BMP1 p.Arg496=
c.1488C>T · rs1333340704 · VCV2919543
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -20 | GERP -5.4 |
| Overall | ||
| CADD | 0.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,884 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000496%
8/1,613,076 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,884 |
| South Asian | 0.0022% | 45,474 |
| Admixed American | 0.00167% | 59,834 |
| African / African-American | 0.00134% | 74,836 |
| European (non-Finnish) | 0.000254% | 393,210 |
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.Arg496=
- Coding
- c.1488C>T
- MANE Select
- NM_006129
- dbSNP
- rs1333340704
- Type
- single nucleotide variant
- Location
- chr8:22194768 (GRCh38)
- Gene constraint
- LOEUF 0.648 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.89 · 8 PDB
- Residue 496
- a disulfide bond; the cub 2 domain
Similar variants
- BMP1 p.Arg496Cys Uncertain significance ★★ ⚠ same residue
- 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
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-arg496 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown