Is BMPR2 p.Ser3= (c.9C>A) pathogenic?

BMPR2 p.Ser3= (c.9C>A) is classified Benign/Likely benign in BMPR2 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-05). Rare (popmax 0.805%, sas); Associated with Inborn genetic diseases.

What condition is associated with BMPR2 p.Ser3= (c.9C>A)?

BMPR2 p.Ser3= (c.9C>A) is associated with Inborn genetic diseases, pulmonary hypertension, primary, 1 (ClinVar).

How common is BMPR2 p.Ser3= (c.9C>A) in the general population?

BMPR2 p.Ser3= (c.9C>A) is rare (popmax 0.805%, sas) (gnomAD).

BMPR2 p.Ser3=

c.9C>A · rs549281044 · VCV695404

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.805%, sas)

Conditions

Inborn genetic diseases

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 0.68	GERP -0.3, phastCons 0.87
Overall
CADD	9.799	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.805% South Asian · 733/91,088 alleles

Filtering AF 0.756% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.737%

Overall 0.0522% 843/1,614,276 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.805%	124
Middle Eastern	0.346%	289
Remaining individualsnot grpmax-eligible	0.0416%	2,404
European (non-Finnish)	0.00517%	19,345
Admixed American	0.00167%	60,030
African / African-American	0.00133%	75,080

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.Ser3=
Coding: c.9C>A
MANE Select: NM_001204
dbSNP: rs549281044
Type: single nucleotide variant
Location: chr2:202377483 (GRCh38)
Gene constraint: LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 58.07 · 7 PDB

Full BMPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: pulmonary hypertension, primary, 1

Similar variants

BMPR2 p.Ser3Pro Uncertain significance ★ ⚠ same residue
BMPR2 c.1276+3A>G Likely pathogenic ★★★ same condition
BMPR2 c.1276+3A>T Likely pathogenic ★★★ same condition
BMPR2 c.1276+4A>G Likely pathogenic ★★★ same condition
BMPR2 c.1277-8A>G Pathogenic ★★★ same condition
BMPR2 c.1277-9A>G Pathogenic ★★★ same condition
BMPR2 c.1413+1G>A Pathogenic ★★★ same condition
BMPR2 c.247+1G>A 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-ser3 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown