Is BPGM p.Leu87= (c.259C>T) pathogenic?

BPGM p.Leu87= (c.259C>T) is classified Likely benign in BPGM (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-04). Very rare (popmax 0.00267%, afr).

How common is BPGM p.Leu87= (c.259C>T) in the general population?

BPGM p.Leu87= (c.259C>T) is very rare (popmax 0.00267%, afr) (gnomAD).

BPGM p.Leu87=

c.259C>T · VCV4691665

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, 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 4	GERP 1.1, phastCons 1
Overall
CADD	11.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,912 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000558% 9/1,614,024 alleles · very rare exomes 4/1,461,866 · genomes 5/152,158 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,456
Remaining individualsnot grpmax-eligible	0.0016%	62,486
European (non-Finnish)	0.000508%	196,671

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.Leu87=
Coding: c.259C>T
MANE Select: NM_001724
Type: single nucleotide variant
Location: chr7:134661766 (GRCh38)
Gene constraint: LOEUF 0.987 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.81 · 17 PDB
Residue 87: an α-helix

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

Similar variants

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
BPGM p.Ala244Val 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-leu87 (accessed [today's date]).

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