Sugi Variant

Sugi Variant/STAG1

STAG1 — 699 ClinVar variants

All ClinVar germline STAG1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 295 flagged for review →

16 Pathogenic · 8 Pathogenic/Likely pathogenic · 36 Likely pathogenic · 26 Conflicting · 30 Benign · 16 Benign/Likely benign · 253 Likely benign · 314 Uncertain significance

Full STAG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 295

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 16

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

Predictors lean, ClinVar uncertain 203

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 203

Predictors split 75

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

All STAG1 variants

Pathogenic 16

Pathogenic/Likely pathogenic 8

  • p.Arg140Ter Multiple submitters intellectual disability, autosomal dominant 47
  • p.Arg216Gly Multiple submitters intellectual disability, autosomal dominant 47
  • p.Arg373Gln Multiple submitters intellectual disability, autosomal dominant 47
  • p.Arg373Ter Multiple submitters
  • p.Arg377Cys Multiple submitters intellectual disability, autosomal dominant 47
  • p.Arg971Ter Multiple submitters
  • p.His478Pro No assertion criteria STAG1-related disorder
  • p.Trp489fs No assertion criteria STAG1-related disorder

Likely pathogenic 36

  • c.1026+2T>C Multiple submitters intellectual disability, autosomal dominant 47
  • p.Arg395Ter Multiple submitters STAG1-related disorder
  • c.1125+1G>C Single submitter intellectual disability, autosomal dominant 47
  • c.132+5G>A Single submitter neurodevelopmental disorder
  • c.1546+1G>T Single submitter
  • c.1744-2A>G Single submitter intellectual disability, autosomal dominant 47
  • c.3446+1G>A Single submitter
  • p.Arg1081Ter Single submitter intellectual disability, autosomal dominant 47
  • p.Arg1187Trp Single submitter
  • p.Arg1231Ter Single submitter intellectual disability, autosomal dominant 47
  • p.Arg1233fs Single submitter
  • p.Arg135fs Single submitter
  • p.Arg301His Single submitter Inborn genetic diseases
  • p.Asn670fs Single submitter intellectual disability, autosomal dominant 47
  • p.Asn941fs Single submitter STAG1-related disorder
  • p.Asp384His Single submitter
  • p.Asp655Ter Single submitter intellectual disability, autosomal dominant 47
  • p.Gln170_Trp171insTer Single submitter intellectual disability, autosomal dominant 47
  • p.Gln190Ter Single submitter intellectual disability, autosomal dominant 47
  • p.Glu1163Gly Single submitter ⚠
  • p.Glu368Lys Single submitter Global developmental delay
  • p.Glu853fs Single submitter intellectual disability, autosomal dominant 47
  • p.Gly209Arg Single submitter intellectual disability, autosomal dominant 47
  • p.Gly316fs Single submitter Neurodevelopmental delay
  • p.His478Leu Single submitter intellectual disability, autosomal dominant 47
  • p.Ile526fs Single submitter intellectual disability, autosomal dominant 47
  • p.Ile573fs Single submitter intellectual disability, autosomal dominant 47
  • p.Leu6Ter Single submitter STAG1-related disorder
  • p.Lys333Glu Single submitter
  • p.Thr1021fs Single submitter
  • p.Tyr322fs Single submitter neurodevelopmental disorder
  • p.Tyr743del Single submitter STAG1-related disorder
  • p.Gln214Arg No assertion criteria STAG1-related disorder
  • p.Leu351Trp No assertion criteria STAG1-related disorder
  • p.Lys1087fs No assertion criteria intellectual disability, autosomal dominant 47
  • p.Lys333Gln No assertion criteria STAG1-related disorder

Conflicting classifications of pathogenicity 26

Benign 30

Benign/Likely benign 16

Likely benign 253

Uncertain significance 314

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