CES2 p.Glu366=
c.1098G>A · rs140590822 · VCV711525
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.225%, nfe)
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 -0.38 | GERP -3.1 |
| Overall | ||
| CADD | 2.041 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.225%
European (non-Finnish) · 2,651/1,180,000 alleles
Filtering AF
0.218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.215%
Overall
0.18%
2,903/1,614,140 alleles · rare
exomes 2,661/1,461,862 · genomes 242/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.225% | 445 |
| Middle Eastern | 0.165% | 606 |
| Admixed American | 0.152% | 660 |
| Remaining individualsnot grpmax-eligible | 0.104% | 962 |
| African / African-American | 0.0533% | 1,876 |
| Finnishnot grpmax-eligible | 0.0328% | 3,049 |
| South Asian | 0.0263% | 3,795 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
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
- CES2
- Protein
- p.Glu366=
- Coding
- c.1098G>A
- MANE Select
- NM_001365405
- dbSNP
- rs140590822
- Type
- single nucleotide variant
- Location
- chr16:66941809 (GRCh38)
- Gene constraint
- LOEUF 1.002 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.96
Similar variants
- CES2 c.-100G>T Uncertain significance ★ same type
- CES2 c.-107C>T Uncertain significance ★ same type
- CES2 c.-108A>T Uncertain significance ★ same type
- CES2 c.-143G>A Uncertain significance ★ same type
- CES2 c.-150G>C Uncertain significance ★ same type
- CES2 c.-16G>T Uncertain significance ★ same type
- CES2 c.-29G>A Uncertain significance ★ same type
- CES2 c.-56C>T 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/ces2-p-glu366 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown