PGR p.Glu786=
c.2358A>G · VCV3931321
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.026 | GERP -1.8, phastCons 0.95 |
| Overall | ||
| CADD | 8.071 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PGR
- Protein
- p.Glu786=
- Coding
- c.2358A>G
- MANE Select
- NM_000926
- Type
- single nucleotide variant
- Location
- chr11:101050059 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 57.66 · 21 PDB
- Residue 786
- the nr lbd domain; the 'af2; mediates transcriptional activation' region; an α-helix
Similar variants
- PGR p.Arg187= Benign ★★ same type
- PGR p.Arg623= Benign ★★ same type
- PGR p.Cys347Ser Benign ★★ same type
- PGR p.Gln536Pro Benign ★★ same type
- PGR p.Gln75Lys Likely benign ★★ same type
- PGR p.Gln868= Benign ★★ same type
- PGR p.Gly263= Benign ★★ same type
- PGR p.Gly435= Likely benign ★★ 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/pgr-p-glu786 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown