Sugi Variant

Sugi Variant/LEF1

LEF1 — 59 ClinVar variants

All ClinVar germline LEF1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 45 flagged for review →

4 Pathogenic · 1 Likely pathogenic · 1 Conflicting · 2 Benign · 1 Benign/Likely benign · 2 Likely benign · 48 Uncertain significance

Full LEF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 45

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, 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 23

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

Predictors split 21

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

All LEF1 variants

Pathogenic 4

  • p.Gln182fs Single submitter split hand-foot malformation
  • p.Tyr349del Single submitter split hand-foot malformation
  • p.His286fs No assertion criteria ectodermal dysplasia 17 with or without limb malformations
  • p.Met23dup No assertion criteria ectrodactyly and ectodermal dysplasia without cleft lip/palate

Likely pathogenic 1

  • p.Ser172fs Single submitter ectodermal dysplasia 17 with or without limb malformations

Conflicting classifications of pathogenicity 1

  • p.Leu157fs Single submitter ectodermal dysplasia 17 with or without limb malformations ⚠

Benign 2

Benign/Likely benign 1

Likely benign 2

Uncertain significance 48