Is BMP1 p.Asn293= (c.879C>T) pathogenic?

BMP1 p.Asn293= (c.879C>T) is classified Benign in BMP1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-31). Low-frequency (popmax 1.65%, afr); Associated with osteogenesis imperfecta type 13.

What condition is associated with BMP1 p.Asn293= (c.879C>T)?

BMP1 p.Asn293= (c.879C>T) is associated with osteogenesis imperfecta type 13 (ClinVar).

How common is BMP1 p.Asn293= (c.879C>T) in the general population?

BMP1 p.Asn293= (c.879C>T) is low-frequency (popmax 1.65%, afr) (gnomAD).

How is Osteogenesis imperfecta inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

BMP1 p.Asn293=

c.879C>T · rs35120584 · VCV716388

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.65%, afr)

Conditions

osteogenesis imperfecta type 13

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 -4.7	GERP -3.8
Overall
CADD	5.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.65% African / African-American · 1,235/75,026 alleles

Filtering AF 1.57% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.54%

Overall 0.0937% 1,512/1,614,026 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.65%	61
Middle Eastern	0.132%	758
Remaining individualsnot grpmax-eligible	0.125%	801
Admixed American	0.1%	1,000
East Asian	0.0735%	1,360
European (non-Finnish)	0.0078%	12,826
South Asian	0.00439%	22,769
Finnishnot grpmax-eligible	0.00312%	32,001

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: BMP1
Protein: p.Asn293=
Coding: c.879C>T
MANE Select: NM_006129
dbSNP: rs35120584
Type: single nucleotide variant
Location: chr8:22179747 (GRCh38)
Gene constraint: LOEUF 0.648 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.89 · 8 PDB
Residue 293: a disulfide bond; the peptidase m12a domain

Full BMP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

osteogenesis imperfecta type 13 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Osteogenesis imperfecta (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: All ages
Prevalence: 1-5 / 10 000 (Worldwide)

Similar variants

BMP1 p.Asn293Lys Uncertain significance ★ ⚠ same residue
BMP1 p.Asn293Ser Uncertain significance ★ ⚠ same residue
BMP1 p.Cys183Ter Pathogenic/Likely pathogenic ★★ same condition
BMP1 c.*452A>C Uncertain significance ★★ same condition
BMP1 p.Arg152Gln Uncertain significance ★★ ⚠ same condition
BMP1 p.Arg393Gln Uncertain significance ★★ ⚠ same condition
BMP1 p.Arg395Leu Uncertain significance ★★ ⚠ same condition
BMP1 p.Arg417Cys Uncertain significance ★★ ⚠ 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/bmp1-p-asn293 (accessed [today's date]).

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