Sugi Variant

Sugi Variant/L1CAM

L1CAM — 1446 ClinVar variants

All ClinVar germline L1CAM variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 382 flagged for review →

111 Pathogenic · 21 Pathogenic/Likely pathogenic · 78 Likely pathogenic · 107 Conflicting · 172 Benign · 82 Benign/Likely benign · 522 Likely benign · 353 Uncertain significance

Full L1CAM gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 382

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 58

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 225

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 225

Predictors split 96

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

All L1CAM variants

Pathogenic 111

Pathogenic/Likely pathogenic 21

  • c.1267+1G>A Multiple submitters L1CAM-related disorders
  • c.1704-1G>A Multiple submitters L1CAM-related disorders
  • c.2431+5G>A Multiple submitters Spastic paraplegia
  • c.3531-12G>A Multiple submitters Spastic paraplegia
  • c.400+5G>A Multiple submitters Spastic paraplegia
  • c.523+12C>T Multiple submitters L1 syndrome
  • c.807-6G>A Multiple submitters Spastic paraplegia
  • c.92-1G>A Multiple submitters Spastic paraplegia
  • p.Ala510fs Multiple submitters L1CAM-related disorder
  • p.Arg473Cys Multiple submitters L1 syndrome
  • p.Gln794Ter Multiple submitters L1 syndrome
  • p.Glu309Lys Multiple submitters Spastic paraplegia
  • p.Gly308= Multiple submitters L1CAM-related disorder
  • p.Ile866fs Multiple submitters X-linked hydrocephalus with stenosis of the aqueduct of Sylvius
  • p.Pro240Leu Multiple submitters L1CAM-related disorder
  • p.Pro333Arg Multiple submitters Spastic paraplegia
  • p.Pro333Leu Multiple submitters L1CAM-related disorders
  • p.Ser1018Ter Multiple submitters L1CAM-related disorders
  • p.Ser1194Leu Multiple submitters hydrops fetalis ⚠
  • p.Ser1224Leu Multiple submitters Inborn genetic diseases
  • p.Tyr811Ter Multiple submitters X-linked hydrocephalus with stenosis of the aqueduct of Sylvius

Likely pathogenic 78

Conflicting classifications of pathogenicity 107

Benign 172

Benign/Likely benign 82

Likely benign 522

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

Uncertain significance 353

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