Sugi Variant

Sugi Variant/FOXP2

FOXP2 — 426 ClinVar variants

All ClinVar germline FOXP2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 130 flagged for review →

39 Pathogenic · 4 Pathogenic/Likely pathogenic · 22 Likely pathogenic · 16 Conflicting · 60 Benign · 14 Benign/Likely benign · 68 Likely benign · 203 Uncertain significance

Full FOXP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 130

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 9

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

Predicted LoF vs a conflicting call 1

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 73

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

Predictors split 46

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

All FOXP2 variants

Pathogenic 39

Pathogenic/Likely pathogenic 4

Likely pathogenic 22

Conflicting classifications of pathogenicity 16

Benign 60

Benign/Likely benign 14

  • c.1266+8C>T Multiple submitters childhood apraxia of speech
  • c.1468+9T>C Multiple submitters childhood apraxia of speech
  • c.1770-5_1770-4dup Multiple submitters Inborn genetic diseases
  • c.598-10C>T Multiple submitters childhood apraxia of speech
  • c.618_620delGCA Multiple submitters Inborn genetic diseases
  • c.618_620dupGCA Multiple submitters Inborn genetic diseases
  • p.Ala615Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Arg477= Multiple submitters Inborn genetic diseases
  • p.Gln161= Multiple submitters Inborn genetic diseases
  • p.Gln174= Multiple submitters childhood apraxia of speech
  • p.Gln184= Multiple submitters Inborn genetic diseases
  • p.Ile457= Multiple submitters Inborn genetic diseases
  • p.Phe562= Multiple submitters Inborn genetic diseases
  • p.Tyr498= Multiple submitters childhood apraxia of speech

Likely benign 68

Uncertain significance 203