BPGM p.Leu196=
c.588A>C · VCV4772648
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, 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 5 | GERP -0.1, phastCons 1 |
| Overall | ||
| CADD | 7.584 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
African / African-American · 5/74,918 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.00031%
5/1,613,996 alleles · very rare
exomes 3/1,461,800 · genomes 2/152,196 · joint denominator
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.Leu196=
- Coding
- c.588A>C
- MANE Select
- NM_001724
- Type
- single nucleotide variant
- Location
- chr7:134662095 (GRCh38)
- Gene constraint
- LOEUF 0.987 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.81 · 17 PDB
- Residue 196
- 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.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-leu196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown