SMC3 — 802 ClinVar variants

All ClinVar germline SMC3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 241 flagged for review →

28 Pathogenic · 3 Pathogenic/Likely pathogenic · 53 Likely pathogenic · 40 Conflicting · 87 Benign · 15 Benign/Likely benign · 281 Likely benign · 295 Uncertain significance

Full SMC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 241

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 14

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 150

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

Predictors split 75

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

All SMC3 variants

Pathogenic 28

Pathogenic/Likely pathogenic 3

  • p.Ala485del Multiple submitters Cornelia de Lange syndrome 3
  • p.Ile196Thr Multiple submitters Cornelia de Lange syndrome 3
  • p.Met648Val Multiple submitters Cornelia de Lange syndrome 3

Likely pathogenic 53

Conflicting classifications of pathogenicity 40

Benign 87

Benign/Likely benign 15

  • c.1092-8T>G Multiple submitters Cornelia de Lange syndrome 3
  • c.1671-4T>C Multiple submitters Inborn genetic diseases
  • c.1671-6A>G Multiple submitters Cornelia de Lange syndrome 3
  • c.2644+6T>A Multiple submitters Cornelia de Lange syndrome 3
  • c.270+18dup Multiple submitters Cornelia de Lange syndrome 3
  • c.2893-17A>G Multiple submitters Cornelia de Lange syndrome 3
  • c.3298-3dup Multiple submitters Cornelia de Lange syndrome 3
  • c.548-5_548-4dup Multiple submitters Inborn genetic diseases
  • c.92-19A>G Multiple submitters Cornelia de Lange syndrome 3
  • c.-99C>A Multiple submitters Cornelia de Lange syndrome 3
  • p.Ala1165= Multiple submitters Inborn genetic diseases
  • p.Asp92= Multiple submitters Cornelia de Lange syndrome 3
  • p.Gln1113= Multiple submitters Inborn genetic diseases
  • p.Leu962= Multiple submitters Cornelia de Lange syndrome 3
  • p.Tyr669= Multiple submitters Inborn genetic diseases

Likely benign 281

Uncertain significance 295