PGM2 p.Asp322=
c.966C>T · rs34893278 · VCV787026
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.72%, 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 -0.005 | GERP 0.19, phastCons 0.78 |
| Overall | ||
| CADD | 6.744 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.72%
African / African-American · 1,287/74,990 alleles
Filtering AF
1.64%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.61%
Overall
0.094%
1,516/1,613,412 alleles · low-frequency
exomes 767/1,461,168 · genomes 749/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.72% | 58 |
| Admixed American | 0.2% | 500 |
| Remaining individualsnot grpmax-eligible | 0.13% | 771 |
| Middle Eastern | 0.066% | 1,515 |
| South Asian | 0.011% | 9,106 |
| European (non-Finnish) | 0.00119% | 84,245 |
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
- PGM2
- Protein
- p.Asp322=
- Coding
- c.966C>T
- MANE Select
- NM_018290
- dbSNP
- rs34893278
- Type
- single nucleotide variant
- Location
- chr4:37845689 (GRCh38)
- Gene constraint
- LOEUF 1.172 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.60
- Residue 322
- a binding site
Similar variants
- PGM2 p.Ala107Thr Uncertain significance ★ ⚠ same type
- PGM2 p.Ala121Val Uncertain significance ★ ⚠ same type
- PGM2 p.Ala124Thr Uncertain significance ★ ⚠ same type
- PGM2 p.Ala277Val Uncertain significance ★ ⚠ same type
- PGM2 p.Ala2Gly Uncertain significance ★ ⚠ same type
- PGM2 p.Ala310Asp Uncertain significance ★ ⚠ same type
- PGM2 p.Ala315Asp Uncertain significance ★ ⚠ same type
- PGM2 p.Ala325Val 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/pgm2-p-asp322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown