Is BMP15 p.Ser284= (c.852C>T) pathogenic?

BMP15 p.Ser284= (c.852C>T) is classified Benign in BMP15 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2018-01-13). Common (popmax 44.8%, afr) — too common for a highly-penetrant pathogenic allele; Associated with ovarian dysgenesis 2.

What condition is associated with BMP15 p.Ser284= (c.852C>T)?

BMP15 p.Ser284= (c.852C>T) is associated with ovarian dysgenesis 2 (ClinVar).

BMP15 p.Ser284=

Q: How common is BMP15 p.Ser284= (c.852C>T) in the general population?

BMP15 p.Ser284= (c.852C>T) is common (popmax 44.8%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.852C>T · rs17003221 · VCV259777

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 44.8%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

ovarian dysgenesis 2

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 -0.89	GERP -3.5
Overall
CADD	0.247	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 44.8% African / African-American · 25,279/56,471 alleles

Filtering AF 44.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 44.1%

Overall 3.4% 40,965/1,204,453 alleles · common exomes 25,942/1,093,762 · genomes 15,023/110,691 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	44.8%	2
South Asian	9.97%	10
East Asian	6.93%	14
Middle Eastern	5.11%	20
Admixed American	4.89%	20
Remaining individualsnot grpmax-eligible	4.63%	22
Ashkenazi Jewishnot grpmax-eligible	1.9%	53
European (non-Finnish)	0.304%	329
Finnishnot grpmax-eligible	0.0151%	6,629

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: BMP15
Protein: p.Ser284=
Coding: c.852C>T
MANE Select: NM_005448
dbSNP: rs17003221
Type: single nucleotide variant
Location: chrX:50916280 (GRCh38)
Structure: AlphaFold pLDDT 72.64

Full BMP15 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ovarian dysgenesis 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BMP15 p.Gly271Cys Uncertain significance ★★ ⚠ same condition
BMP15 c.-9C>G Benign ★★ same condition
BMP15 c.*13G>A Benign ★★ same condition
BMP15 p.Asn103Ser Benign ★★ same condition
BMP15 p.Gly54= Benign/Likely benign ★★ same condition
BMP15 p.His337= Benign ★★ same condition
BMP15 p.Leu148Pro Benign/Likely benign ★★ same condition
BMP15 p.Phe194Ser Benign/Likely benign ★★ 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/bmp15-p-ser284 (accessed [today's date]).

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