GPI p.Pro317=
c.951C>T · rs369354841 · VCV755594
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00988%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -4.7 |
| Overall | ||
| CADD | 0.128 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00988%
South Asian · 9/91,078 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.00198%
32/1,613,772 alleles · very rare
exomes 27/1,461,456 · genomes 5/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00988% | 10,120 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| African / African-American | 0.00267% | 37,523 |
| European (non-Finnish) | 0.0017% | 58,995 |
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
- GPI
- Protein
- p.Pro317=
- Coding
- c.951C>T
- MANE Select
- NM_000175
- dbSNP
- rs369354841
- Type
- single nucleotide variant
- Location
- chr19:34393955 (GRCh38)
- Structure
- AlphaFold pLDDT 93.81 · 1 PDB
Similar variants
- GPI p.Ala337Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- GPI p.Arg347Cys Pathogenic/Likely pathogenic ★★ same type
- GPI p.Arg347His Pathogenic/Likely pathogenic ★★ ⚠ same type
- GPI p.Arg446Ter Pathogenic/Likely pathogenic ★★ same type
- GPI p.Arg472Cys Pathogenic ★★ ⚠ same type
- GPI p.Arg96Ter Pathogenic/Likely pathogenic ★★ same type
- GPI p.Gln343Arg Pathogenic/Likely pathogenic ★★ same type
- GPI c.909+5G>A Uncertain significance ★★ 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/gpi-p-pro317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown