Sugi Variant

Sugi Variant/SATB1

SATB1 — 246 ClinVar variants

All ClinVar germline SATB1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 133 flagged for review →

16 Pathogenic · 2 Pathogenic/Likely pathogenic · 19 Likely pathogenic · 4 Conflicting · 5 Benign · 2 Benign/Likely benign · 31 Likely benign · 167 Uncertain significance

Full SATB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 133

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 1

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

Predictors lean, ClinVar uncertain 93

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

Predictors split 38

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

All SATB1 variants

Pathogenic 16

  • p.Arg553Ter Multiple submitters developmental delay with dysmorphic facies and dental anomalies
  • p.Arg642Ter Multiple submitters developmental delay with dysmorphic facies and dental anomalies
  • p.Glu407Gln Multiple submitters developmental delay with dysmorphic facies and dental anomalies
  • p.Arg335fs Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Asn268fs Single submitter Inborn genetic diseases
  • p.Gln402Arg Single submitter
  • p.Gln616fs Single submitter Inborn genetic diseases
  • p.Glu413fs Single submitter Inborn genetic diseases
  • p.Gly46fs Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Leu321fs Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Leu545fs Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Pro626fs Single submitter
  • p.Arg385fs No assertion criteria developmental delay with dysmorphic facies and dental anomalies
  • p.Arg410Ter No assertion criteria developmental delay with dysmorphic facies and dental anomalies
  • p.Gln525Arg No assertion criteria Kohlschutter-Tonz syndrome-like
  • p.Gln694Ter No assertion criteria developmental delay with dysmorphic facies and dental anomalies

Pathogenic/Likely pathogenic 2

  • p.Glu530Lys Multiple submitters Kohlschutter-Tonz syndrome-like
  • p.Pro352fs Multiple submitters developmental delay with dysmorphic facies and dental anomalies

Likely pathogenic 19

  • p.Arg427Gln Multiple submitters Kohlschutter-Tonz syndrome-like ⚠
  • p.Tyr144Ter Multiple submitters developmental delay with dysmorphic facies and dental anomalies
  • c.211+2T>C Single submitter Inborn genetic diseases
  • p.Arg508Cys Single submitter
  • p.Arg533Cys Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Gln402Glu Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Gln420Arg Single submitter Inborn genetic diseases ⚠
  • p.Gln420Ter Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Gln594fs Single submitter neurodevelopmental disorder
  • p.Glu407Gly Single submitter SATB1-related disorder
  • p.Glu530Gln Single submitter ⚠
  • p.Glu713Ter Single submitter Kohlschutter-Tonz syndrome-like
  • p.Pro181Leu Single submitter developmental delay with dysmorphic facies and dental anomalies ⚠
  • p.Pro610fs Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Ser309fs Single submitter Kohlschutter-Tonz syndrome-like
  • p.Ser451Arg Single submitter SATB1-related disorder ⚠
  • p.Ser633fs Single submitter developmental delay with dysmorphic facies and dental anomalies
  • p.Val574fs Single submitter Kohlschutter-Tonz syndrome-like
  • p.Asp150fs No assertion criteria developmental delay with dysmorphic facies and dental anomalies

Conflicting classifications of pathogenicity 4

Benign 5

Benign/Likely benign 2

Likely benign 31

Uncertain significance 167