PTGS1 p.Phe366=
c.1098C>T · rs201018159 · VCV756558
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 -3.6 | GERP -4 |
| Overall | ||
| CADD | 2.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,084 alleles
Filtering AF
0.00676%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00565%
Overall
0.00657%
106/1,614,020 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,042 |
| South Asian | 0.0121% | 8,280 |
| European (non-Finnish) | 0.00737% | 13,564 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| African / African-American | 0.00267% | 37,445 |
| Admixed American | 0.00167% | 60,004 |
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
- PTGS1
- Protein
- p.Phe366=
- Coding
- c.1098C>T
- MANE Select
- NM_000962
- dbSNP
- rs201018159
- Type
- single nucleotide variant
- Location
- chr9:122386534 (GRCh38)
- Gene constraint
- LOEUF 0.82 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.19 · 1 PDB
- Residue 366
- a β-strand
Similar variants
- PTGS1 p.Gln240Pro Uncertain significance ★★ ⚠ same type
- PTGS1 c.762+10G>A Benign ★★ same type
- PTGS1 p.Ala499= Benign ★★ same type
- PTGS1 p.Cys68= Benign ★★ same type
- PTGS1 p.Gln41= Benign ★★ same type
- PTGS1 p.Val481Ile Likely benign ★★ same type
- PTGS1 p.Arg108Ter Uncertain significance ★ same type
- PTGS1 p.Arg178Cys 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/ptgs1-p-phe366 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown