Is BMPR1A p.Phe58= (c.174T>C) pathogenic?

BMPR1A p.Phe58= (c.174T>C) is classified Likely benign in BMPR1A (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-25). Very rare (popmax 8.47e-05%, nfe); Associated with juvenile polyposis syndrome.

What condition is associated with BMPR1A p.Phe58= (c.174T>C)?

BMPR1A p.Phe58= (c.174T>C) is associated with juvenile polyposis syndrome, hereditary neoplastic syndrome (ClinVar).

How common is BMPR1A p.Phe58= (c.174T>C) in the general population?

BMPR1A p.Phe58= (c.174T>C) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is Juvenile polyposis syndrome inherited?

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

BMPR1A p.Phe58=

c.174T>C · rs1554888126 · VCV490985

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

juvenile polyposis 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 1.2	GERP 0.38, phastCons 1
Overall
CADD	10.3	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,028 alleles

Overall 6.2e-05% 1/1,614,194 alleles · very rare exomes 1/1,461,834 · genomes 0/152,360 · joint denominator

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: BMPR1A
Protein: p.Phe58=
Coding: c.174T>C
MANE Select: NM_004329
dbSNP: rs1554888126
Type: single nucleotide variant
Location: chr10:86890168 (GRCh38)
Gene constraint: LOEUF 0.195 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 82.86 · 11 PDB
Residue 58: a UniProt-annotated variant site (in a renal clear cell carcinoma sample; somatic mutation)

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

Disease context

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

Also linked: hereditary neoplastic syndrome

For Juvenile polyposis syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

BMPR1A p.Phe58Cys Uncertain significance ★ ⚠ same residue
BMPR1A p.Phe58Leu Uncertain significance ★ ⚠ same residue
BMPR1A p.Phe58Ser Uncertain significance ★ ⚠ same residue
BMPR1A p.Phe58Tyr Uncertain significance ★ ⚠ same residue
BMPR1A p.Phe58_Leu59insTer Pathogenic ★★ same residue
BMPR1A c.1166+1G>A Likely pathogenic ★★ same condition
BMPR1A c.1343-2A>G 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-phe58 (accessed [today's date]).

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