PRPS1 p.Phe189=
c.567T>C · rs1602904724 · VCV724822
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.46 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 9.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PRPS1
- Protein
- p.Phe189=
- Coding
- c.567T>C
- MANE Select
- NM_002764
- dbSNP
- rs1602904724
- Type
- single nucleotide variant
- Location
- chrX:107645213 (GRCh38)
- Structure
- AlphaFold pLDDT 94.77 · 27 PDB
Similar variants
- PRPS1 p.Phe189Leu Uncertain significance ★ ⚠ same residue
- PRPS1 p.Arg196Trp Pathogenic/Likely pathogenic ★★ same type
- PRPS1 p.Arg214Trp Pathogenic/Likely pathogenic ★★ same type
- PRPS1 p.Arg84Trp Pathogenic/Likely pathogenic ★★ same type
- PRPS1 p.Asn114Ser Likely pathogenic ★★ ⚠ same type
- PRPS1 p.Ile107Val Likely pathogenic ★★ same type
- PRPS1 p.Met115Thr Pathogenic/Likely pathogenic ★★ same type
- PRPS1 p.Met115Val Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/prps1-p-phe189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown