BMP2 p.Phe112=
c.336C>T · VCV3676702
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00189%, nfe)
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 6 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 14.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00189%
European (non-Finnish) · 22/1,166,072 alleles
Filtering AF
0.00123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00106%
Overall
0.00144%
23/1,593,064 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00189% | 53,003 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,414 |
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.Phe112=
- Coding
- c.336C>T
- MANE Select
- NM_001200
- Type
- single nucleotide variant
- Location
- chr20:6770462 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.37 · 21 PDB
- Residue 112
- a UniProt-annotated variant site (in ssfsc1); the 'disordered' region
Similar variants
- 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
- BMP2 p.Ala106Thr 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-phe112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown