PRPS1 p.Cys60=
c.180T>C · rs2147681429 · VCV1660423
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -1.4 | GERP -0.18, phastCons 0.001 |
| Overall | ||
| CADD | 10.65 | 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.Cys60=
- Coding
- c.180T>C
- MANE Select
- NM_002764
- dbSNP
- rs2147681429
- Type
- single nucleotide variant
- Location
- chrX:107639352 (GRCh38)
- Structure
- AlphaFold pLDDT 94.77 · 27 PDB
Similar variants
- PRPS1 p.Cys60Tyr Uncertain significance ★★ ⚠ 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
- PRPS1 p.Arg260Cys 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-cys60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown