Sugi Variant

Sugi Variant/STX3

STX3 — 231 ClinVar variants

All ClinVar germline STX3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 82 flagged for review →

10 Pathogenic · 3 Likely pathogenic · 2 Conflicting · 4 Benign · 5 Benign/Likely benign · 118 Likely benign · 89 Uncertain significance

Full STX3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 82

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 agree, ClinVar conflicts 1

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

Predictors lean, ClinVar uncertain 62

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

Predictors split 19

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

All STX3 variants

Pathogenic 10

  • p.Arg247Ter Multiple submitters STX3-related disorder
  • p.Ala253fs Single submitter
  • p.Arg142Ter Single submitter
  • p.Arg148fs Single submitter
  • p.Arg148Ter Single submitter
  • p.Tyr60fs Single submitter retinal dystrophy and microvillus inclusion disease
  • p.Val240fs Single submitter
  • c.115-2A>G No assertion criteria retinal dystrophy and microvillus inclusion disease
  • p.Arg125fs No assertion criteria retinal dystrophy and microvillus inclusion disease
  • p.Val122fs No assertion criteria retinal dystrophy and microvillus inclusion disease

Likely pathogenic 3

Conflicting classifications of pathogenicity 2

  • p.Arg197Ter Single submitter diarrhea 12, with microvillus atrophy
  • p.Gln15Arg Single submitter Inborn genetic diseases ⚠

Benign 4

Benign/Likely benign 5

Likely benign 118

Uncertain significance 89