BMP2 p.Thr347=
c.1041G>A · rs143654141 · VCV593765
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0441%, afr)
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 -2.4 | GERP -5.5 |
| Overall | ||
| CADD | 4.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0441%
African / African-American · 33/74,822 alleles
Filtering AF
0.0322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0281%
Overall
0.00328%
53/1,613,764 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0441% | 2,267 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,926 |
| Admixed American | 0.00834% | 11,991 |
| European (non-Finnish) | 0.000678% | 147,501 |
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
- BMP2
- Protein
- p.Thr347=
- Coding
- c.1041G>A
- MANE Select
- NM_001200
- dbSNP
- rs143654141
- Type
- single nucleotide variant
- Location
- chr20:6778939 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.37 · 21 PDB
- Residue 347
- a disulfide bond; a UniProt-annotated variant site (in ssfsc1); an α-helix
Similar variants
- BMP2 p.Thr347Met Likely benign ★★ same residue
- BMP2 p.Arg154Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Arg170Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Cys329Ter Likely pathogenic ★★ same type
- BMP2 p.Gln89Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Glu229Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Ser92Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Ala103Thr 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/bmp2-p-thr347 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown