BCHE p.Asn587=
c.1761T>C · VCV3389180
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, 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 6 | GERP 0.32, phastCons 1 |
| Overall | ||
| CADD | 8.598 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,914 alleles
Filtering AF
0.000956%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000788%
Overall
0.0013%
21/1,610,386 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,957 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,316 |
| European (non-Finnish) | 0.00153% | 65,403 |
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.Asn587=
- Coding
- c.1761T>C
- MANE Select
- NM_000055
- Type
- single nucleotide variant
- Location
- chr3:165773430 (GRCh38)
- Gene constraint
- LOEUF 1.195 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.30 · 111 PDB
Similar variants
- 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
- BCHE p.Tyr528Ter 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-asn587 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown