BMP1 p.Arg125=
c.373C>A · rs747988703 · VCV2787861
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0154%, sas)
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 2.6 | GERP -1.5, phastCons 0.96 |
| Overall | ||
| CADD | 4.402 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0154%
South Asian · 14/90,978 alleles
Filtering AF
0.0092%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00736%
Overall
0.000868%
14/1,613,494 alleles · ultra-rare
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
- BMP1
- Protein
- p.Arg125=
- Coding
- c.373C>A
- MANE Select
- NM_006129
- dbSNP
- rs747988703
- Type
- single nucleotide variant
- Location
- chr8:22176253 (GRCh38)
- Gene constraint
- LOEUF 0.648 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.89 · 8 PDB
- Residue 125
- the 'disordered' region; the peptidase m12a domain
Similar variants
- BMP1 p.Cys183Ter Pathogenic/Likely pathogenic ★★ same type
- BMP1 p.Gln70Ter Pathogenic/Likely pathogenic ★★ same type
- BMP1 c.1443+6T>C Uncertain significance ★★ same type
- BMP1 c.1639+4C>G Uncertain significance ★★ same type
- BMP1 c.2233+4C>T Uncertain significance ★★ same type
- BMP1 c.*452A>C Uncertain significance ★★ same type
- BMP1 p.Ala538Val Uncertain significance ★★ ⚠ same type
- BMP1 p.Ala657Thr 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/bmp1-p-arg125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown