Computational evidence
| Protein change | ||
| AlphaMissense | 0.0658 | likely benign |
|---|---|---|
| REVEL | 0.04 | moderately benign-leaning |
| SaProt | LLR -6.76 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -2.3 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 26 kb · p 0.68 · regional, not allelic |
| Overall | ||
| CADD | 0.444 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.07% | 33 |
| Remaining individualsnot grpmax-eligible | 0.219% | 456 |
| Middle Eastern | 0.066% | 1,516 |
| Admixed American | 0.015% | 6,669 |
| South Asian | 0.0132% | 7,591 |
| European (non-Finnish) | 0.00246% | 40,691 |
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
- BMS1
- Protein
- p.Ser552Pro
- Coding
- c.1654T>C
- MANE Select
- NM_014753
- dbSNP
- rs3814621
- Type
- single nucleotide variant
- Location
- chr10:42796898 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 72.04 · 3 PDB
- Residue 552
- a modified residue (phosphoserine); a UniProt-annotated variant site (in); the 'disordered' region
Similar variants
- BMS1 p.Ala214Val Benign/Likely benign ★★ same type
- BMS1 p.Ala500= Benign/Likely benign ★★ same type
- BMS1 p.Arg237His Benign ★★ same type
- BMS1 p.Arg38Trp Benign/Likely benign ★★ ⚠ same type
- BMS1 p.Arg863= Benign ★★ same type
- BMS1 p.Asp768Asn Benign ★★ same type
- BMS1 p.Glu1278= Likely benign ★★ same type
- BMS1 p.Ile942= Benign/Likely benign ★★ 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/bms1-p-ser552pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown