Is BMPR1A p.Arg9fs (c.24_31del) pathogenic?

BMPR1A p.Arg9fs (c.2431del) is classified Likely pathogenic in BMPR1A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-27). No gnomAD frequency available for this variant; Associated with hereditary neoplastic syndrome.

What condition is associated with BMPR1A p.Arg9fs (c.24_31del)?

BMPR1A p.Arg9fs (c.24_31del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BMPR1A p.Arg9fs (c.24_31del) in the general population?

BMPR1A p.Arg9fs (c.24_31del) is no gnomAD frequency available for this variant (gnomAD).

BMPR1A p.Arg9fs

c.24_31del · rs2539350478 · VCV3223950

Likely pathogenic Single submitter

Classification

Likely 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 3 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.31	GERP -4.8, phastCons 0.15

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.Arg9fs
Coding: c.24_31del
MANE Select: NM_004329
dbSNP: rs2539350478
Type: Deletion
Location: chr10:86876040 (GRCh38)
Gene constraint: LOEUF 0.195 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 82.86 · 11 PDB

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.Arg9Ter Pathogenic/Likely pathogenic ★★ same residue
BMPR1A p.Arg9Lys Uncertain significance ★★ ⚠ same residue
BMPR1A p.Arg9Thr Uncertain significance ★★ ⚠ same residue
BMPR1A p.Arg9= Conflicting classifications of pathogenicity ★ same residue
BMPR1A p.Glu256fs Pathogenic ★★ same condition
BMPR1A p.Glu276fs Pathogenic ★★ same condition
BMPR1A p.Glu45fs Pathogenic ★★ same condition
BMPR1A p.Gly92fs 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-arg9fs (accessed [today's date]).

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