Sugi Variant

Sugi Variant/FOXC2

FOXC2 — 330 ClinVar variants

All ClinVar germline FOXC2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 184 flagged for review →

33 Pathogenic · 2 Pathogenic/Likely pathogenic · 27 Likely pathogenic · 12 Conflicting · 10 Benign · 4 Benign/Likely benign · 43 Likely benign · 199 Uncertain significance

Full FOXC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 184

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 2

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

Predictors agree, ClinVar conflicts 8

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 144

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

Predictors split 29

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

All FOXC2 variants

Pathogenic 33

Pathogenic/Likely pathogenic 2

  • p.Arg121Cys Multiple submitters lymphedema-distichiasis syndrome
  • p.Tyr99Ter Multiple submitters lymphedema-distichiasis syndrome

Likely pathogenic 27

  • p.Leu124Phe Multiple submitters lymphedema-distichiasis syndrome
  • c.(?_1 Single submitter lymphedema-distichiasis syndrome
  • p.Ala196fs Single submitter lymphedema-distichiasis syndrome
  • p.Arg242fs Single submitter
  • p.Asp151fs Single submitter
  • p.Gln330Ter Single submitter Inborn genetic diseases
  • p.Gln407fs Single submitter lymphedema-distichiasis syndrome
  • p.Gln47Ter Single submitter
  • p.Gln63fs Single submitter FOXC2-related disorders
  • p.Glu343Ter Single submitter non-immune hydrops fetalis
  • p.Ile102Asn Single submitter lymphedema-distichiasis syndrome
  • p.Leu369fs Single submitter lymphedema-distichiasis syndrome
  • p.Leu80Val Single submitter lymphedema-distichiasis syndrome
  • p.Lys68fs Single submitter FOXC2-related disorders
  • p.Met333fs Single submitter
  • p.Pro403fs Single submitter lymphedema-distichiasis syndrome
  • p.Pro412fs Single submitter FOXC2-related disorders
  • p.Ser125Leu Single submitter lymphedema-distichiasis syndrome
  • p.Thr385fs Single submitter FOXC2-related disorders
  • p.Trp116Ter Single submitter lymphedema-distichiasis syndrome
  • p.Tyr305Ter Single submitter FOXC2-related disorders
  • p.Tyr313Ter Single submitter lymphedema-distichiasis syndrome
  • p.Tyr329Ter Single submitter FOXC2-related disorder
  • p.Val298fs Single submitter FOXC2-related disorders
  • p.Gln63Ter No assertion criteria FOXC2-related disorder
  • p.Gly250fs No assertion criteria FOXC2-related disorder
  • p.Tyr329fs No assertion criteria FOXC2-related disorder

Conflicting classifications of pathogenicity 12

Benign 10

Benign/Likely benign 4

Likely benign 43

Uncertain significance 199