Is BGN p.Pro52= (c.156G>A) pathogenic?

BGN p.Pro52= (c.156G>A) is classified Likely benign in BGN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-02-12). Very rare (popmax 0.00436%, amr); Associated with Cardiovascular phenotype.

What condition is associated with BGN p.Pro52= (c.156G>A)?

BGN p.Pro52= (c.156G>A) is associated with Cardiovascular phenotype (ClinVar).

How common is BGN p.Pro52= (c.156G>A) in the general population?

BGN p.Pro52= (c.156G>A) is very rare (popmax 0.00436%, amr) (gnomAD).

BGN p.Pro52=

c.156G>A · rs374777271 · VCV1775484

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00436%, amr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.4	GERP -3.5, phastCons 1
Overall
CADD	2.575	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00436% Admixed American · 2/45,888 alleles

Filtering AF 0.000722% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000278%

Overall 0.000909% 11/1,209,988 alleles · very rare exomes 10/1,097,727 · genomes 1/112,261 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00436%	22,944
East Asian	0.00296%	33,770
European (non-Finnish)	0.000894%	111,907

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: BGN
Protein: p.Pro52=
Coding: c.156G>A
MANE Select: NM_001711
dbSNP: rs374777271
Type: single nucleotide variant
Location: chrX:153504787 (GRCh38)
Structure: AlphaFold pLDDT 85.72

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

Disease context

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

Similar variants

BGN p.Pro52Leu Uncertain significance ★ ⚠ same residue
BGN p.Pro52Ser Uncertain significance ★ ⚠ same residue
BGN c.909+4A>G Uncertain significance ★★ same condition
BGN p.Ala330Asp Uncertain significance ★★ ⚠ same condition
BGN p.Ala330Pro Uncertain significance ★★ ⚠ same condition
BGN p.Ala41Ser Uncertain significance ★★ ⚠ same condition
BGN p.Ala44Thr Uncertain significance ★★ ⚠ same condition
BGN p.Arg106His 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/bgn-p-pro52 (accessed [today's date]).

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