases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
potassium chromate(VI)increases expression1
nickel sulfatedecreases expression1
pentanalincreases expression1
perfluorooctane sulfonic aciddecreases expression1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
clothianidinincreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangaffects cotreatment, increases expression1
Temozolomidedecreases expression1
Vorinostatincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Cisplatinaffects cotreatment, increases expression1
Doxorubicindecreases expression1

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.