PGM1 p.Ser100=
c.300C>G · rs2100981874 · VCV2740429
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
PGM1-congenital disorder of glycosylation
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 0.27 | GERP -0.79, phastCons 0.97 |
| Overall | ||
| CADD | 8.454 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PGM1
- Protein
- p.Ser100=
- Coding
- c.300C>G
- MANE Select
- NM_002633
- dbSNP
- rs2100981874
- Type
- single nucleotide variant
- Location
- chr1:63629478 (GRCh38)
- Gene constraint
- LOEUF 1.189 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 97.27 · 16 PDB
- Residue 100
- an α-helix
Disease context
PGM1-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor PGM1-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- PGM1 p.Arg217Ter Pathogenic ★★ same condition
- PGM1 p.Arg293Ter Pathogenic/Likely pathogenic ★★ same condition
- PGM1 p.Arg499Ter Pathogenic/Likely pathogenic ★★ same condition
- PGM1 p.Arg503Ter Pathogenic ★★ same condition
- PGM1 p.Arg515Gln Pathogenic/Likely pathogenic ★★ same condition
- PGM1 p.Asp263Tyr Pathogenic/Likely pathogenic ★★ same condition
- PGM1 p.Gly291Arg Pathogenic/Likely pathogenic ★★ same condition
- PGM1 p.Gly330Arg Pathogenic/Likely pathogenic ★★ same condition
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/pgm1-p-ser100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown