PRX p.Ser1065=
c.3195C>T · rs2079420208 · VCV916924
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 disease
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 0.79 | GERP -0.57, phastCons 1 |
| Overall | ||
| CADD | 6.955 | 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
- PRX
- Protein
- p.Ser1065=
- Coding
- c.3195C>T
- MANE Select
- NM_181882
- dbSNP
- rs2079420208
- Type
- single nucleotide variant
- Location
- chr19:40395157 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 35.74 · 1 PDB
Similar variants
- PRX p.Ser1065Ala Uncertain significance ★ ⚠ same residue
- PRX p.Arg196Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Arg364Ter Pathogenic ★★ same condition
- PRX p.Arg953Ter Pathogenic ★★ same condition
- PRX p.Cys715Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Gln622Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Glu197Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Ala1000Val 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/prx-p-ser1065 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown