APRT adenine phosphoribosyltransferase [Homo sapiens (human)] - Gene

Summary

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Official Symbol: APRTprovided by HGNC
Official Full Name: adenine phosphoribosyltransferaseprovided by HGNC
Primary source: HGNC:626
See related: Ensembl:ENSG00000198931; HPRD:00029; MIM:102600; Vega:OTTHUMG00000175454
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: AMP; APRTD
Summary: 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. [provided by RefSeq, Jul 2008]

Genomic context

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Location :: 16q24

Sequence :: Chromosome: 16; NC_000016.9 (88875877..88878342, complement)

See APRT in Epigenomics, MapViewer

Chromosome 16 - NC_000016.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

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.
Title: A Japanese boy with adenine phosphoribosyltransferase (APRT) deficiency caused by compound heterozygosity including a novel missense mutation in APRT gene.
The phosphorylation status of membrane-bound nucleoside diphosphate kinase in epithelia and the role of AMP are reported.
Title: The phosphorylation status of membrane-bound nucleoside diphosphate kinase in epithelia and the role of AMP.
Data indicates that the flexible loop structure adopts an open conformation before and after binding of both substrates adenine and phosphoribosyl pyrophosphate.
Title: Structural complexes of human adenine phosphoribosyltransferase reveal novel features of the APRT catalytic mechanism.
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).
Title: Clinical, biochemical and molecular diagnosis of a compound homozygote for the 254 bp deletion-8 bp insertion of the APRT gene suffering from severe renal failure.
kinetic, regulatory and thermostability properties of APRT from erythrocytes of HGPRT deficient patients
Title: APRT from erythrocytes of HGPRT deficient patients: kinetic, regulatory and thermostability properties.
determination of structure and examination of role of deficiency in DHA-urolithiasis
Title: Three-dimensional structure of human adenine phosphoribosyltransferase and its relation to DHA-urolithiasis.
two novel mutations, G133D and V84M, were found in the APRT gene in Japanese patients with APRT deficiency
Title: Identification of two novel mutations in adenine phosphoribosyltransferase gene in patients with 2,8-dihydroxyadenine urolithiasis.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Deficiency of AMP pyrophorylase

MIM: 614723

Genetic Testing Registry

Summary from GeneReviews: Adenine Phosphoribosyltransferase Deficiency

Adenine phosphoribosyltransferase (APRT) deficiency is characterized by excessive production of and urinary excretion of 2,8-dihydroxyadenine (DHA) leading to kidney stone formation and chronic kidney disease. Kidney stones, the most common clinical manifestation of APRT deficiency, can occur at any age; in at least 50% of individuals symptoms do not occur until adulthood. In a significant number of individuals, intratubular precipitation of DHA crystals can result in renal failure (i.e., DHA crystalline nephropathy).

Diagnosis Testing

The round, brown DHA crystals detected by urine microscopy are pathognomonic. The diagnosis is confirmed by absence of APRT enzyme activity in red cell lysates or identification of functionally significant biallelic mutations in APRT.

Genetic Counseling

APRT deficiency is inherited in an autosomal recessive manner. At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being normal. Carrier testing for at-risk relatives and prenatal diagnosis for pregnancies at increased risk are possible if the disease-causing mutations in the family have been identified.

References

PMID: 22934314

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
P07741	P07741	APRT	HPRD	PubMed
BioGRID:106849	BioGRID:106848	APP	BioGRID	PubMed	Reconstituted Complex
BioGRID:106849	BioGRID:108621	FN1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:106849	BioGRID:114360	GMPS	BioGRID	PubMed	Co-fractionation
BioGRID:106849	BioGRID:121581	HECW2	BioGRID	PubMed	Co-fractionation
BioGRID:106849	BioGRID:109488	HPRT1	BioGRID	PubMed	Co-fractionation
BioGRID:106849	BioGRID:114089	IKBKG	BioGRID	PubMed	Reconstituted Complex
BioGRID:106849	BioGRID:109883	ITGA4	BioGRID	PubMed	Affinity Capture-MS
BioGRID:106849	BioGRID:110438	MLH1	BioGRID	PubMed	Two-hybrid
BioGRID:106849	BioGRID:125001	NAPRT1	BioGRID	PubMed	Co-fractionation
BioGRID:106849	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS
BioGRID:106849	BioGRID:113218	UMPS	BioGRID	PubMed	Co-fractionation
BioGRID:106849	BioGRID:113255	VCAM1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:106849	BioGRID:113269	VHL	BioGRID	PubMed	Affinity Capture-MS

Pathways from BioSystems

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Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
Metabolism of nucleotides, organism-specific biosystem (from REACTOME)
Metabolism of nucleotides, organism-specific biosystemNucleotides and their derivatives are used for short-term energy storage (ATP, GTP), for intra- and extra-cellular signaling (cAMP; adenosine), as enzyme cofactors (NAD, FAD), and for the synthesis o...
Purine metabolism, organism-specific biosystem (from KEGG)
Purine metabolism, organism-specific biosystem
Purine metabolism
Purine metabolism, organism-specific biosystem (from REACTOME)
Purine metabolism, organism-specific biosystemThe events of human purine metabolism are conveniently, if somewhat arbitrarily, grouped into four pathways: de novo synthesis of inosine 5'-monophosphate (IMP), the biosynthesis of other purine ribo...
Purine metabolism, conserved biosystem (from KEGG)
Purine metabolism, conserved biosystem
Purine metabolism
Purine salvage, organism-specific biosystem (from REACTOME)
Purine salvage, organism-specific biosystemNucleosides and free bases generated by DNA and RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathway of purine biosynthesis. Nucleosides and free bases...
adenine and adenosine salvage I, organism-specific biosystem (from BIOCYC)
adenine and adenosine salvage I, organism-specific biosystemAdenosine nucleotides can be synthesized de novo. In that route : AMP (AMP) is synthesized via : IMP (IMP) and : ADENYLOSUCC , which is converted to AMP by the action of : ASL-MONOMER (see : PWY-6126...

General gene information

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Markers

NoName (e-PCR)
- UniSTS:486660

RH68125 (e-PCR)
- UniSTS:27274

RH70957 (e-PCR)
- UniSTS:15081

GDB:180915 (e-PCR)
- UniSTS:155120

Genotypes

See APRT SNP Geneview Report
See APRT SNP Genotype Report
See APRT SNP Variation Viewer Report

Homology

Homologs of the APRT gene: The APRT gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, and rice.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Clone Names

MGC125856, MGC125857, MGC129961, DKFZp686D13177

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
AMP binding	IDA Inferred from Direct Assay more info	PubMed
adenine binding	IEA Inferred from Electronic Annotation more info
adenine phosphoribosyltransferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
AMP salvage	IEA Inferred from Electronic Annotation more info
adenine salvage	IEA Inferred from Electronic Annotation more info
cellular response to insulin stimulus	IEA Inferred from Electronic Annotation more info
grooming behavior	IEA Inferred from Electronic Annotation more info
lactation	IEA Inferred from Electronic Annotation more info
nucleobase-containing small molecule metabolic process	TAS Traceable Author Statement more info
purine nucleobase metabolic process	TAS Traceable Author Statement more info
purine ribonucleoside salvage	IEA Inferred from Electronic Annotation more info
purine-containing compound salvage	TAS Traceable Author Statement more info
small molecule metabolic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
cytoplasm	IDA Inferred from Direct Assay more info
cytoplasm	TAS Traceable Author Statement more info	PubMed
cytosol	TAS Traceable Author Statement more info
NOT nucleolus	IDA Inferred from Direct Assay more info
nucleus	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: adenine phosphoribosyltransferase

Names: adenine phosphoribosyltransferase; AMP diphosphorylase; AMP pyrophosphorylase; transphosphoribosidase

NP_000476.1

EC 2.4.2.7

NP_001025189.1

EC 2.4.2.7

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008013.1 RefSeqGene

Range

5001..7466

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000485.2 → NP_000476.1 adenine phosphoribosyltransferase isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

BM423481, BU507629

Consensus CDS

CCDS32511.1

UniProtKB/Swiss-Prot

P07741

Related

ENSP00000367615, OTTHUMP00000253666, ENST00000378364, OTTHUMT00000430000

Conserved Domains (1) summary

cd06223
Location:42 – 177
Blast Score: 241

PRTases_typeI; Phosphoribosyl transferase (PRT)-type I domain
NM_001030018.1 → NP_001025189.1 adenine phosphoribosyltransferase isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate segment compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.

Source sequence(s)

BM423481, BM550173

Consensus CDS

CCDS45546.1

UniProtKB/Swiss-Prot

P07741

Related

ENSP00000397007, OTTHUMP00000253667, ENST00000426324, OTTHUMT00000430003

Conserved Domains (1) summary

cd06223
Location:42 – 133
Blast Score: 165

PRTases_typeI; Phosphoribosyl transferase (PRT)-type I domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000016.9 Reference GRCh37.p10 Primary Assembly

Range

88875877..88878342, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000148.1 Alternate HuRef

Range

74573103..74575568, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018927.1 Alternate CHM1_1.0

Range

89876349..89878814, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01013586.1 (13..2478)	None
genomic	AC092384.5 (42228..44693)	None
genomic	AMYH01007914.1 (5265..7730)	None
genomic	AY306126.1	AAP45051.1
genomic	CH471184.2	EAW66760.1
		EAW66761.1
genomic	HH961760.1	CBX51353.1
genomic	M16446.1	AAA51769.1
genomic	U09817.1	AAB84304.1
genomic	Y00486.1	CAA68543.1
mRNA	BC106894.2	None
mRNA	BC106895.2	None
mRNA	BC107151.2	AAI07152.1
mRNA	BM423481.1	None
mRNA	BM550173.1	None
mRNA	BU507629.1	None
mRNA	CR749423.1	CAH18261.1