Sugi Variant

Sugi Variant/LGI4

LGI4 — 155 ClinVar variants

All ClinVar germline LGI4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 82 flagged for review →

9 Pathogenic · 10 Likely pathogenic · 2 Conflicting · 23 Benign · 1 Benign/Likely benign · 25 Likely benign · 85 Uncertain significance

Full LGI4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 82

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 61

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

Predictors split 19

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

All LGI4 variants

Pathogenic 9

  • p.Arg145Ter Single submitter arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Met1Thr Single submitter arthrogryposis multiplex congenita 2, neurogenic type
  • c.1299+5G>T No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • c.793+5G>C No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Ala265Thr No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect ⚠
  • p.Arg258Pro No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Gln385Ter No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Trp288Ter No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Val434Asp No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect

Likely pathogenic 10

  • p.Ser279fs Multiple submitters LGI4-related disorder
  • p.Cys424Ter Single submitter arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Glu260fs Single submitter arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Gly277fs Single submitter
  • p.Leu344Gln Single submitter arthrogryposis multiplex congenita
  • p.Phe88del Single submitter arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Ser291fs Single submitter arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Tyr104Ter Single submitter arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Glu321Lys No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Leu67Arg No assertion criteria arthrogryposis multiplex congenita 1, neurogenic, with myelin defect

Conflicting classifications of pathogenicity 2

  • p.Arg21Ter Single submitter arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Trp168Cys Single submitter arthrogryposis multiplex congenita ⚠

Benign 23

  • c.1299+221A>G Multiple submitters
  • c.1299+52T>C Multiple submitters
  • c.1300-134C>T Multiple submitters
  • c.1300-151G>C Multiple submitters
  • c.1300-53C>G Multiple submitters
  • c.170+97C>T Multiple submitters
  • c.242+47G>A Multiple submitters
  • c.314+49C>T Multiple submitters
  • c.459-33G>A Multiple submitters arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • c.*102G>A Multiple submitters
  • c.*10C>T Multiple submitters arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • c.*11G>A Multiple submitters arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • c.*81C>T Multiple submitters
  • p.Gln465= Multiple submitters arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Glu210= Multiple submitters
  • p.Gly394Ser Multiple submitters
  • p.His152= Multiple submitters arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Leu466= Multiple submitters arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Pro278= Multiple submitters arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Thr401= Multiple submitters arthrogryposis multiplex congenita 1, neurogenic, with myelin defect
  • p.Thr62Met Multiple submitters
  • p.Gly98= Single submitter
  • p.Ser471= Single submitter

Benign/Likely benign 1

Likely benign 25

Uncertain significance 85