BCHE p.Thr52=
c.156G>A · rs150673481 · VCV731432
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.189%, 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 -7.5 | GERP -4.7 |
| Overall | ||
| CADD | 0.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.189%
African / African-American · 142/74,990 alleles
Filtering AF
0.164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.154%
Overall
0.0111%
179/1,613,878 alleles · rare
exomes 94/1,461,680 · genomes 85/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.189% | 528 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,208 |
| Admixed American | 0.0117% | 8,565 |
| East Asian | 0.00223% | 44,864 |
| European (non-Finnish) | 0.00144% | 69,406 |
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
- BCHE
- Protein
- p.Thr52=
- Coding
- c.156G>A
- MANE Select
- NM_000055
- dbSNP
- rs150673481
- Type
- single nucleotide variant
- Location
- chr3:165830878 (GRCh38)
- Gene constraint
- LOEUF 1.195 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.30 · 111 PDB
- Residue 52
- a UniProt-annotated variant site (in bched); a β-strand
Similar variants
- BCHE p.Thr52Met Uncertain significance ★★ ⚠ same residue
- BCHE p.Arg414Cys Pathogenic/Likely pathogenic ★★ same type
- BCHE p.Arg452Ter Pathogenic/Likely pathogenic ★★ same type
- BCHE p.Asp98Gly Pathogenic/Likely pathogenic ★★ same type
- BCHE p.Glu377Ter Pathogenic/Likely pathogenic ★★ same type
- BCHE p.Gly143Asp Pathogenic ★★ same type
- BCHE p.Gly393Arg Pathogenic ★★ same type
- BCHE p.Leu358Ile Pathogenic/Likely pathogenic ★★ ⚠ 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/bche-p-thr52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown