PRPS1 p.Ile290=
c.870T>C · rs754068855 · VCV698965
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0459%, amr)
Conditions
1
Charcot-Marie-Tooth Neuropathy X
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 -4.5 | GERP -4.5 |
| Overall | ||
| CADD | 2.357 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0459%
Admixed American · 21/45,762 alleles
Filtering AF
0.0307%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0258%
Overall
0.00173%
21/1,210,533 alleles · ultra-rare
exomes 15/1,098,213 · genomes 6/112,320 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PRPS1
- Protein
- p.Ile290=
- Coding
- c.870T>C
- MANE Select
- NM_002764
- dbSNP
- rs754068855
- Type
- single nucleotide variant
- Location
- chrX:107649945 (GRCh38)
- Structure
- AlphaFold pLDDT 94.77 · 27 PDB
- Residue 290
- a UniProt-annotated variant site (in dfnx1); a β-strand
Similar variants
- PRPS1 p.Ile290Val Likely benign ★ same residue
- PRPS1 p.Ile290Thr Pathogenic same residue
- PRPS1 p.Ile107Val Likely pathogenic ★★ same condition
- PRPS1 p.Met115Thr Pathogenic/Likely pathogenic ★★ same condition
- PRPS1 p.Ser169Leu Pathogenic ★★ same condition
- PRPS1 p.Ala216Thr Uncertain significance ★★ ⚠ same condition
- PRPS1 p.Arg204Cys Uncertain significance ★★ ⚠ same condition
- PRPS1 p.Arg204His Uncertain significance ★★ same condition
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-ile290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown