Sugi Variant

Sugi Variant/PGM3

PGM3 — 604 ClinVar variants

All ClinVar germline PGM3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 164 flagged for review →

45 Pathogenic · 10 Pathogenic/Likely pathogenic · 13 Likely pathogenic · 14 Conflicting · 17 Benign · 6 Benign/Likely benign · 301 Likely benign · 198 Uncertain significance

Full PGM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 164

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors vs ClinVar 1

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 6

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 133

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 23

The independent predictors disagree with each other — read with care.

All PGM3 variants

Pathogenic 45

Pathogenic/Likely pathogenic 10

  • c.-2-185C>T Multiple submitters immunodeficiency 23
  • p.Arg104Ter Multiple submitters immunodeficiency 23
  • p.Arg127Ter Multiple submitters immunodeficiency 23
  • p.Arg492Ter Multiple submitters severe combined immunodeficiency
  • p.Asn246Ser Multiple submitters Inborn genetic diseases
  • p.Asn482fs Multiple submitters immunodeficiency 23
  • p.Gln22Ter Multiple submitters immunodeficiency 23
  • p.Gln262Ter Multiple submitters PGM3-related disorder
  • p.Glu340del Multiple submitters immunodeficiency 23
  • p.Met385fs Multiple submitters immunodeficiency 23

Likely pathogenic 13

Conflicting classifications of pathogenicity 14

Benign 17

Benign/Likely benign 6

  • c.389+12A>T Multiple submitters immunodeficiency 23
  • c.-2-190T>A Multiple submitters immunodeficiency 23
  • p.Ala11= Multiple submitters immunodeficiency 23
  • p.Asn17Ser Multiple submitters Inborn genetic diseases
  • p.Glu427= Multiple submitters immunodeficiency 23
  • p.Lys489= Multiple submitters immunodeficiency 23

Likely benign 301

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 198