GPX1 p.Pro77=
c.231G>T · rs201340744 · VCV784004
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.38%, afr)
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 -2.6 | |
| Overall | ||
| CADD | 10.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.38%
African / African-American · 1,028/74,712 alleles
Filtering AF
1.31%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.28%
Overall
0.0718%
1,157/1,610,376 alleles · low-frequency
exomes 579/1,458,528 · genomes 578/151,848 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.38% | 73 |
| Remaining individualsnot grpmax-eligible | 0.109% | 915 |
| Admixed American | 0.0852% | 1,174 |
| South Asian | 0.0033% | 30,297 |
| European (non-Finnish) | 0.000594% | 168,447 |
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
- GPX1
- Protein
- p.Pro77=
- Coding
- c.231G>T
- MANE Select
- NM_000581
- dbSNP
- rs201340744
- Type
- single nucleotide variant
- Location
- chr3:49358048 (GRCh38)
- Gene constraint
- LOEUF 1.38 · pLI <0.01 (gnomAD)
- Residue 77
- a β-strand
Similar variants
- GPX1 p.Ala132Val Uncertain significance ★★ same type
- GPX1 p.Ala140Ser Uncertain significance ★★ same type
- GPX1 p.Ile42Thr Uncertain significance ★★ same type
- GPX1 p.Pro190Ser Uncertain significance ★★ same type
- GPX1 c.-46C>T Benign ★★ same type
- GPX1 p.Pro200Leu Benign ★★ same type
- GPX1 p.Ala10Val Uncertain significance ★ same type
- GPX1 p.Ala11Thr Uncertain significance ★ same type
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/gpx1-p-pro77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown