BMP2 p.Ter397Ser
c.1190A>C · rs1986568109 · VCV986057
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
stop-loss
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | stop-loss | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.1 | GERP 2.8, phastCons 1 |
| Overall | ||
| CADD | 15.07 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BMP2
- Protein
- p.Ter397Ser
- Coding
- c.1190A>C
- MANE Select
- NM_001200
- dbSNP
- rs1986568109
- Type
- single nucleotide variant
- Location
- chr20:6779088 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.37 · 21 PDB
Similar variants
- BMP2 p.Ter397Tyr Likely pathogenic ★ same residue
- BMP2 p.Arg215Gln Uncertain significance ★★ ⚠ same condition
- BMP2 p.Arg291His Uncertain significance ★★ ⚠ same condition
- BMP2 p.Arg6Cys Uncertain significance ★★ ⚠ same condition
- BMP2 p.Glu234Gly Uncertain significance ★★ ⚠ same condition
- BMP2 p.Glu235Asp Uncertain significance ★★ ⚠ same condition
- BMP2 p.Gly327Arg Uncertain significance ★★ ⚠ same condition
- BMP2 p.His168Asn Uncertain significance ★★ ⚠ same condition
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-ter397ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown