Sugi Variant

Sugi Variant/GDI1

GDI1 — 161 ClinVar variants

All ClinVar germline GDI1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 83 flagged for review →

7 Pathogenic · 7 Likely pathogenic · 13 Conflicting · 5 Benign · 5 Benign/Likely benign · 39 Likely benign · 85 Uncertain significance

Full GDI1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 83

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 7

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

Predictors lean, ClinVar uncertain 57

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

Predictors split 18

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

All GDI1 variants

Pathogenic 7

  • p.Ala148fs Single submitter Inborn genetic diseases
  • p.Asp392delinsThrTer Single submitter intellectual disability, X-linked 41
  • p.Glu363fs Single submitter intellectual disability, X-linked 41
  • p.Arg423Pro No assertion criteria intellectual disability, X-linked 41
  • p.Arg70Ter No assertion criteria intellectual disability, X-linked 41
  • p.Ser354fs No assertion criteria intellectual disability, X-linked 41
  • p.Ser396fs No assertion criteria intellectual disability, X-linked 41

Likely pathogenic 7

  • c.45+1G>A Single submitter intellectual disability, X-linked 41
  • c.819+1G>A Single submitter Inborn genetic diseases
  • p.Gln236fs Single submitter intellectual disability, X-linked 41
  • p.Gln236Ter Single submitter intellectual disability, X-linked 41
  • p.Gly263fs Single submitter intellectual disability, X-linked 41
  • p.Phe158Ser Single submitter ⚠
  • p.Tyr224Cys Single submitter non-syndromic X-linked intellectual disability

Conflicting classifications of pathogenicity 13

Benign 5

Benign/Likely benign 5

  • c.154-3C>T Multiple submitters Inborn genetic diseases
  • p.Asn312= Multiple submitters
  • p.Asp196= Multiple submitters Inborn genetic diseases
  • p.Asp257= Multiple submitters
  • p.Ser108= Multiple submitters intellectual disability, X-linked 41

Likely benign 39

Uncertain significance 85