BPGM p.Arg62=
c.186G>A · rs184531591 · VCV2081153
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.11%, amr)
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 0.47 | GERP -3.2, phastCons 0.98 |
| Overall | ||
| CADD | 9.301 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.11%
Admixed American · 66/59,990 alleles
Filtering AF
0.0887%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0809%
Overall
0.00527%
85/1,614,086 alleles · rare
exomes 31/1,461,838 · genomes 54/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.11% | 909 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,167 |
| African / African-American | 0.00533% | 18,755 |
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.Arg62=
- Coding
- c.186G>A
- MANE Select
- NM_001724
- dbSNP
- rs184531591
- Type
- single nucleotide variant
- Location
- chr7:134661693 (GRCh38)
- Gene constraint
- LOEUF 0.987 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.81 · 17 PDB
- Residue 62
- a UniProt-annotated variant site (in ecyt8); an α-helix; a binding site
Similar variants
- BPGM p.Arg62Gln Pathogenic 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.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-arg62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown