Is BMPR1A p.Ile169= (c.507C>T) pathogenic?

BMPR1A p.Ile169= (c.507C>T) is classified Conflicting classifications of pathogenicity in BMPR1A (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-08-26). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BMPR1A p.Ile169= (c.507C>T)?

BMPR1A p.Ile169= (c.507C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BMPR1A p.Ile169= (c.507C>T) in the general population?

BMPR1A p.Ile169= (c.507C>T) is absent from gnomAD v4.1 (gnomAD).

BMPR1A p.Ile169=

c.507C>T · rs2539495484 · VCV1745204

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

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	GERP 0.8, phastCons 1
Overall
CADD	12.39	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BMPR1A
Protein: p.Ile169=
Coding: c.507C>T
MANE Select: NM_004329
dbSNP: rs2539495484
Type: single nucleotide variant
Location: chr10:86900103 (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.Ile169Leu Uncertain significance ★★ ⚠ same residue
BMPR1A p.Ile169Thr Uncertain significance ★★ ⚠ same residue
BMPR1A p.Ile169Val Uncertain significance ★★ ⚠ same residue
BMPR1A p.Ile169Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
BMPR1A p.Ile169_Phe170insPro Uncertain significance ★★ same residue
BMPR1A p.Ile169del Uncertain significance ★★ same residue
BMPR1A c.1166+1G>A Likely pathogenic ★★ same condition
BMPR1A c.1473+1G>A Pathogenic/Likely 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-ile169 (accessed [today's date]).

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