GP1BB p.Val119=
c.357G>A · VCV4946936
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0316%, mid)
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 -2.7 |
| Overall | ||
| CADD | 5.181 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0316%
Middle Eastern · 1/3,164 alleles
Filtering AF
0.00107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0004%
Overall
0.000808%
10/1,237,900 alleles · ultra-rare
exomes 9/1,087,298 · genomes 1/150,602 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0316% | 3,164 |
| South Asian | 0.00646% | 15,485 |
| European (non-Finnish) | 0.000703% | 142,179 |
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.Val119=
- Coding
- c.357G>A
- MANE Select
- NM_000407
- Type
- single nucleotide variant
- Location
- chr22:19724200 (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 119
- a β-strand; the lrrct domain
Similar variants
- GP1BB p.Val119Met 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-val119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown