PPAT

phosphoribosyl pyrophosphate amidotransferase, the group of Purinosome

Basic information

Region (hg38): 4:56393362-56435615

Links

ENSG00000128059 ∙ NCBI:5471 ∙ OMIM:172450 ∙ HGNC:9238 ∙ Uniprot:Q06203 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPAT gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	7	2	0

Variants in PPAT

This is a list of pathogenic ClinVar variants found in the PPAT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-56396648-G-A		not specified	Uncertain significance (Jun 27, 2022)
4-56396649-G-A		not specified	Uncertain significance (Oct 25, 2023)
4-56399364-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
4-56400825-G-T		not specified	Uncertain significance (Apr 19, 2024)
4-56401337-C-T		not specified	Likely benign (Apr 28, 2022)
4-56401410-A-G		not specified	Uncertain significance (Dec 20, 2023)
4-56403162-G-A		not specified	Uncertain significance (Mar 01, 2023)
4-56403307-G-A		not specified	Uncertain significance (May 17, 2023)
4-56406664-T-C		not specified	Uncertain significance (Oct 31, 2023)
4-56407657-G-A		not specified	Uncertain significance (Jan 02, 2024)
4-56435340-T-A			Likely benign (Aug 16, 2018)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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