PPAT
phosphoribosyl pyrophosphate amidotransferase, the group of Purinosome
Basic information
Region (hg38): 4:56393362-56435615
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (25 variants)
- not_provided (1 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPAT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002703.5. 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 | 0 | |||||
| missense | 24 | 26 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 24 | 2 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPAT | protein_coding | protein_coding | ENST00000264220 | 11 | 42254 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.986 | 0.0139 | 125736 | 0 | 10 | 125746 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.06 | 137 | 281 | 0.487 | 0.0000140 | 3349 |
| Missense in Polyphen | 35 | 120.35 | 0.29082 | 1391 | ||
| Synonymous | 1.66 | 77 | 97.9 | 0.786 | 0.00000487 | 1009 |
| Loss of Function | 4.20 | 3 | 26.2 | 0.115 | 0.00000134 | 332 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000868 | 0.0000868 |
| Ashkenazi Jewish | 0.000107 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Pathway
- Antimetabolite Pathway - Folate Cycle, Pharmacodynamics;Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Methotrexate Pathway (Cancer Cell), Pharmacodynamics;Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;2-Hydroxyglutric Aciduria (D And L Form);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;Homocarnosinosis;Hyperinsulinism-Hyperammonemia Syndrome;Succinic semialdehyde dehydrogenase deficiency;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Mercaptopurine Metabolism Pathway;4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Glutamate Metabolism;Fluoropyrimidine Activity;Metabolism of nucleotides;Metabolism;Pentose phosphate cycle;Nucleobase biosynthesis;Purine nucleotides nucleosides metabolism;Purine ribonucleoside monophosphate biosynthesis;5-aminoimidazole ribonucleotide biosynthesis;purine nucleotides <i>de novo</i> biosynthesis
(Consensus)
Recessive Scores
- pRec
- 0.379
Intolerance Scores
- loftool
- 0.216
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.51
Haploinsufficiency Scores
- pHI
- 0.891
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.633
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppat
- Phenotype
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;kidney development;purine nucleotide biosynthetic process;'de novo' IMP biosynthetic process;glutamine catabolic process;lactation;purine nucleobase biosynthetic process;nucleoside metabolic process;purine ribonucleoside monophosphate biosynthetic process;animal organ regeneration;cellular response to insulin stimulus;cellular response to drug;protein homotetramerization;maternal process involved in female pregnancy
- Cellular component
- cytosol
- Molecular function
- amidophosphoribosyltransferase activity;metal ion binding;4 iron, 4 sulfur cluster binding