Sugi Variant

Sugi Variant/TCF4

TCF4 — 1165 ClinVar variants

All ClinVar germline TCF4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 281 flagged for review →

152 Pathogenic · 17 Pathogenic/Likely pathogenic · 89 Likely pathogenic · 22 Conflicting · 97 Benign · 32 Benign/Likely benign · 340 Likely benign · 416 Uncertain significance

Full TCF4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 281

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 9

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 9

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

Predicted LoF vs a conflicting call 2

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 199

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 199

Predictors split 62

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

All TCF4 variants

Pathogenic 152

Pathogenic/Likely pathogenic 17

Likely pathogenic 89

Conflicting classifications of pathogenicity 22

Benign 97

Benign/Likely benign 32

  • c.146-11C>G Multiple submitters Pitt-Hopkins syndrome
  • c.1486+6T>C Multiple submitters Pitt-Hopkins syndrome
  • c.1650-14C>T Multiple submitters Pitt-Hopkins syndrome
  • c.207+13A>G Multiple submitters Pitt-Hopkins syndrome
  • c.208-8A>G Multiple submitters Pitt-Hopkins syndrome
  • c.305-14G>A Multiple submitters Pitt-Hopkins syndrome
  • c.369+12T>G Multiple submitters Pitt-Hopkins syndrome
  • c.369+1365del Multiple submitters
  • c.370-14T>C Multiple submitters Pitt-Hopkins syndrome
  • c.549+28099AG[2] Multiple submitters
  • c.73-3T>C Multiple submitters Inborn genetic diseases
  • c.923-17G>T Multiple submitters Pitt-Hopkins syndrome
  • c.990+12T>C Multiple submitters Pitt-Hopkins syndrome
  • c.991-18del Multiple submitters Pitt-Hopkins syndrome
  • c.991-18dup Multiple submitters Pitt-Hopkins syndrome
  • c.-125C>T Multiple submitters Pitt-Hopkins syndrome
  • c.*3404G>C Multiple submitters Pitt-Hopkins syndrome
  • c.*5-10C>T Multiple submitters Pitt-Hopkins syndrome
  • c.*53C>A Multiple submitters Pitt-Hopkins syndrome
  • p.Ala315= Multiple submitters Pitt-Hopkins syndrome
  • p.Asn70Ser Multiple submitters Pitt-Hopkins syndrome
  • p.Asp322= Multiple submitters Inborn genetic diseases
  • p.Asp517= Multiple submitters Inborn genetic diseases
  • p.Glu22= Multiple submitters Pitt-Hopkins syndrome
  • p.Glu568= Multiple submitters Inborn genetic diseases
  • p.Glu641= Multiple submitters Pitt-Hopkins syndrome
  • p.Leu433= Multiple submitters Inborn genetic diseases
  • p.Ser110= Multiple submitters Inborn genetic diseases
  • p.Ser213= Multiple submitters Pitt-Hopkins syndrome
  • p.Ser312= Multiple submitters Inborn genetic diseases
  • p.Ser665= Multiple submitters Pitt-Hopkins syndrome
  • p.Thr526Met Multiple submitters Pitt-Hopkins syndrome

Likely benign 340

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

Uncertain significance 416

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