GP1BB p.Ala102=
c.306C>T · rs566833759 · VCV727504
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.678%, afr)
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 1.9 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 15.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.678%
African / African-American · 441/65,040 alleles
Filtering AF
0.626%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.605%
Overall
0.0374%
498/1,330,532 alleles · rare
exomes 187/1,179,438 · genomes 311/151,094 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.678% | 147 |
| Admixed American | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.0283% | 3,533 |
| Middle Eastern | 0.0275% | 3,640 |
| South Asian | 0.00395% | 25,321 |
| European (non-Finnish) | 0.000384% | 260,315 |
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
- GP1BB
- Protein
- p.Ala102=
- Coding
- c.306C>T
- MANE Select
- NM_000407
- dbSNP
- rs566833759
- Type
- single nucleotide variant
- Location
- chr22:19724149 (GRCh38)
- Gene constraint
- LOEUF 1.922 · pLI 0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.43 · 3 PDB
- Residue 102
- an α-helix; the lrrct domain
Similar variants
- GP1BB p.Asn89Asp Likely pathogenic ★★★ same type
- GP1BB p.Asn89Thr Likely pathogenic ★★★ same type
- GP1BB p.Cys141Ter Pathogenic ★★★ same type
- GP1BB p.Cys147Ser Likely pathogenic ★★★ ⚠ same type
- GP1BB p.Cys30Tyr Likely pathogenic ★★★ same type
- GP1BB p.Cys32Ter Likely pathogenic ★★★ same type
- GP1BB p.Glu136Ter Likely pathogenic ★★★ same type
- GP1BB p.Leu16Pro 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/gp1bb-p-ala102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown