PRPS2
Basic information
Region (hg38): X:12791355-12824222
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPS2 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 | 1 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 0 |
Variants in PRPS2
This is a list of pathogenic ClinVar variants found in the PRPS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-12791602-C-A | not specified | Uncertain significance (Jan 23, 2023) | ||
| X-12799396-A-G | not specified | Likely benign (Jul 25, 2023) | ||
| X-12819587-G-A | not specified | Uncertain significance (Apr 22, 2022) | ||
| X-12819661-A-G | not specified | Uncertain significance (Oct 25, 2022) | ||
| X-12820693-A-C | not specified | Uncertain significance (Jan 24, 2023) | ||
| X-12820744-G-A | not specified | Uncertain significance (May 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRPS2 | protein_coding | protein_coding | ENST00000398491 | 7 | 32868 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.935 | 0.0643 | 123049 | 0 | 1 | 123050 | 0.00000406 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.05 | 39 | 141 | 0.277 | 0.0000116 | 2116 |
| Missense in Polyphen | 3 | 35.846 | 0.083691 | 615 | ||
| Synonymous | 0.462 | 58 | 62.6 | 0.926 | 0.00000595 | 638 |
| Loss of Function | 2.73 | 0 | 8.71 | 0.00 | 6.24e-7 | 156 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000734 | 0.0000557 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000734 | 0.0000557 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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);Nucleotide Metabolism;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
- 0.225
Intolerance Scores
- loftool
- 0.0654
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.142
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.507
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.966
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Prps2
- Phenotype
- cellular phenotype; neoplasm; 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); immune system phenotype;
Gene ontology
- Biological process
- 5-phosphoribose 1-diphosphate biosynthetic process;nucleobase-containing compound metabolic process;purine nucleotide biosynthetic process;AMP biosynthetic process;nucleoside metabolic process;nucleotide biosynthetic process;phosphorylation;animal organ regeneration
- Cellular component
- ribose phosphate diphosphokinase complex;cytoplasm
- Molecular function
- magnesium ion binding;ribose phosphate diphosphokinase activity;protein binding;ATP binding;AMP binding;kinase activity;GDP binding;carbohydrate binding;identical protein binding;protein homodimerization activity;ADP binding