Is BMPR1A p.Asp69fs (c.199_203dup) pathogenic?

BMPR1A p.Asp69fs (c.199203dup) is classified Pathogenic in BMPR1A (ClinVar, Single submitter, 1 submitter; last evaluated 2017-11-22). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with BMPR1A p.Asp69fs (c.199_203dup)?

BMPR1A p.Asp69fs (c.199_203dup) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BMPR1A p.Asp69fs (c.199_203dup) in the general population?

BMPR1A p.Asp69fs (c.199_203dup) is absent from gnomAD (gnomAD).

BMPR1A p.Asp69fs

c.199_203dup · rs1554888134 · VCV482872

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 4 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BMPR1A
Protein: p.Asp69fs
Coding: c.199_203dup
MANE Select: NM_004329
dbSNP: rs1554888134
Type: Duplication
Location: chr10:86890191 (GRCh38)
Gene constraint: LOEUF 0.195 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 82.86 · 11 PDB
Residue 69: a disulfide bond

Full BMPR1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BMPR1A p.Asp69Tyr Uncertain significance ★★ ⚠ same residue
BMPR1A p.Asp69= Benign/Likely benign ★★ same residue
BMPR1A p.Asp69Asn Uncertain significance ★ ⚠ same residue
BMPR1A p.Asp69Gly Uncertain significance ★ ⚠ same residue
BMPR1A p.Arg442fs Pathogenic ★★ same condition
BMPR1A p.Asn73Ter Pathogenic ★★ same condition
BMPR1A p.Asp38fs Pathogenic ★★ same condition
BMPR1A p.Ile308fs 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/bmpr1a-p-asp69fs (accessed [today's date]).

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