GP1BB p.Glu59=
c.177G>A · rs749912012 · VCV3047263
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0564%, 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 -3.2 | GERP -3 |
| Overall | ||
| CADD | 1.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0564%
South Asian · 47/83,360 alleles
Filtering AF
0.0435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.039%
Overall
0.00319%
49/1,534,816 alleles · ultra-rare
exomes 45/1,382,634 · genomes 4/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0564% | 1,774 |
| Remaining individualsnot grpmax-eligible | 0.00168% | 59,628 |
| European (non-Finnish) | 8.71e-05% | 1,147,544 |
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.Glu59=
- Coding
- c.177G>A
- MANE Select
- NM_000407
- dbSNP
- rs749912012
- Type
- single nucleotide variant
- Location
- chr22:19724020 (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 59
- a β-strand
Similar variants
- GP1BB p.Glu59Ala Uncertain significance ★★★ ⚠ same residue
- 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
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-glu59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown