Is BMPR1B p.Asp50= (c.150C>T) pathogenic?

BMPR1B p.Asp50= (c.150C>T) is classified Likely benign in BMPR1B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-22). Ultra-rare (popmax 0.0144%, nfe); Associated with brachydactyly.

What condition is associated with BMPR1B p.Asp50= (c.150C>T)?

BMPR1B p.Asp50= (c.150C>T) is associated with brachydactyly, brachydactyly type A2, acromesomelic dysplasia 3 (ClinVar).

How common is BMPR1B p.Asp50= (c.150C>T) in the general population?

BMPR1B p.Asp50= (c.150C>T) is ultra-rare (popmax 0.0144%, nfe) (gnomAD).

BMPR1B p.Asp50=

c.150C>T · rs147320212 · VCV350114

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0144%, nfe)

Conditions

brachydactyly

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.41 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.22	GERP -4.6, phastCons 0.49
Overall
CADD	14.87	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0144% European (non-Finnish) · 170/1,179,268 alleles

Filtering AF 0.0126% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0119%

Overall 0.0113% 183/1,612,854 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0144%	6,937
Remaining individualsnot grpmax-eligible	0.00801%	12,490
Finnishnot grpmax-eligible	0.00469%	21,335
African / African-American	0.00401%	24,916
East Asian	0.00223%	44,840
South Asian	0.0011%	91,052

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: BMPR1B
Protein: p.Asp50=
Coding: c.150C>T
MANE Select: NM_001203
dbSNP: rs147320212
Type: single nucleotide variant
Location: chr4:95114726 (GRCh38)
Gene constraint: LOEUF 0.331 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 85.36 · 1 PDB
Residue 50: a disulfide bond

Full BMPR1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

brachydactyly — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: brachydactyly type A2 acromesomelic dysplasia 3

Similar variants

BMPR1B c.585+1G>C Likely pathogenic ★★ same condition
BMPR1B p.Arg486Trp Pathogenic ★★ same condition
BMPR1B c.*828T>G Uncertain significance ★★ same condition
BMPR1B c.*83C>G Uncertain significance ★★ same condition
BMPR1B p.Arg412Gly Uncertain significance ★★ ⚠ same condition
BMPR1B p.Arg91Ile Uncertain significance ★★ ⚠ same condition
BMPR1B p.Asn257Asp Uncertain significance ★★ ⚠ same condition
BMPR1B p.Asp166Gly Uncertain significance ★★ ⚠ 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/bmpr1b-p-asp50 (accessed [today's date]).

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