PTGER1 p.Pro91=
c.273G>T · rs1390260305 · VCV2649423
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00211%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -2.7 |
| Overall | ||
| CADD | 9.189 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00211%
Admixed American · 1/47,468 alleles
Filtering AF
7.1e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2e-05%
Overall
0.000334%
5/1,497,670 alleles · very rare
exomes 5/1,346,092 · genomes 0/151,578 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00211% | 47,468 |
| Remaining individualsnot grpmax-eligible | 0.00173% | 57,902 |
| European (non-Finnish) | 0.000266% | 376,254 |
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
- PTGER1
- Protein
- p.Pro91=
- Coding
- c.273G>T
- MANE Select
- NM_000955
- dbSNP
- rs1390260305
- Type
- single nucleotide variant
- Location
- chr19:14474048 (GRCh38)
- Gene constraint
- LOEUF 1.889 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.11 · 1 PDB
- Residue 91
- an α-helix
Similar variants
- PTGER1 p.Ala147Val Uncertain significance ★ ⚠ same type
- PTGER1 p.Ala154Thr Uncertain significance ★ ⚠ same type
- PTGER1 p.Ala160Val Uncertain significance ★ ⚠ same type
- PTGER1 p.Ala165Asp Uncertain significance ★ ⚠ same type
- PTGER1 p.Ala19Thr Uncertain significance ★ ⚠ same type
- PTGER1 p.Ala19Val Uncertain significance ★ ⚠ same type
- PTGER1 p.Ala204Thr Uncertain significance ★ ⚠ same type
- PTGER1 p.Ala34Gly 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/ptger1-p-pro91 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown