BOC p.Cys200=
c.600T>C · rs772157582 · VCV747269
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0911%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.2 | GERP -4.6 |
| Overall | ||
| CADD | 4.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0911%
South Asian · 83/91,084 alleles
Filtering AF
0.0752%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0694%
Overall
0.00898%
145/1,614,086 alleles · ultra-rare
exomes 139/1,461,880 · genomes 6/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0911% | 1,097 |
| Middle Eastern | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,498 |
| European (non-Finnish) | 0.00466% | 21,456 |
| Admixed American | 0.00167% | 60,010 |
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
- BOC
- Protein
- p.Cys200=
- Coding
- c.600T>C
- MANE Select
- NM_001378074
- dbSNP
- rs772157582
- Type
- single nucleotide variant
- Location
- chr3:113270877 (GRCh38)
- Gene constraint
- LOEUF 0.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.98 · 3 PDB
- Residue 200
- a disulfide bond; the ig-like c2-type 2 domain
Similar variants
- BOC p.Ala715= Benign ★★ same type
- BOC p.Lys884Asn Benign ★★ same type
- BOC p.Pro829Arg Benign ★★ same type
- BOC p.Pro913Ser Benign ★★ same type
- BOC p.Ala226Thr Uncertain significance ★ ⚠ same type
- BOC p.Ala424Thr Uncertain significance ★ ⚠ same type
- BOC p.Ala470Val Uncertain significance ★ ⚠ same type
- BOC p.Ala503Val 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/boc-p-cys200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown