PRX p.Phe94del
c.281_283del · rs1424434006 · VCV575102
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Conditions
2
Charcot-Marie-Tooth disease type 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.2, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,082 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.0013%
21/1,614,052 alleles · very rare
exomes 21/1,461,782 · genomes 0/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,541 |
| European (non-Finnish) | 0.00161% | 62,104 |
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
- PRX
- Protein
- p.Phe94del
- Coding
- c.281_283del
- MANE Select
- NM_181882
- dbSNP
- rs1424434006
- Type
- Deletion
- Location
- chr19:40398718 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 35.74 · 1 PDB
- Residue 94
- the pdz domain; a β-strand
Similar variants
- PRX p.Ala210fs Pathogenic ★★ same condition
- PRX p.Asp765fs Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Ile1096fs Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Lys930fs Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Thr1033fs Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Val525fs Pathogenic/Likely pathogenic ★★ same condition
- PRX p.629MKLPE[1] Uncertain significance ★★ same condition
- PRX p.Ala1447fs 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-phe94del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown