ACHE p.Leu282=
c.846G>C · rs1584774926 · VCV748832
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
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 0.04 | phastCons 0.82 |
| Overall | ||
| CADD | 5.316 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,950 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.000372%
6/1,613,038 alleles · very rare
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
- ACHE
- Protein
- p.Leu282=
- Coding
- c.846G>C
- MANE Select
- NM_000665
- dbSNP
- rs1584774926
- Type
- single nucleotide variant
- Location
- chr7:100893387 (GRCh38)
- Gene constraint
- LOEUF 0.546 · pLI 0.81 (gnomAD)
- Structure
- AlphaFold pLDDT 93.04 · 81 PDB
- Residue 282
- an α-helix
Similar variants
- ACHE p.Arg34Gln Benign ★★ same type
- ACHE p.Glu344= Benign/Likely benign ★★ same type
- ACHE p.Gly89Glu Benign ★★ ⚠ same type
- ACHE p.Pro135Ala Likely benign ★★ ⚠ same type
- ACHE p.Pro441= Likely benign ★★ same type
- ACHE p.Thr269= Benign/Likely benign ★★ same type
- ACHE p.Ala14Thr Uncertain significance ★ ⚠ same type
- ACHE p.Ala256Thr 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/ache-p-leu282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown