PGM2 p.Ser104=
c.312T>C · VCV4684783
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 63.7%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.6 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 8.108 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
63.7%
African / African-American · 47,379/74,324 alleles
Filtering AF
63.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 63.1%
Overall
23.2%
370,094/1,597,158 alleles · common
exomes 319,452/1,445,072 · genomes 50,642/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 63.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 30.7% | 3 |
| Admixed American | 28.3% | 4 |
| Middle Eastern | 26.4% | 4 |
| East Asian | 25.4% | 4 |
| Remaining individualsnot grpmax-eligible | 25.2% | 4 |
| European (non-Finnish) | 20.9% | 5 |
| Amishnot grpmax-eligible | 19.3% | 5 |
| South Asian | 17% | 6 |
| Finnishnot grpmax-eligible | 14.1% | 7 |
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.Ser104=
- Coding
- c.312T>C
- MANE Select
- NM_018290
- Type
- single nucleotide variant
- Location
- chr4:37834680 (GRCh38)
- Gene constraint
- LOEUF 1.172 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.60
Similar variants
- PGM2 p.Asp322= Benign ★★ same type
- 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
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-ser104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown