PGM3 p.Gly4=
c.12T>A · VCV4691697
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0033%, sas)
Conditions
1
immunodeficiency 23
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 0.23 | GERP -3.9, phastCons 0.011 |
| Overall | ||
| CADD | 4.087 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0033%
South Asian · 3/91,040 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000186%
3/1,612,762 alleles · very rare
exomes 3/1,460,456 · genomes 0/152,306 · joint denominator
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
- PGM3
- Protein
- p.Gly4=
- Coding
- c.12T>A
- MANE Select
- NM_015599
- Type
- single nucleotide variant
- Location
- chr6:83191001 (GRCh38)
- Gene constraint
- LOEUF 0.962 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 95.54
Disease context
immunodeficiency 23 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor PGM3-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy, Neonatal
Similar variants
- PGM3 p.Gly4Asp Uncertain significance ★ ⚠ same residue
- PGM3 c.-2-185C>T Pathogenic/Likely pathogenic ★★ same condition
- PGM3 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same condition
- PGM3 p.Asn246Ser Pathogenic/Likely pathogenic ★★ same condition
- PGM3 p.Gln22Ter Pathogenic/Likely pathogenic ★★ same condition
- PGM3 p.Gln262Ter Pathogenic/Likely pathogenic ★★ same condition
- PGM3 c.389+6G>A Uncertain significance ★★ same condition
- PGM3 c.-2-226T>C Uncertain significance ★★ 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/pgm3-p-gly4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown