CES2 p.His147=
c.441C>T · rs150573301 · VCV2646608
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0275%, amr)
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 -15 | GERP -3.7 |
| Overall | ||
| CADD | 0.162 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0275%
Admixed American · 15/54,606 alleles
Filtering AF
0.0169%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0141%
Overall
0.0141%
217/1,538,998 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0275% | 3,640 |
| European (non-Finnish) | 0.0168% | 5,950 |
| Remaining individualsnot grpmax-eligible | 0.0134% | 7,454 |
| Finnishnot grpmax-eligible | 0.00165% | 60,680 |
| African / African-American | 0.00152% | 65,936 |
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.His147=
- Coding
- c.441C>T
- MANE Select
- NM_001025195 · reported on NM_001365405
- dbSNP
- rs150573301
- Type
- single nucleotide variant
- Location
- chr16:66940239 (GRCh38)
- Structure
- AlphaFold pLDDT 93.27 · 21 PDB
Similar variants
- CES1 p.Val166Met Uncertain significance ★★ ⚠ same type
- CES2 p.Glu366= Benign ★★ same type
- CES1 p.Ala126Asp Uncertain significance ★ ⚠ same type
- CES1 p.Ala126Val Uncertain significance ★ ⚠ same type
- CES1 p.Ala149Glu Uncertain significance ★ ⚠ same type
- CES1 p.Ala160Thr Uncertain significance ★ ⚠ same type
- CES1 p.Ala197Asp Uncertain significance ★ ⚠ same type
- CES1 p.Ala338Gly 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-his147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown