PRPS1L1

phosphoribosyl pyrophosphate synthetase 1 like 1

Basic information

Region (hg38): 7:18026770-18027846

Previous symbols: [ "PRPSL" ]

Links

ENSG00000229937 ∙ NCBI:221823 ∙ OMIM:611566 ∙ HGNC:9463 ∙ Uniprot:P21108 ∙ 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 PRPS1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPS1L1 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			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	0	0

Variants in PRPS1L1

This is a list of pathogenic ClinVar variants found in the PRPS1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-18026848-A-G		not specified	Uncertain significance (Dec 14, 2024)
7-18026869-T-G		not specified	Uncertain significance (Feb 09, 2025)
7-18026881-C-T		not specified	Uncertain significance (Jan 20, 2023)
7-18026914-A-G		not specified	Uncertain significance (Aug 09, 2021)
7-18026932-C-A		not specified	Uncertain significance (Nov 09, 2023)
7-18026933-A-T		not specified	Uncertain significance (Nov 09, 2023)
7-18026947-T-C		not specified	Uncertain significance (Aug 30, 2022)
7-18027007-G-A		not specified	Uncertain significance (Jun 10, 2024)
7-18027028-A-C		not specified	Uncertain significance (Jan 03, 2024)
7-18027037-G-A		not specified	Uncertain significance (Jul 10, 2024)
7-18027082-T-G		not specified	Uncertain significance (Aug 12, 2021)
7-18027089-C-T		not specified	Uncertain significance (Jan 31, 2024)
7-18027125-C-G		not specified	Uncertain significance (May 10, 2023)
7-18027184-T-C		not specified	Uncertain significance (Oct 01, 2024)
7-18027194-T-C		not specified	Uncertain significance (Dec 08, 2023)
7-18027210-C-G		not specified	Uncertain significance (Jan 08, 2025)
7-18027244-G-C		not specified	Uncertain significance (Nov 17, 2022)
7-18027259-G-T		not specified	Uncertain significance (Nov 03, 2022)
7-18027334-G-A		not specified	Uncertain significance (May 30, 2024)
7-18027339-C-G		not specified	Uncertain significance (Dec 19, 2022)
7-18027350-A-C		not specified	Uncertain significance (Oct 10, 2023)
7-18027399-G-C		not specified	Uncertain significance (Jul 13, 2021)
7-18027404-T-C		not specified	Uncertain significance (Nov 12, 2021)
7-18027412-A-G		not specified	Uncertain significance (Jan 10, 2023)
7-18027430-A-G		not specified	Uncertain significance (Aug 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPS1L1	protein_coding	protein_coding	ENST00000506618	1	1082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.287	0.694	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.444	192	175	1.09	0.00000973	2108
Missense in Polyphen		51	42.911	1.1885		539
Synonymous	-0.649	73	66.3	1.10	0.00000379	645
Loss of Function	1.97	2	8.01	0.250	6.28e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.
• Pathway: Purine metabolism - Homo sapiens (human);Pentose phosphate pathway - Homo sapiens (human);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Pentose Phosphate 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;Glucose-6-phosphate dehydrogenase deficiency;Ribose-5-phosphate isomerase deficiency;Transaldolase deficiency;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Pentose phosphate pathway (hexose monophosphate shunt);Metabolism of carbohydrates;PRPP biosynthesis;5-Phosphoribose 1-diphosphate biosynthesis;Metabolism;Pentose phosphate cycle;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.303

Intolerance Scores

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.741

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Prps1l1

Gene ontology

• Biological process: 5-phosphoribose 1-diphosphate biosynthetic process;purine nucleotide biosynthetic process;nucleoside metabolic process;ribonucleoside monophosphate biosynthetic process;nucleotide biosynthetic process;phosphorylation
• Cellular component: ribose phosphate diphosphokinase complex;cellular_component;cytoplasm
• Molecular function: magnesium ion binding;ribose phosphate diphosphokinase activity;ATP binding;kinase activity;protein homodimerization activity