Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 13 submitters
gnomAD v4.1
Common
common (popmax 80.1%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
4
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 -3.2 | GERP -4 |
| Overall | ||
| CADD | 0.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
80.1%
African / African-American · 59,922/74,850 alleles
Filtering AF
79.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 79.3%
Overall
52.7%
849,893/1,613,490 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 80.1% | 1 |
| Amishnot grpmax-eligible | 65.2% | 2 |
| European (non-Finnish) | 53.4% | 2 |
| Admixed American | 51.8% | 2 |
| Remaining individualsnot grpmax-eligible | 51.5% | 2 |
| South Asian | 47.1% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 46.1% | 2 |
| Middle Eastern | 45% | 2 |
| Finnishnot grpmax-eligible | 44.9% | 2 |
| East Asian | 18.6% | 5 |
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.Pro885=
- Coding
- c.2655T>C
- MANE Select
- NM_181882
- dbSNP
- rs268672
- Type
- single nucleotide variant
- Location
- chr19:40395697 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 35.74 · 1 PDB
Similar variants
- PRX c.184+2T>C Likely pathogenic ★★ same condition
- PRX p.Arg1070Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Arg196Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Arg364Ter Pathogenic ★★ same condition
- PRX p.Arg368Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Arg392Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Arg464Ter Pathogenic/Likely pathogenic ★★ same condition
- PRX p.Arg897Ter Pathogenic/Likely pathogenic ★★ 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-pro885 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown