GP1BB p.Ser48=
c.144G>T · rs762805097 · VCV1013202
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000436%, nfe)
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 1.5 | GERP 0.08, phastCons 1 |
| Overall | ||
| CADD | 11.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000436%
European (non-Finnish) · 5/1,147,494 alleles
Filtering AF
0.000128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.3e-05%
Overall
0.000326%
5/1,533,280 alleles · very rare
exomes 4/1,381,238 · genomes 1/152,042 · joint denominator
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.Ser48=
- Coding
- c.144G>T
- MANE Select
- NM_000407
- dbSNP
- rs762805097
- Type
- single nucleotide variant
- Location
- chr22:19723987 (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 48
- a turn; the lrrnt domain
Similar variants
- GP1BB p.Ser48Ter Likely pathogenic ★★★ same residue
- GP1BB p.Ser48Leu 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
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-ser48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown