GP1BA p.Pro411=
c.1233A>G · rs12940222 · VCV3050960
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.135%, 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 -2.8 | GERP -2.8 |
| Overall | ||
| CADD | 1.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.135%
African / African-American · 70/51,856 alleles
Filtering AF
0.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.1%
Overall
0.0212%
300/1,414,614 alleles · rare
exomes 292/1,324,884 · genomes 8/89,730 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.135% | 741 |
| Middle Eastern | 0.0941% | 1,062 |
| Admixed American | 0.0374% | 2,672 |
| Remaining individualsnot grpmax-eligible | 0.0294% | 3,400 |
| European (non-Finnish) | 0.0171% | 5,844 |
| South Asian | 0.00551% | 18,135 |
| Finnishnot grpmax-eligible | 0.00211% | 47,450 |
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
- GP1BA
- Protein
- p.Pro411=
- Coding
- c.1233A>G
- MANE Select
- NM_000173
- dbSNP
- rs12940222
- Type
- single nucleotide variant
- Location
- chr17:4933837 (GRCh38)
- Gene constraint
- LOEUF 1.289 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 64.65 · 22 PDB
- Residue 411
- the 'disordered' region
Similar variants
- GP1BA p.Pro411Leu Benign ★★★ same residue
- GP1BA p.Cys225Arg Likely pathogenic ★★★ same type
- GP1BA p.Cys81Arg Pathogenic ★★★ same type
- GP1BA p.Gln346Ter Likely pathogenic ★★★ same type
- GP1BA p.Glu347Ter Likely pathogenic ★★★ same type
- GP1BA p.Leu145Pro Likely pathogenic ★★★ same type
- GP1BA p.Ser267Ter Likely pathogenic ★★★ same type
- GP1BA p.Ser486Ter 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/gp1ba-p-pro411 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown