BPGM p.Leu162=
c.486G>A · rs145982146 · VCV2759959
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.219%, nfe)
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 3.4 | GERP 0.009, phastCons 1 |
| Overall | ||
| CADD | 7.329 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.219%
European (non-Finnish) · 2,585/1,180,022 alleles
Filtering AF
0.212%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.209%
Overall
0.17%
2,740/1,614,154 alleles · rare
exomes 2,582/1,461,866 · genomes 158/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.219% | 456 |
| Remaining individualsnot grpmax-eligible | 0.126% | 791 |
| African / African-American | 0.0307% | 3,262 |
| South Asian | 0.0274% | 3,644 |
| Finnishnot grpmax-eligible | 0.025% | 4,002 |
| Admixed American | 0.0183% | 5,456 |
| East Asian | 0.00223% | 44,882 |
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.Leu162=
- Coding
- c.486G>A
- MANE Select
- NM_001724
- dbSNP
- rs145982146
- Type
- single nucleotide variant
- Location
- chr7:134661993 (GRCh38)
- Gene constraint
- LOEUF 0.987 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.81 · 17 PDB
- Residue 162
- an α-helix
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.Arg90Cys Pathogenic ★ same type
- BPGM p.Ala243Val Uncertain significance ★ ⚠ same type
- BPGM p.Ala244Val Uncertain significance ★ same type
- BPGM p.Arg10Thr 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-leu162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown