GP1BA p.Pro424=
c.1272G>A · rs868035529 · VCV3030172
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00287%, amr)
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 -3.3 | GERP -2.4 |
| Overall | ||
| CADD | 0.512 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00287%
Admixed American · 1/34,826 alleles
Filtering AF
5.7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.1e-05%
Overall
0.00048%
4/834,030 alleles · very rare
exomes 4/768,482 · genomes 0/65,548 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00287% | 34,826 |
| Remaining individualsnot grpmax-eligible | 0.00267% | 37,410 |
| European (non-Finnish) | 0.000343% | 291,724 |
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.Pro424=
- Coding
- c.1272G>A
- MANE Select
- NM_000173
- dbSNP
- rs868035529
- Type
- single nucleotide variant
- Location
- chr17:4933876 (GRCh38)
- Gene constraint
- LOEUF 1.289 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 64.65 · 22 PDB
- Residue 424
- the 'disordered' region
Similar variants
- GP1BA p.Pro424Leu Uncertain significance ★★ ⚠ 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-pro424 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown