BMP2 p.Ser87=

Q: Is BMP2 p.Ser87= (c.261A>G) pathogenic?

BMP2 p.Ser87= (c.261A>G) is classified Benign in BMP2 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-04). Common (popmax 86.3%, afr) — too common for a highly-penetrant pathogenic allele; Associated with short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies.

Q: What condition is associated with BMP2 p.Ser87= (c.261A>G)?

BMP2 p.Ser87= (c.261A>G) is associated with short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies (ClinVar).

Q: How common is BMP2 p.Ser87= (c.261A>G) in the general population?

BMP2 p.Ser87= (c.261A>G) is common (popmax 86.3%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.261A>G · rs1049007 · VCV195136

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 86.3%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies

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 2.1	GERP -3.8, phastCons 1
Overall
CADD	6.909	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 86.3% African / African-American · 64,723/74,996 alleles

Filtering AF 85.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 85.5%

Overall 64.4% 1,038,242/1,612,632 alleles · common exomes 931,010/1,460,578 · genomes 107,232/152,054 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	86.3%	1
East Asian	82.2%	1
Ashkenazi Jewishnot grpmax-eligible	80.9%	1
Middle Eastern	76.5%	1
Admixed American	70%	1
Remaining individualsnot grpmax-eligible	67%	1
Amishnot grpmax-eligible	62.1%	2
European (non-Finnish)	62%	2
South Asian	61%	2
Finnishnot grpmax-eligible	58.6%	2

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.Ser87=
Coding: c.261A>G
MANE Select: NM_001200
dbSNP: rs1049007
Type: single nucleotide variant
Location: chr20:6770387 (GRCh38)
Gene constraint: LOEUF 0.213 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.37 · 21 PDB
Residue 87: a UniProt-annotated variant site (in ssfsc1); the 'disordered' region; a modified residue (phosphoserine)

Full BMP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BMP2 p.Arg154Ter Pathogenic/Likely pathogenic ★★ same condition
BMP2 p.Arg170Ter Pathogenic/Likely pathogenic ★★ same condition
BMP2 p.Cys329Ter Likely pathogenic ★★ same condition
BMP2 p.Arg190Ser Benign ★★ same condition
BMP2 p.Glu205Ter Pathogenic ★ same condition
BMP2 p.Glu27Ter Likely pathogenic ★ same condition
BMP2 p.Trp313Ter Likely pathogenic ★ same condition
BMP2 p.Val74fs 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-ser87 (accessed [today's date]).

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