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APRT

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Summary

APRT (adenine phosphoribosyltransferase, HGNC:626) is a protein-coding gene on chromosome 16q24.3, encoding Adenine phosphoribosyltransferase (P07741). Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.

Adenine phosphoribosyltransferase belongs to the purine/pyrimidine phosphoribosyltransferase family. A conserved feature of this gene is the distribution of CpG dinucleotides. This enzyme catalyzes the formation of AMP and inorganic pyrophosphate from adenine and 5-phosphoribosyl-1-pyrophosphate (PRPP). It also produces adenine as a by-product of the polyamine biosynthesis pathway. A homozygous deficiency in this enzyme causes 2,8-dihydroxyadenine urolithiasis. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 353 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): adenine phosphoribosyltransferase deficiency (Definitive, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 222 total — 56 pathogenic, 24 likely-pathogenic
  • GTEx eGene: eQTL in 46 tissues, sQTL in 36 (q < 0.05)
  • Phenotypes (HPO): 28
  • ChEMBL bioactivity: 1 clinical-phase molecule tested; no curated mechanism-of-action drug
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.79 (unconstrained)
  • MANE Select transcript: NM_000485
  • Interaction hub: 3,125 STRING partners (top 2% of genes corpus-wide)

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:626
Approved symbolAPRT
Nameadenine phosphoribosyltransferase
Location16q24.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000198931
Ensembl biotypeprotein_coding
OMIM102600
Entrez353

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 21 protein_coding, 7 nonsense_mediated_decay, 4 retained_intron

MANE Select: ENST00000378364

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 4, TSL 3: 3, TSL 5: 3

ENST00000378364, ENST00000426324, ENST00000562464, ENST00000563655, ENST00000564858, ENST00000567057, ENST00000567391, ENST00000567713, ENST00000568319, ENST00000568575, ENST00000569616, ENST00000880214, ENST00000880215, ENST00000912467, ENST00000912468, ENST00000912469, ENST00000912470, ENST00000912471, ENST00000912472, ENST00000912473, ENST00000974599, ENST00001041525, ENST00001068262, ENST00001068263, ENST00001068266, ENST00001068267, ENST00001068268, ENST00001068273, ENST00001068277, ENST00001068278, ENST00001068283, ENST00001140439

RefSeq mRNA: 2 — MANE Select: NM_000485 NM_000485, NM_001030018

CCDS: CCDS32511, CCDS45546

Canonical transcript exons

ENST00000378364 — 5 exons

ExonStartEnd
ENSE000015039178881042388810556
ENSE000015039188881155088811656
ENSE000025849248880933988809840
ENSE000025991638881182088811928
ENSE000034734858881007088810148

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 98.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 117.1645 / max 545.9404, expressed in 1823 samples.

Highest expression (Bgee): skin of abdomen, skin of leg, lower esophagus mucosa, granulocyte, mucosa of transverse colon.

Genetic regulation across tissues (GTEx eQTL / sQTL)

APRT is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 46 tissues and its splicing (sQTL) in 36 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 82 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Skin Not Sun Exposed Suprapubicsqtl1.8e-29-1.5616:88809297:G:A
Muscle Skeletaleqtl1.8e-26-0.4816:88811949:G:T
Skin Sun Exposed Lower legsqtl2.8e-25-1.2916:88809297:G:A
Artery Tibialeqtl9.2e-24-0.3816:88811949:G:T
Nerve Tibialeqtl8.4e-22-0.3416:88811949:G:T
Adipose Subcutaneouseqtl1.0e-20-0.4016:88811949:G:T
Esophagus Mucosasqtl1.2e-19-1.8116:88809297:G:A
Whole Bloodeqtl1.2e-19-0.5916:88862191:C:G
Adipose Subcutaneoussqtl1.6e-19-1.2916:88809297:G:A
Cells Cultured fibroblastssqtl6.7e-19-1.3516:88809297:G:A
Esophagus Musculariseqtl1.8e-17-0.4316:88811949:G:T
Artery Aortaeqtl2.8e-17-0.4216:88811949:G:T
Lungeqtl6.2e-17-0.3116:88811949:G:T
Skin Sun Exposed Lower legeqtl6.7e-17-0.2616:88811949:G:T
Heart Left Ventricleeqtl1.8e-16-0.5116:88811949:G:T
Thyroideqtl2.5e-16-0.3316:88811949:G:T
Muscle Skeletalsqtl6.0e-15-1.3616:88809297:G:A
Cells EBV-transformed lymphocyteseqtl1.3e-14-1.2116:88862191:C:G
Skin Not Sun Exposed Suprapubiceqtl2.4e-14-0.6916:88812826:G:A
Brain Caudate basal gangliaeqtl6.1e-14-0.5716:88811949:G:T

FANTOM5 promoters

2 alternative TSS:

Promoter IDTPM avgSamples expressed
158581116.45931823
1585800.7052337

Top tissues by expression

showing 100 of 295 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
skin of abdomenUBERON:000141698.73gold quality
skin of legUBERON:000151198.72gold quality
lower esophagus mucosaUBERON:003583498.63gold quality
granulocyteCL:000009498.59gold quality
mucosa of transverse colonUBERON:000499198.31gold quality
body of pancreasUBERON:000115098.26gold quality
right adrenal glandUBERON:000123398.25gold quality
esophagus mucosaUBERON:000246998.23gold quality
right adrenal gland cortexUBERON:003582798.11gold quality
left adrenal gland cortexUBERON:003582598.10gold quality
left adrenal glandUBERON:000123498.09gold quality
body of stomachUBERON:000116197.94gold quality
adrenal cortexUBERON:000123597.82gold quality
zone of skinUBERON:000001497.80gold quality
transverse colonUBERON:000115797.59gold quality
minor salivary glandUBERON:000183097.59gold quality
right lobe of liverUBERON:000111497.58gold quality
endometrium epitheliumUBERON:000481197.57gold quality
right lobe of thyroid glandUBERON:000111997.50gold quality
left lobe of thyroid glandUBERON:000112097.38gold quality
small intestine Peyer’s patchUBERON:000345497.29gold quality
esophagusUBERON:000104397.26gold quality
left uterine tubeUBERON:000130397.26gold quality
mouth mucosaUBERON:000372997.25gold quality
adrenal glandUBERON:000236997.24gold quality
ectocervixUBERON:001224997.21gold quality
spleenUBERON:000210697.19gold quality
omental fat padUBERON:001041497.16gold quality
peritoneumUBERON:000235897.13gold quality
metanephros cortexUBERON:001053397.05gold quality
endocervixUBERON:000045897.03gold quality
left coronary arteryUBERON:000162697.00gold quality
saliva-secreting glandUBERON:000104496.98gold quality
olfactory segment of nasal mucosaUBERON:000538696.98gold quality
right uterine tubeUBERON:000130296.91gold quality
adipose tissue of abdominal regionUBERON:000780896.91gold quality
thyroid glandUBERON:000204696.80gold quality
coronary arteryUBERON:000162196.73gold quality
upper lobe of left lungUBERON:000895296.71gold quality
lymph nodeUBERON:000002996.69gold quality
stomachUBERON:000094596.67gold quality
body of uterusUBERON:000985396.64gold quality
vaginaUBERON:000099696.57gold quality
monocyteCL:000057696.46gold quality
cervix squamous epitheliumUBERON:000692296.46gold quality
leukocyteCL:000073896.44gold quality
right ovaryUBERON:000211896.40gold quality
small intestineUBERON:000210896.32gold quality
esophagogastric junction muscularis propriaUBERON:003584196.30gold quality
mononuclear cellCL:000084296.29gold quality
left ovaryUBERON:000211996.26gold quality
tibial nerveUBERON:000132396.22gold quality
gingival epitheliumUBERON:000194996.22gold quality
lower esophagusUBERON:001347396.21gold quality
adenohypophysisUBERON:000219696.20gold quality
lower esophagus muscularis layerUBERON:003583396.20gold quality
mucosa of stomachUBERON:000119996.19gold quality
tonsilUBERON:000237296.19gold quality
upper lobe of lungUBERON:000894896.19gold quality
right lungUBERON:000216796.15gold quality
right coronary arteryUBERON:000162596.14gold quality
ascending aortaUBERON:000149696.02gold quality
thoracic aortaUBERON:000151596.02gold quality
fundus of stomachUBERON:000116095.89gold quality
nippleUBERON:000203095.73gold quality
bloodUBERON:000017895.67gold quality
muscle layer of sigmoid colonUBERON:003580595.61gold quality
gingivaUBERON:000182895.60gold quality
apex of heartUBERON:000209895.57gold quality
prostate glandUBERON:000236795.56gold quality
aortaUBERON:000094795.50gold quality
right atrium auricular regionUBERON:000663195.49gold quality
stromal cell of endometriumCL:000225595.48gold quality
descending thoracic aortaUBERON:000234595.46gold quality
colonUBERON:000115595.39gold quality
liverUBERON:000210795.26gold quality
penisUBERON:000098995.25gold quality
pituitary glandUBERON:000000795.23gold quality
tibial arteryUBERON:000761095.22gold quality
popliteal arteryUBERON:000225095.21gold quality
large intestineUBERON:000005995.20gold quality
tendon of biceps brachiiUBERON:000818895.20gold quality
vermiform appendixUBERON:000115495.19gold quality
intestineUBERON:000016095.13gold quality
subcutaneous adipose tissueUBERON:000219095.11gold quality
uterine cervixUBERON:000000295.01gold quality
caecumUBERON:000115394.95gold quality
mammalian vulvaUBERON:000099794.86gold quality
adipose tissueUBERON:000101394.84gold quality
upper arm skinUBERON:000426394.70gold quality
buccal mucosa cellCL:000233694.61silver quality
adult mammalian kidneyUBERON:000008294.48gold quality
connective tissueUBERON:000238494.46gold quality
pharyngeal mucosaUBERON:000035594.40gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.37gold quality
pancreasUBERON:000126494.33gold quality
rectumUBERON:000105294.27gold quality
periodontal ligamentUBERON:000826694.27gold quality
sigmoid colonUBERON:000115994.22gold quality
nasal cavity mucosaUBERON:000182694.19gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-8271yes10.74
E-MTAB-10596no954.26
E-HCAD-8no50.82
E-ANND-3no0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 77 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Vaginatissue148.2not detected
Pancreastissue112.0not detected
Salivary glandtissue97.6medium
Bone marrowtissue97.2not detected
Skin 1tissue91.3low
Lymph nodetissue78.4medium
Thymustissue71.9
Appendixtissue69.4not detected
Duodenumtissue67.8not detected
Stomach 1tissue65.8not detected
Esophagustissue65.1low
Pituitary glandtissue63.4
Livertissue62.7medium
Colontissue62.6not detected
Frontal cortextissue62.2
Parathyroid glandtissue62.1low
Adrenal glandtissue60.8medium
Tonsiltissue60.5medium
Small intestinetissue55.9not detected
Spleentissue55.6medium
Fallopian tubetissue51.0medium
Prostatetissue49.6medium
Breasttissue49.0low
Choroid plexustissue46.8
Adipose tissuetissue45.9not detected
Urinary bladdertissue45.5medium
Cervixtissue42.6low
Ovarytissue42.3medium
Seminal vesicletissue42.0medium
Lungtissue39.5not detected
Kidneytissue38.8medium
Rectumtissue37.8not detected
Caudate putamentissue36.4
Placentatissue34.8low
Thyroid glandtissue34.7medium
Skeletal muscletissue34.0not detected
Gallbladdertissue29.4medium
Locus coeruleustissue29.1
Smooth muscletissue27.8not detected
Heart muscletissue27.5not detected
Nucleus accumbenstissue26.0
Endometrium 1tissue25.7medium
Hippocampustissue24.3low
Epididymistissue24.2medium
Tonguetissue22.2
Postcentral gyrustissue17.1
Basal gangliatissue16.9not detected
Testistissue16.4medium
Superior colliculitissue16.1
Cerebellumtissue15.6low
Putamentissue15.4
Cerebral cortextissue15.3low
Somatosensory cortextissue15.3
Hippocampal formationtissue15.0
Ponstissue14.9
Septumtissue14.7
Motor cortextissue14.4
Hypothalamustissue14.2
Temporal cortextissue13.8
Thalamustissue13.7

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Blood vessel (85.5), Anterior thalamic nucleus, ventral (39.4), Lateral funiculus (white matter) (39.4), Cervical spinal cord, ventral horn (35.4), Anterior funiculus (white matter) (34.9).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, ATF5, CEBPB, CREM, E2F4, E4F1, ESR1, NFKB, NKX2-1, NR1H3, NR5A1, RARA, REST, SP1, SP3

miRNA regulators (miRDB)

Targeting APRT by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

8 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-426799.9666.532368
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-314799.5266.34388
HSA-MIR-429299.1665.571767
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-3135B98.6165.331470
HSA-MIR-642B-5P96.3767.26745

Functional genomics

gnomAD constraint: pLI 4.74e-11, LOEUF 1.79, missense Z -1.83 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000378364 — one region, missense o/e 1.26.

Literature-anchored findings (GeneRIF, showing 13)

  • kinetic, regulatory and thermostability properties of APRT from erythrocytes of HGPRT deficient patients (PMID:14674717)
  • determination of structure and examination of role of deficiency in DHA-urolithiasis (PMID:15196008)
  • two novel mutations, G133D and V84M, were found in the APRT gene in Japanese patients with APRT deficiency (PMID:15571218)
  • APRT assay in a sample of patient hemolysate showed no detectable activity of the enzyme (25.56+/-9.55 U/L red blood cells in control healthy subjects). (PMID:17126311)
  • Data indicates that the flexible loop structure adopts an open conformation before and after binding of both substrates adenine and phosphoribosyl pyrophosphate. (PMID:18399692)
  • The phosphorylation status of membrane-bound nucleoside diphosphate kinase in epithelia and the role of AMP are reported. (PMID:19399589)
  • Case study of 2 year old Japanese boy with APRT deficiency. Genetic analysis showed compound heterozygote APRT*J and missense mutation L33P. APRT deficiency should be suspected in patients with radiolucent kidney stones and urinary 2,8-DHA crystals. (PMID:21635362)
  • A new mutation, p.Gln147X, in APRT gene, was found in a patient with adenine phosphoribosyltransferase deficiency. (PMID:24986359)
  • A long TA repeat in the promoter region of IL28B was associated with spontaneous HCV clearance. (PMID:25735432)
  • We found large differences between tumour types and individual tumours in their expression of XDH and APRT Variations in locus-specific DNA methylation and gene copy number correlated with the expression levels of XDH and APRT in human tumours respectively (PMID:30104401)
  • binding to hAPRT is substrate shape-specific in the forward reaction, whereas it is base-specific in the reverse reaction. The forward reaction is mainly a nucleophilic substitution of type 2 (SN2) with a mix of SN1-type molecular mechanism. Based on our structural analysis, a magnesium-assisted SN2-type mechanism would be involved in the reverse reaction. (PMID:31160323)
  • Allele frequency of variants reported to cause adenine phosphoribosyltransferase deficiency. (PMID:33707627)
  • Amp(1q) and tetraploidy are commonly acquired chromosomal abnormalities in relapsed multiple myeloma. (PMID:36433728)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioaprtENSDARG00000003519
mus_musculusAprtENSMUSG00000006589
drosophila_melanogasterAprtFBGN0000109
caenorhabditis_elegansT19B4.3WBGENE00020557

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:88061) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 46 distinct phenotype terms.

Mouse phenotype (MP)Records
nephrolithiasis5
hunched posture3
reduced fertility3
premature death3
renal interstitial fibrosis3
weight loss2
decreased body size2
kidney inflammation2
abnormal kidney morphology2
dilated renal tubule2
renal fibrosis2
renal tubular necrosis2
postnatal lethality, incomplete penetrance2
preweaning lethality, incomplete penetrance2
abnormal urine nucleoside level2
cystolithiasis2
decreased hematocrit1
hydronephrosis1
abnormal urinary bladder morphology1
abnormal retina morphology1
dehydration1
abnormal coat appearance1
disheveled coat1
polyuria1
small kidney1

+21 more (showing top 25).

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Mus spicilegusP47957100.0%Diamond
Mycobacterium ulcerans Agy99A0PPE499.5%Diamond
Mycobacterium marinum MB2HN7599.5%Diamond
Mycobacterium avium 104A0QIA998.9%Diamond
Mycobacterium avium subsp. paratuberculosis K-10Q741P398.9%Diamond
Mus pahariP4795698.3%Diamond
Rhodococcus opacus B4C1B4D696.6%Diamond
Rattus norvegicusP3697295.6%Diamond
Stochomys longicaudatusP4795895.6%Diamond
Dipodillus campestrisQ6441495.6%Diamond
Mastomys natalensisQ6442795.6%Diamond
Cricetulus griseusP4795295.0%Diamond
Mycolicibacterium vanbaalenii PYR-1A1T89491.3%Diamond
Mycolicibacterium gilvum PYR-GCKA4TBR291.3%Diamond
Bos taurusQ56JW491.1%Diamond
Drosophila pseudoobscura pseudoobscuraP5436386.5%Diamond
Debaryomyces hansenii CBS767Q6BZF979.6%Diamond
Mycolicibacterium smegmatis MC2 155A0QWJ576.7%Diamond
Acidiphilium cryptum JF-5A5FVJ476.3%Diamond
Granulibacter bethesdensis CGDNIH1Q0BVB876.3%Diamond
Saccharomyces cerevisiae S288CP4943574.1%Diamond
Kluyveromyces lactis NRRL Y-1140Q6CWV074.1%Diamond
Eremothecium gossypii ATCC 10895Q756E274.1%Diamond
Rhodospirillum rubrum ATCC 11170Q2RWT472.3%Diamond
Paramagnetospirillum magneticum AMB-1Q2W3C272.3%Diamond
Nocardia farcinica IFM 10152Q5YTF568.5%Diamond
Mycoplasmoides genitalium G37P4751868.3%Diamond
Corynebacterium kroppenstedtii DSM 44385C4LIX268.0%Diamond
Corynebacterium jeikeium K411Q4JVE467.2%Diamond
Bifidobacterium animalis subsp. lactis AD011B8DUE564.2%Diamond
Yarrowia lipolytica CLIB122Q6CA5362.6%Diamond
Saccharopolyspora erythraea NRRL 2338A4FBB257.0%Diamond
Prochlorococcus marinus subsp. marinus str. CCMP1375Q7VAL556.5%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
GALNSprotein-coding2588
PABPN1Lprotein-coding390748
TRAPPC2Lprotein-coding51693
CDT1protein-coding81620
CBFA2T3protein-coding863
HSALR1ncRNA100289580
PIEZO1-AS1ncRNA339059
PIEZO1protein-coding9780
MIR4722ncRNA100616167
RNF166protein-coding115992
SNAI3-AS1ncRNA197187
SNAI3protein-coding333929
CTU2protein-coding348180

Protein

Protein identifiers

Adenine phosphoribosyltransferase — P07741 (reviewed: P07741)

All UniProt accessions (5): H3BQB1, H3BQF1, H3BQZ9, H3BSW3, P07741

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.

Subunit / interactions. Homodimer.

Subcellular location. Cytoplasm.

Disease relevance. Adenine phosphoribosyltransferase deficiency (APRTD) [MIM:614723] An enzymatic deficiency that can lead to urolithiasis and renal failure. Patients have 2,8-dihydroxyadenine (DHA) urinary stones. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Purine metabolism; AMP biosynthesis via salvage pathway; AMP from adenine: step 1/1.

Similarity. Belongs to the purine/pyrimidine phosphoribosyltransferase family.

Isoforms (2)

UniProt IDNamesCanonical?
P07741-11yes
P07741-22

RefSeq proteins (2): NP_000476, NP_001025189 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000836PRTase_domDomain
IPR005764Ade_phspho_transFamily
IPR029057PRTase-likeHomologous_superfamily
IPR050054UPRTase/APRTaseFamily

Pfam: PF00156

Catalyzed reactions (Rhea)

  • AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine (RHEA:16609)

UniProt features (40 total): sequence variant 10, strand 10, helix 9, modified residue 8, initiator methionine 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

16 structures by resolution:

PDBTitleMethodResolution (Å)
6FCHCrystal Structure of Human APRT wild type in complex with PRPP and Mg2+X-RAY DIFFRACTION1.45
6FCLCrystal Structure of Human APRT wild type in complex with AMPX-RAY DIFFRACTION1.5
6FD4Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+ …X-RAY DIFFRACTION1.5
6HGRCrystal Structure of Human APRT wild type in complex with IMPX-RAY DIFFRACTION1.52
6FD5Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+ …X-RAY DIFFRACTION1.55
6HGSCrystal Structure of Human APRT wild type in complex with GMPX-RAY DIFFRACTION1.55
6HGPCrystal Structure of Human APRT wild type in complex with Phosphate ion.X-RAY DIFFRACTION1.7
4X45Crystal Structure of F173G Mutant of Human APRTX-RAY DIFFRACTION1.75
1ZN8Human Adenine Phosphoribosyltransferase Complexed with AMP, in Space Group P1 at 1.76 A …X-RAY DIFFRACTION1.76
6FD6Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+ …X-RAY DIFFRACTION1.8
1ZN7Human Adenine Phosphoribosyltransferase Complexed with PRPP, ADE and R5PX-RAY DIFFRACTION1.83
6HGQCrystal Structure of Human APRT wild type in complex with Hypoxanthine, PRPP and Mg2+X-RAY DIFFRACTION1.9
6FCICrystal Structure of Human APRT wild type in complex with Adenine, PRPP and Mg2+X-RAY DIFFRACTION1.94
1ZN9Human Adenine Phosphoribosyltransferase in Apo and AMP Complexed FormsX-RAY DIFFRACTION2.05
4X44Crystal Structure of Mutant R89Q of human Adenine phosphoribosyltransferaseX-RAY DIFFRACTION2.05
1OREHuman Adenine PhosphoribosyltransferaseX-RAY DIFFRACTION2.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P07741-F196.910.96

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Transferases, Metabolic proteins, Predicted intracellular proteins, Plasma proteins, Disease related genes, Potential drug targets, Human disease related genes, Congenital disorders of metabolism, Congenital disorders of nucleotide metabolism

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nucleoplasm

Antibody reliability (HPA): IH approved · IF approved

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 (8)

TypePositions
N-acetylalanine2
Phosphoserine4, 15, 30, 66
Phosphotyrosine60
N6-acetyllysine114
Phosphothreonine135

Function

Pathways and Gene Ontology

Reactome pathways

3 curated (TAS) of 12; 5 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

12 pathways:

IDPathwayEvidence
R-HSA-9734195Defective APRT disrupts adenine salvage ⚕curated
R-HSA-6798695Neutrophil degranulationcurated
R-HSA-74217Purine salvagecurated
R-HSA-1643685Disease ⚕—
R-HSA-5668914Diseases of metabolism ⚕—
R-HSA-9735804Diseases of nucleotide metabolism ⚕—
R-HSA-9734207Nucleotide salvage defects ⚕—
R-HSA-168256Immune System—
R-HSA-168249Innate Immune System—
R-HSA-1430728Metabolism—
R-HSA-15869Metabolism of nucleotides—
R-HSA-8956321Nucleotide salvage—

MSigDB gene sets: 305 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, HONMA_DOCETAXEL_RESISTANCE, REACTOME_INNATE_IMMUNE_SYSTEM, CHIBA_RESPONSE_TO_TSA_UP, GOBP_BEHAVIOR, XU_GH1_AUTOCRINE_TARGETS_UP, MODULE_56, GOCC_SECRETORY_GRANULE, MODULE_151, ENK_UV_RESPONSE_KERATINOCYTE_UP, GCM_NPM1, DAZARD_UV_RESPONSE_CLUSTER_G4, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS

GO Biological Process (5): purine ribonucleoside salvage (GO:0006166), adenine salvage (GO:0006168), IMP salvage (GO:0032264), AMP salvage (GO:0044209), GMP salvage (GO:0032263)

GO Molecular Function (7): adenine binding (GO:0002055), adenine phosphoribosyltransferase activity (GO:0003999), AMP binding (GO:0016208), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757), heterocyclic compound binding (GO:1901363)

GO Cellular Component (5): extracellular region (GO:0005576), cytoplasm (GO:0005737), cytosol (GO:0005829), secretory granule lumen (GO:0034774), extracellular exosome (GO:0070062)

Reactome top-level categories

9 top-level categories:

CategoryPathways
Innate Immune System1
Nucleotide salvage1
Nucleotide salvage defects1
Metabolism1
Immune System1
Disease1
Metabolism of nucleotides1
Diseases of nucleotide metabolism1
Diseases of metabolism1

GO top-level categories

24 GO namespaces:

CategoryTerms
purine ribonucleotide salvage3
cellular anatomical structure3
purine-containing compound salvage1
nucleoside salvage1
purine ribonucleoside biosynthetic process1
purine nucleobase salvage1
adenine biosynthetic process1
IMP biosynthetic process1
AMP biosynthetic process1
GMP biosynthetic process1
purine nucleobase binding1
purine phosphoribosyltransferase activity1
adenyl ribonucleotide binding1
anion binding1
cation binding1
binding1
catalytic activity1
transferase activity1
small molecule binding1
intracellular anatomical structure1
cytoplasm1
secretory granule1
cytoplasmic vesicle lumen1
extracellular vesicle1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 4 of 17 annotations. The rest are phylogenetic / computational / electronic (IEA).

4 experimentally-supported GO terms:

GO termNSEvidence
cytosolCCdirect assay
extracellular exosomeCChigh-throughput assay
AMP bindingMFdirect assay
adenine phosphoribosyltransferase activityMFdirect assay

Protein interactions and networks

STRING

showing 15 of 3,125 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
APRTADKP55263921
APRTHPRT1P00492919
APRTGALNSP34059833
APRTPNPP00491774
APRTADSLP30566768
APRTTATP17735741
APRTGDAQ9Y2T3706
APRTGMPSP49915686
APRTAMPD3Q01432685
APRTADAP00813671
APRTAMPD2Q01433662
APRTAMPD1P23109658
APRTPPATQ06203657
APRTIMPDH2P12268648
APRTUMPSP11172645

IntAct

Human interaction partners of APRT in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

11 partners by confidence:

PartnerInteraction typeMIscoreRecords
SPRED1physical association0.5603
TTC19physical association0.5603
KLHL24physical association0.4001
UNC45Bphysical association0.4001
MLH1physical association0.3701
FTSJ1physical association0.0001
GH1physical association0.0001
IKBKEphysical association0.0001
MCCphysical association0.0001
TRAF6physical association0.0001
VHLphysical association0.0001

BioGRID (137 interactions; top human partners by supporting records): SQSTM1 (Proximity Label-MS; 3 records), PARK2 (Affinity Capture-MS; 2 records), RAF1 (Affinity Capture-MS; 2 records), UMPS (Co-fractionation; 2 records), AAR2 (Affinity Capture-MS), ACE2 (Affinity Capture-MS), ADA (Co-fractionation), ADIPOR2 (Affinity Capture-MS), AGR2 (Proximity Label-MS), ANKZF1 (Affinity Capture-MS), APP (Reconstituted Complex), AR (Affinity Capture-MS), ATG16L1 (Proximity Label-MS), ATG5 (Proximity Label-MS), BAG1 (Affinity Capture-MS)

SIGNOR signaling

4 signaling interactions:

AEffectBMechanism
APRT“down-regulates quantity”adenine“chemical modification”
APRT“down-regulates quantity”“5-phospho-α-D-ribose 1-diphosphate”“chemical modification”
APRT“up-regulates quantity”AMP“chemical modification”
APRT“up-regulates quantity”diphosphate(3-)“chemical modification”

Disease & clinical

Genetic variants

Variant evidence for APRT: 222 ClinVar records (80 pathogenic / likely pathogenic); 1 GWAS association. Per-variant detail is on Sugi Variant.

ClinVar

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

ClassificationCount (floor)
Pathogenic56
Likely pathogenic24
Uncertain significance74
Likely benign31
Benign10

Top pathogenic / likely-pathogenic (15)

Showing the 15 best-reviewed of 80 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
18298NM_000485.3(APRT):c.294G>A (p.Trp98Ter)Pathogeniccriteria provided, multiple submitters, no conflicts6
18297NM_000485.3(APRT):c.194A>T (p.Asp65Val)Pathogeniccriteria provided, multiple submitters, no conflicts4
988053NM_000485.3(APRT):c.289_290del (p.Leu97fs)Pathogeniccriteria provided, multiple submitters, no conflicts4
988028NM_000485.3(APRT):c.1A>G (p.Met1Val)Pathogeniccriteria provided, multiple submitters, no conflicts3
988045NM_000485.3(APRT):c.199C>T (p.Arg67Ter)Pathogeniccriteria provided, multiple submitters, no conflicts3
988049NM_000485.3(APRT):c.259C>T (p.Arg87Ter)Pathogeniccriteria provided, multiple submitters, no conflicts2
4074265NM_000485.3(APRT):c.3G>C (p.Met1Ile)Pathogeniccriteria provided, multiple submitters, no conflicts2
988046NM_000485.3(APRT):c.200G>A (p.Arg67Gln)Likely pathogeniccriteria provided, multiple submitters, no conflicts4
988044NM_000485.3(APRT):c.188G>A (p.Gly63Asp)Likely pathogeniccriteria provided, multiple submitters, no conflicts3
3777188NM_000485.3(APRT):c.397G>C (p.Gly133Arg)Likely pathogeniccriteria provided, multiple submitters, no conflicts2
18296NM_000485.3(APRT):c.407T>C (p.Met136Thr)Pathogeniccriteria provided, single submitter4
988068NM_000485.3(APRT):c.472_474del (p.Glu158del)Pathogeniccriteria provided, single submitter2
988021NM_000485.3(APRT):c.522_524del (p.Ser175del)Pathogeniccriteria provided, single submitter1
988029NM_000485.3(APRT):c.2T>C (p.Met1Thr)Pathogeniccriteria provided, single submitter1
988031NM_000485.3(APRT):c.23dup (p.Val9fs)Pathogeniccriteria provided, single submitter1

Per-variant reference — Sugi Variant

Explore APRT’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 30 predictions of 477):

Position(s)EffectΔscoreSites
16:88810421–88810422donor_loss1.00005
16:88810068–88810069donor_loss0.99005
16:88810149–88810150acceptor_loss0.99006
16:88810184acceptor_gain0.9900
16:88810425donor_gain0.9900
16:88810557–88810558acceptor_loss0.99006
16:88810068donor_loss0.9800
16:88811549donor_loss0.98003
16:88810426donor_gain0.9500
16:88810474donor_gain0.9500

AlphaMissense

460 missense substitutions predicted likely pathogenic (of 1,127 scored), across 126 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
D12880.9880.995
D12780.9800.995
D2880.9760.988
F2680.9440.996
F6980.9370.993
D6580.8900.976
F1970.9720.996
E10470.9280.968
E15870.8430.943
F3970.8210.924
F7170.8200.943
K8860.9780.992
G6860.9430.982
K9160.9260.967
G13360.9180.985
Y10560.9060.986
P2060.9010.946
P9360.8750.950
G16460.8710.958
A13160.8530.963

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

CancerPrognosticp-value
Liver Hepatocellular Carcinoma (validation)unfavorable0.000154
Liver Hepatocellular Carcinoma (TCGA)unfavorable0.000693
Kidney Renal Papillary Cell Carcinoma (TCGA)favorable0.000942

Disease associations

OMIM: gene MIM:102600 | disease phenotypes: MIM:253000, MIM:614723

GenCC curated gene-disease

1 curated gene-disease records:

DiseaseClassificationInheritanceRecords
adenine phosphoribosyltransferase deficiencyDefinitiveAutosomal recessive4

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (9 panels, 8 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

9 panels:

PanelRating
Hypotonic infantgreen
Leukodystrophy, childhood onsetgreen
Likely inborn error of metabolismgreen
Nephrocalcinosis or nephrolithiasisgreen
Paediatric disordersgreen
Undiagnosed metabolic disordersgreen
Unexplained death in infancy and sudden unexplained death in childhoodgreen
Unexplained young onset end-stage renal diseasegreen
Unexplained kidney failure in young peopleamber

Mondo (2): mucopolysaccharidosis type 4A (MONDO:0009659), adenine phosphoribosyltransferase deficiency (MONDO:0013869)

Orphanet (3): Mucopolysaccharidosis type 4A (Orphanet:309297), Mucopolysaccharidosis type 4 (Orphanet:582), Adenine phosphoribosyltransferase deficiency (Orphanet:976)

HPO phenotypes

28 phenotypes (HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000010Recurrent urinary tract infections
HP:0000016Urinary retention
HP:0000019Urinary hesitancy
HP:0000083Renal insufficiency
HP:0000093Proteinuria
HP:0000787Kidney stone
HP:0000790Hematuria
HP:0000791Uric acid nephrolithiasis
HP:0000822Hypertension
HP:0001919Acute kidney injury
HP:0001942Metabolic acidosis
HP:0002027Abdominal pain
HP:0003259Elevated circulating creatinine concentration
HP:0003621Juvenile onset
HP:0003774Stage 5 chronic kidney disease
HP:0005110Atrial fibrillation
HP:0011463Childhood onset
HP:0011848Abdominal colic
HP:0012379Abnormal circulating enzyme concentration or activity
HP:0012587Macroscopic hematuria
HP:0012622Chronic kidney disease
HP:0030157Flank pain
HP:00342792,8-dihydroxyadenine crystalluria
HP:0034368Urolithiasis
HP:0100518Dysuria
HP:0100520Oliguria
HP:6000803Elevated urinary 2,8-dihydroxyadenine level

GWAS associations

1 associations:

StudyTraitp-value
GCST003479_9Hair color1e-7

MeSH disease descriptors

1 disease descriptors:

DescriptorNameTree numbers
C538228Adenine phosphoribosyltransferase deficiency *(supp.)*

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105819 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

Phase ≥1, by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 2,278 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

1 molecules by phase:

MoleculeNamePhasePatents
CHEMBL2105728CRENOLANIB32,278

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (1 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
CHEMBL5653589KD1440 nM

ChEMBL bioactivities

3 potent at pChembl≥5 of 3 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.88Kd13.08nMCHEMBL5653589
7.88ED5013.08nMCHEMBL5653589
7.54Kd29nMCRENOLANIB

PubChem BioAssay actives

2 with measured affinity, of 186 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2147877: Binding affinity to human APRT incubated for 45 mins by Kinobead based pull down assaykd0.0131uM
1-[2-[5-[(3-methyloxetan-3-yl)methoxy]benzimidazol-1-yl]quinolin-8-yl]piperidin-4-amine1424914: Kinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by mass spectrometry.kd0.0290uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression4
perfluorooctane sulfonic aciddecreases expression, increases expression3
Tobacco Smoke Pollutionaffects expression, decreases expression, increases expression3
perfluorooctanoic aciddecreases expression, increases expression2
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
bisphenol Fincreases expression1
beauvericindecreases expression1
bufotalinincreases expression1
pirinixic acidincreases activity, affects binding, decreases expression1
bisphenol Adecreases expression1
lead acetatedecreases activity1
beta-lapachoneincreases expression1
arseniteaffects binding, increases reaction1
cobaltous chloridedecreases expression1
ochratoxin Aincreases expression1
2-amino-3-methylimidazo(4,5-f)quinolineincreases mutagenesis, increases response to substance1
perfluoro-n-nonanoic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
perfluorohexanesulfonic aciddecreases expression1
ICG 001decreases expression1
bisphenol Bincreases expression1
hexabrominated diphenyl ether 153increases expression1
bisphenol Sincreases expression1
LDN 193189affects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
MT19c compounddecreases expression1
bisphenol AFincreases expression1
Sunitinibincreases expression1
Aspirindecreases expression1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3991627BindingKinobeads (epsilon), multiple immobilized ATP-competitive broad spectrum kinase inhibitors, used to assess residual binding of ~300 proteins simultaneously from cell lysate in the presence of a compound. Quantitative readout performed by maThe target landscape of clinical kinase drugs. — *Science*

Cellosaurus cell lines

22 cell lines: 20 transformed cell line, 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_0R03GM07290Transformed cell lineMale
CVCL_0R04GM07291Transformed cell lineFemale
CVCL_0R06GM10807Transformed cell lineMale
CVCL_5606WR216Transformed cell line
CVCL_B2RWAbcam HEK293T APRT KOTransformed cell lineFemale
CVCL_SD05HAP1 APRT (-) 1Cancer cell lineMale
CVCL_SD06HAP1 APRT (-) 2Cancer cell lineMale
CVCL_W060WR002Transformed cell line
CVCL_W061WR004Transformed cell line
CVCL_W062WR005Transformed cell line

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

26 trials:

NCTPhaseStatusTitle
NCT02752633Phase 4COMPLETEDEffect of Allopurinol and Febuxostat on Urinary 2,8-Dihydroxyadenine Excretion
NCT01275066Phase 3COMPLETEDA Double-Blind Study to Evaluate the Efficacy and Safety of BMN 110 in Patients With Mucopolysaccharidosis IVA (Morquio A Syndrome)
NCT01415427Phase 3COMPLETEDLong-Term Efficacy and Safety Extension Study of BMN 110 in Patients With Mucopolysaccharidosis IVA (Morquio A Syndrome)
NCT01515956Phase 2COMPLETEDStudy of BMN 110 in Pediatric Patients < 5 Years of Age With Mucopolysaccharidosis IVA (Morquio A Syndrome)
NCT01609062Phase 2TERMINATEDSafety and Exercise Study of Two Doses of BMN 110 for Morquio A Syndrome
NCT01697319Phase 2TERMINATEDEfficacy and Safety Study of BMN 110 for Morquio A Syndrome Patients Who Have Limited Ambulation
NCT03632213Phase 2UNKNOWNEvaluation of Losartan on Cardiovascular Disease in Patients With Mucopolysaccharidoses IV A and VI
NCT04532047Phase 1RECRUITINGPEARL (PrEnAtal Enzyme Replacement Therapy for Lysosomal Storage Disorders)
NCT00588562Not specifiedRECRUITINGRare Kidney Stone Consortium Patient Registry
NCT02026388Not specifiedRECRUITINGRare Kidney Stone Consortium Biobank
NCT02780297Not specifiedRECRUITINGProspective Research Rare Kidney Stones (ProRKS)
NCT03655223Not specifiedACTIVE_NOT_RECRUITINGEarly Check: Expanded Screening in Newborns
NCT06065852Not specifiedRECRUITINGNational Registry of Rare Kidney Diseases
NCT00884949Phase 1/2COMPLETEDA Study to Evaluate the Safety, Tolerability and Efficacy of BMN 110 in Subjects With Mucopolysaccharidosis IVA
NCT01242111Phase 1/2TERMINATEDA Study to Evaluate the Long-Term Efficacy and Safety of BMN 110 in Patients With Mucopolysaccharidosis IVA (Morquio A Syndrome)
NCT05845749Phase 1/2ACTIVE_NOT_RECRUITINGSafety and Efficacy of Voxzogo for Growth Deficits in MPS IVA and VI
NCT00787995Not specifiedTERMINATEDA Clinical Assessment Study of Subjects With Mucopolysaccharidosis IVA (Morquio Syndrome)
NCT01457456Not specifiedWITHDRAWNBiomarker for Morquio Disease (BioMorquio)
NCT01733615Not specifiedTERMINATEDDiscovering New Biomarkers For Monitoring Disease Progression in Patients With Mucopolysaccharidosis IVA
NCT01858103Not specifiedAPPROVED_FOR_MARKETINGBMN 110 US Expanded Access Program
NCT01920828Not specifiedCOMPLETEDGait Analysis in MPS IVA
NCT01961518Not specifiedCOMPLETEDScreening an Orthopedic Population for Mildly-affected Individuals With Morquio Syndrome A and Maroteaux-Lamy Syndrome
NCT02153255Not specifiedWITHDRAWNDynamic Gait Analysis in Children With Mucopolysaccharidosis Type IVa
NCT02294877Not specifiedCOMPLETEDA Multicenter, Multinational, Observational Morquio A Registry Study (MARS)
NCT05284006Not specifiedRECRUITINGNon-invasive Functional Assessment and Pathogenesis of Morquio A
NCT07361536Not specifiedRECRUITINGCardiac Structure and Function in MPS

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for APRT across ~30M SureChEMBL compounds — explore on Sugi Predict.