BMPR2 p.Asn55=
c.165T>C · rs200976092 · VCV1567918
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.225%, eas)
Conditions
1
Primary pulmonary hypertension
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 -1.8 | GERP -4 |
| Overall | ||
| CADD | 8.811 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.225%
East Asian · 101/44,872 alleles
Filtering AF
0.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.176%
Overall
0.00644%
104/1,614,076 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.225% | 444 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00167% | 59,996 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
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
- BMPR2
- Protein
- p.Asn55=
- Coding
- c.165T>C
- MANE Select
- NM_001204
- dbSNP
- rs200976092
- Type
- single nucleotide variant
- Location
- chr2:202464897 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.07 · 7 PDB
- Residue 55
- a disulfide bond; a turn
Similar variants
- BMPR2 c.1128+1G>A Pathogenic ★★ same condition
- BMPR2 c.1128+1G>C Pathogenic ★★ same condition
- BMPR2 c.621+1G>T Pathogenic/Likely pathogenic ★★ same condition
- BMPR2 c.853-2A>G Pathogenic ★★ same condition
- BMPR2 p.Arg147Ter Pathogenic ★★ same condition
- BMPR2 p.Arg213Ter Pathogenic ★★ same condition
- BMPR2 p.Arg491Trp Pathogenic ★★ same condition
- BMPR2 p.Arg873Ter Pathogenic/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/bmpr2-p-asn55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown