BCHE p.Ser598=
c.1794T>C · rs148569288 · VCV2571193
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0824%, mid)
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 0.53 | GERP -4, phastCons 0.98 |
| Overall | ||
| CADD | 6.617 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0824%
Middle Eastern · 5/6,070 alleles
Filtering AF
0.0324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.0129%
208/1,611,122 alleles · ultra-rare
exomes 196/1,459,020 · genomes 12/152,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0824% | 1,214 |
| Remaining individualsnot grpmax-eligible | 0.0321% | 3,117 |
| South Asian | 0.022% | 4,546 |
| European (non-Finnish) | 0.0134% | 7,456 |
| Admixed American | 0.00835% | 11,980 |
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.Ser598=
- Coding
- c.1794T>C
- MANE Select
- NM_000055
- dbSNP
- rs148569288
- Type
- single nucleotide variant
- Location
- chr3:165773397 (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-ser598 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown