PGR p.His204=
c.612C>T · rs10160726 · VCV768475
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 10.3%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.75 | |
| Overall | ||
| CADD | 0.668 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.3%
African / African-American · 7,748/75,028 alleles
Filtering AF
10.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.1%
Overall
0.604%
9,714/1,609,528 alleles · common
exomes 5,290/1,457,208 · genomes 4,424/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.3% | 10 |
| Middle Eastern | 1.29% | 78 |
| Remaining individualsnot grpmax-eligible | 0.855% | 117 |
| Admixed American | 0.785% | 127 |
| Ashkenazi Jewishnot grpmax-eligible | 0.497% | 201 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| European (non-Finnish) | 0.058% | 1,725 |
| South Asian | 0.056% | 1,785 |
| Finnishnot grpmax-eligible | 0.00166% | 60,172 |
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.His204=
- Coding
- c.612C>T
- MANE Select
- NM_000926
- dbSNP
- rs10160726
- Type
- single nucleotide variant
- Location
- chr11:101128459 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 57.66 · 21 PDB
- Residue 204
- the 'modulating, pro-rich' region; the 'mediates transcriptional transrepression (in isoform a)' 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-his204 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown