PGAM1 p.Ser152=
c.456C>T · rs141766981 · VCV782534
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.588%, 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 0.83 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 10.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.588%
African / African-American · 441/75,036 alleles
Filtering AF
0.542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.525%
Overall
0.032%
517/1,613,948 alleles · rare
exomes 266/1,461,668 · genomes 251/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.588% | 170 |
| Admixed American | 0.0583% | 1,715 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,717 |
| Middle Eastern | 0.0165% | 6,058 |
| East Asian | 0.00669% | 14,954 |
| South Asian | 0.0022% | 45,537 |
| European (non-Finnish) | 0.00102% | 98,323 |
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
- PGAM1
- Protein
- p.Ser152=
- Coding
- c.456C>T
- MANE Select
- NM_002629
- dbSNP
- rs141766981
- Type
- single nucleotide variant
- Location
- chr10:97430996 (GRCh38)
- Structure
- AlphaFold pLDDT 94.21
Similar variants
- PGAM1 p.Asn99= Benign ★★ same type
- PGAM1 p.Ala105Gly Uncertain significance ★ ⚠ same type
- PGAM1 p.Ala105Val Uncertain significance ★ ⚠ same type
- PGAM1 p.Ala163Thr Uncertain significance ★ ⚠ same type
- PGAM1 p.Ala248Thr Uncertain significance ★ ⚠ same type
- PGAM1 p.Ala2Val Uncertain significance ★ same type
- PGAM1 p.Ala48Val Uncertain significance ★ ⚠ same type
- PGAM1 p.Ala73Gly 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/pgam1-p-ser152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown