Is BMPR2 p.Arg459fs (c.1376_1377del) pathogenic?

BMPR2 p.Arg459fs (c.13761377del) is classified Pathogenic in BMPR2 (ClinVar, Single submitter, 2 submitters; last evaluated 2019-09-13). Absent from gnomAD; Associated with pulmonary hypertension, primary, 1.

What condition is associated with BMPR2 p.Arg459fs (c.1376_1377del)?

BMPR2 p.Arg459fs (c.1376_1377del) is associated with pulmonary hypertension, primary, 1 (ClinVar).

How common is BMPR2 p.Arg459fs (c.1376_1377del) in the general population?

BMPR2 p.Arg459fs (c.1376_1377del) is absent from gnomAD (gnomAD).

BMPR2 p.Arg459fs

c.1376_1377del · rs1085307342 · VCV425931

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

pulmonary hypertension, primary, 1

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 10 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.6, 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: BMPR2
Protein: p.Arg459fs
Coding: c.1376_1377del
MANE Select: NM_001204
dbSNP: rs1085307342
Type: Microsatellite
Location: chr2:202542407 (GRCh38)
Gene constraint: LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 58.07 · 7 PDB
Residue 459: a UniProt-annotated variant site (in pph1; changed localization to the plasma membrane); the protein kinase domain; a UniProt-annotated variant site (in pph1; loss of localization to the plasma membrane; localized to the cytoplasm)

Full BMPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pulmonary hypertension, primary, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BMPR2 c.1587-7_1587-4del Likely benign ★★★ same condition
BMPR2 p.Ser52_His53insTer Pathogenic/Likely pathogenic ★★ same condition
BMPR2 p.Glu661del Uncertain significance ★★ same condition
BMPR2 p.Arg459= Likely benign ★★ same residue
BMPR2 p.Arg266fs Pathogenic ★ same condition
BMPR2 p.Leu293fs Likely pathogenic ★ same condition
BMPR2 p.Arg459Lys Uncertain significance ★ ⚠ same residue
BMPR2 p.Arg459Ser Uncertain significance ★ same residue

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/bmpr2-p-arg459fs (accessed [today's date]).

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