Sugi Variant

Sugi Variant/EDEM3

EDEM3 — 138 ClinVar variants

All ClinVar germline EDEM3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 114 flagged for review →

13 Pathogenic · 3 Likely pathogenic · 2 Benign · 5 Likely benign · 115 Uncertain significance

Full EDEM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 114

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 lean, ClinVar uncertain 77

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

Predictors split 36

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

All EDEM3 variants

Pathogenic 13

  • c.346-1G>A Single submitter
  • p.Arg283fs Single submitter congenital disorder of glycosylation, type 2v
  • p.Arg648Ter Single submitter
  • p.Pro667fs Single submitter congenital disorder of glycosylation, type 2v
  • c.853+1G>T No assertion criteria congenital disorder of glycosylation, type 2v
  • p.Ala668fs No assertion criteria congenital disorder of glycosylation, type 2v
  • p.Arg314Ter No assertion criteria congenital disorder of glycosylation, type 2v
  • p.Arg457fs No assertion criteria congenital disorder of glycosylation, type 2v
  • p.Asp456Asn No assertion criteria congenital disorder of glycosylation, type 2v
  • p.Asp61Gly No assertion criteria congenital disorder of glycosylation, type 2v ⚠
  • p.Ile620fs No assertion criteria congenital disorder of glycosylation, type 2v
  • p.Phe461fs No assertion criteria congenital disorder of glycosylation, type 2v
  • p.Tyr469Ter No assertion criteria congenital disorder of glycosylation, type 2v

Likely pathogenic 3

  • p.Arg265Ter Single submitter congenital disorder of glycosylation, type 2v
  • p.Asp364fs Single submitter congenital disorder of glycosylation, type 2v
  • p.Leu402Val No assertion criteria Short stature

Benign 2

Likely benign 5

Uncertain significance 115