GPI p.Ala232=
c.696G>A · rs142635084 · VCV771217
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.147%, 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 -11 | GERP -5.2 |
| Overall | ||
| CADD | 0.594 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.147%
African / African-American · 110/75,048 alleles
Filtering AF
0.124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.116%
Overall
0.0201%
324/1,613,958 alleles · rare
exomes 220/1,461,618 · genomes 104/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.147% | 682 |
| Admixed American | 0.123% | 811 |
| Middle Eastern | 0.099% | 1,010 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| European (non-Finnish) | 0.00865% | 11,567 |
| East Asian | 0.00223% | 44,890 |
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
- GPI
- Protein
- p.Ala232=
- Coding
- c.696G>A
- MANE Select
- NM_000175
- dbSNP
- rs142635084
- Type
- single nucleotide variant
- Location
- chr19:34378996 (GRCh38)
- Structure
- AlphaFold pLDDT 93.81 · 1 PDB
Similar variants
- GPI p.Ala232Glu Uncertain significance ★ ⚠ same residue
- GPI p.Ala232Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- GPI p.Ala337Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- GPI p.Arg347Cys Pathogenic/Likely pathogenic ★★ same type
- GPI p.Arg347His Pathogenic/Likely pathogenic ★★ ⚠ same type
- GPI p.Arg446Ter Pathogenic/Likely pathogenic ★★ same type
- GPI p.Arg472Cys Pathogenic ★★ ⚠ same type
- GPI p.Arg96Ter Pathogenic/Likely pathogenic ★★ 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/gpi-p-ala232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown