APRT
adenine phosphoribosyltransferase
Basic information
Region (hg38): 16:88809339-88811937
Links
Phenotypes
GenCC
Source:
- adenine phosphoribosyltransferase deficiency (Definitive), mode of inheritance: AR
- adenine phosphoribosyltransferase deficiency (Strong), mode of inheritance: AR
- adenine phosphoribosyltransferase deficiency (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Adenine phosphoribosyltransferase deficiency | AR | Biochemical; Renal | Medical and dietary interventions (eg, purine-restricted diet with adequate hydration and allopurinol or febuxostat, in instances where allopurinol can not be used) may be beneficial in order to decrease the severity of manifestations including nephrolithiasis and renal sequelae, as well as to treat individuals with relatively advanced disease; Renal transplant has been described, and disease-specific considerations (eg, immediate postoperative pharmacotherapy) may impact transplant outcomes | Biochemical; Musculoskeletal; Renal | 5676523; 5763607; 4852180; 1061547; 7766; 865583; 420519; 7311997; 6701033; 3876264; 3680503; 1353080; 806829; 3077470; 3409638; 3343350; 1986109; 1985452; 1353080; 1349689; 1349687; 7915931; 8825602; 9298830; 9521589; 11532677; 14767036; 15025810; 15077874; 15571218; 17126311; 19435978; 20101413; 20150536; 20303634; 20553441; 21635362; 22212387; 22934314; 22988602; 23430916 |
ClinVar
This is a list of variants' phenotypes submitted to
- Adenine_phosphoribosyltransferase_deficiency (114 variants)
- not_provided (69 variants)
- Inborn_genetic_diseases (16 variants)
- APRT-related_disorder (4 variants)
- APRT_deficiency,_Japanese_type (1 variants)
- Morquio_syndrome (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the APRT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000485.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 15 | 16 | ||||
| missense | 17 | 12 | 57 | 90 | ||
| nonsense | 9 | |||||
| start loss | 4 | 4 | ||||
| frameshift | 15 | 20 | ||||
| splice donor/acceptor (+/-2bp) | 9 | |||||
| Total | 46 | 25 | 58 | 18 | 1 |
Highest pathogenic variant AF is 0.00018537
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APRT | protein_coding | protein_coding | ENST00000378364 | 5 | 2606 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.45e-13 | 0.00218 | 125581 | 0 | 33 | 125614 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.238 | 110 | 103 | 1.07 | 0.00000563 | 1109 |
| Missense in Polyphen | 43 | 39.128 | 1.099 | 438 | ||
| Synonymous | -2.97 | 73 | 47.1 | 1.55 | 0.00000266 | 395 |
| Loss of Function | -2.03 | 15 | 8.57 | 1.75 | 5.06e-7 | 80 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000235 | 0.000235 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000382 | 0.000381 |
| Finnish | 0.0000952 | 0.0000924 |
| European (Non-Finnish) | 0.000145 | 0.000141 |
| Middle Eastern | 0.000382 | 0.000381 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.;
- Disease
- DISEASE: 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. {ECO:0000269|PubMed:11243733, ECO:0000269|PubMed:1353080, ECO:0000269|PubMed:15571218, ECO:0000269|PubMed:1746557, ECO:0000269|PubMed:21635362, ECO:0000269|PubMed:3343350, ECO:0000269|PubMed:3680503, ECO:0000269|PubMed:7915931}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Purine metabolism - Homo sapiens (human);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Purine metabolism;Neutrophil degranulation;adenine and adenosine salvage I;Metabolism of nucleotides;Innate Immune System;Immune System;Metabolism;Nucleotide salvage;Purine salvage;Purine nucleotides nucleosides metabolism;superpathway of purine nucleotide salvage
(Consensus)
Recessive Scores
- pRec
- 0.0946
Intolerance Scores
- loftool
- 0.271
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.49
Haploinsufficiency Scores
- pHI
- 0.612
- hipred
- N
- hipred_score
- 0.239
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Aprt
- Phenotype
- hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- purine ribonucleoside salvage;adenine salvage;lactation;grooming behavior;cellular response to insulin stimulus;purine-containing compound salvage;neutrophil degranulation;AMP salvage
- Cellular component
- extracellular region;nucleoplasm;cytoplasm;cytosol;secretory granule lumen;extracellular exosome
- Molecular function
- adenine binding;adenine phosphoribosyltransferase activity;AMP binding