GP1BA p.Ser199=
c.597G>A · rs770552079 · VCV3036754
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, eas)
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 2.9 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 6.732 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
East Asian · 9/44,898 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00905%
Overall
0.00409%
66/1,613,826 alleles · ultra-rare
exomes 51/1,461,674 · genomes 15/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.02% | 4,989 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,205 |
| African / African-American | 0.0187% | 5,350 |
| Admixed American | 0.01% | 10,000 |
| South Asian | 0.0022% | 45,546 |
| European (non-Finnish) | 0.00195% | 51,300 |
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.Ser199=
- Coding
- c.597G>A
- MANE Select
- NM_000173
- dbSNP
- rs770552079
- Type
- single nucleotide variant
- Location
- chr17:4933201 (GRCh38)
- Gene constraint
- LOEUF 1.289 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 64.65 · 22 PDB
Similar variants
- GP1BA p.Ser199Leu 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-ser199 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown