Is BPGM p.Gln151= (c.453A>G) pathogenic?

BPGM p.Gln151= (c.453A>G) is classified Likely benign in BPGM (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-09). Ultra-rare (popmax 0.0147%, afr).

How common is BPGM p.Gln151= (c.453A>G) in the general population?

BPGM p.Gln151= (c.453A>G) is ultra-rare (popmax 0.0147%, afr) (gnomAD).

BPGM p.Gln151=

c.453A>G · VCV3730415

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0147%, afr)

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 -0.88	GERP -5.7
Overall
CADD	0.465	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0147% African / African-American · 11/74,936 alleles

Filtering AF 0.00815% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00633%

Overall 0.00105% 17/1,614,070 alleles · ultra-rare exomes 9/1,461,864 · genomes 8/152,206 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0147%	6,812
Remaining individualsnot grpmax-eligible	0.0032%	31,243
Admixed American	0.00167%	59,998
South Asian	0.0011%	91,090
European (non-Finnish)	0.000169%	590,016

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: BPGM
Protein: p.Gln151=
Coding: c.453A>G
MANE Select: NM_001724
Type: single nucleotide variant
Location: chr7:134661960 (GRCh38)
Gene constraint: LOEUF 0.987 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.81 · 17 PDB
Residue 151: an α-helix

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

Similar variants

BPGM p.Gln151His Uncertain significance ★ ⚠ same residue
BPGM p.Glu176Lys Uncertain significance ★★ ⚠ same type
BPGM p.His11Asn Uncertain significance ★★ ⚠ same type
BPGM p.His198Gln Uncertain significance ★★ ⚠ same type
BPGM p.Arg62= Likely benign ★★ same type
BPGM p.Leu162= Likely benign ★★ same type
BPGM p.Arg90Cys Pathogenic ★ same type
BPGM p.Ala243Val Uncertain significance ★ ⚠ same type

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/bpgm-p-gln151 (accessed [today's date]).

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