GPI p.Pro340=
c.1020C>T · rs1377978035 · VCV751023
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -0.077 | GERP -1.5, phastCons 0.53 |
| Overall | ||
| CADD | 9.842 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,874 alleles
Overall
6.2e-05%
1/1,613,194 alleles · very rare
exomes 1/1,460,888 · genomes 0/152,306 · 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
- GPI
- Protein
- p.Pro340=
- Coding
- c.1020C>T
- MANE Select
- NM_000175
- dbSNP
- rs1377978035
- Type
- single nucleotide variant
- Location
- chr19:34394024 (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-pro340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown