PGM3 p.Leu75=
c.223T>C · rs2538211910 · VCV2841502
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
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 1.3 | GERP -5, phastCons 0.66 |
| Overall | ||
| CADD | 12.22 | 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
- PGM3
- Protein
- p.Leu75=
- Coding
- c.223T>C
- MANE Select
- NM_015599
- dbSNP
- rs2538211910
- Type
- single nucleotide variant
- Location
- chr6:83188780 (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 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
- PGM3 p.Ala402Thr 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-leu75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown