GP1BA p.Pro603=
c.1809C>T · VCV4932798
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0812%, 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 -0.75 | GERP -2.8, phastCons 0.003 |
| Overall | ||
| CADD | 5.706 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0812%
South Asian · 74/91,090 alleles
Filtering AF
0.0663%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0608%
Overall
0.00502%
81/1,614,086 alleles · ultra-rare
exomes 80/1,461,690 · genomes 1/152,396 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0812% | 1,231 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,498 |
| European (non-Finnish) | 0.00017% | 589,957 |
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.Pro603=
- Coding
- c.1809C>T
- MANE Select
- NM_000173
- Type
- single nucleotide variant
- Location
- chr17:4934413 (GRCh38)
- Gene constraint
- LOEUF 1.289 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 64.65 · 22 PDB
Similar variants
- 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
- GP1BA p.Trp223Gly 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-pro603 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown