GP1BA p.Pro523=
c.1569C>T · VCV4684183
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00769%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -2.8 |
| Overall | ||
| CADD | 1.097 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/91,084 alleles
Filtering AF
0.00462%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00423%
Overall
0.00533%
86/1,613,916 alleles · very rare
exomes 80/1,461,554 · genomes 6/152,362 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 13,012 |
| East Asian | 0.00668% | 14,965 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| European (non-Finnish) | 0.00576% | 17,351 |
| Admixed American | 0.00333% | 30,009 |
| African / African-American | 0.00266% | 37,529 |
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.Pro523=
- Coding
- c.1569C>T
- MANE Select
- NM_000173
- Type
- single nucleotide variant
- Location
- chr17:4934173 (GRCh38)
- Gene constraint
- LOEUF 1.289 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 64.65 · 22 PDB
Similar variants
- GP1BA p.Pro523Arg 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-pro523 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown