PGR p.Pro52=
c.156T>A · rs138237815 · VCV743649
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.345%, afr)
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 0.1 | phastCons 0.015 |
| Overall | ||
| CADD | 2.814 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.345%
African / African-American · 259/75,016 alleles
Filtering AF
0.311%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.297%
Overall
0.0179%
289/1,613,468 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.345% | 290 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,676 |
| Admixed American | 0.015% | 6,669 |
| European (non-Finnish) | 0.000339% | 294,934 |
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
- PGR
- Protein
- p.Pro52=
- Coding
- c.156T>A
- MANE Select
- NM_000926
- dbSNP
- rs138237815
- Type
- single nucleotide variant
- Location
- chr11:101128915 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 57.66 · 21 PDB
- Residue 52
- the 'modulating, pro-rich' region; the 'af3; mediates transcriptional activation (in isoform b)' region; the 'disordered' region
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-pro52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown