BMP2 p.Ser42Ter
c.125C>A · VCV4854977
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 3 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 1.8, phastCons 0.93 |
| Overall | ||
| CADD | 36.0 | 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.Ser42Ter
- Coding
- c.125C>A
- MANE Select
- NM_001200
- Type
- single nucleotide variant
- Location
- chr20:6770251 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.37 · 21 PDB
- Residue 42
- a UniProt-annotated variant site (in ssfsc1)
Similar variants
- BMP2 p.Arg170Ter Pathogenic/Likely pathogenic ★★ same condition
- BMP2 p.Cys329Ter Likely pathogenic ★★ same condition
- BMP2 p.Ser92Ter Pathogenic/Likely pathogenic ★★ same condition
- BMP2 p.Arg170Gln Uncertain significance ★★ ⚠ same condition
- BMP2 p.His269Tyr Uncertain significance ★★ same condition
- BMP2 p.His299Arg Uncertain significance ★★ ⚠ same condition
- BMP2 p.Glu27Ter Likely pathogenic ★ same condition
- BMP2 p.Pro363Leu Likely pathogenic ★ 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-ser42ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown