Sugi Variant

Sugi Variant/SHANK2

SHANK2 — 518 ClinVar variants

All ClinVar germline SHANK2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 94 flagged for review →

21 Pathogenic · 3 Pathogenic/Likely pathogenic · 24 Likely pathogenic · 24 Conflicting · 15 Benign · 9 Benign/Likely benign · 184 Likely benign · 238 Uncertain significance

Full SHANK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 94

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 6

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 5

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 72

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

Predictors split 10

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

All SHANK2 variants

Pathogenic 21

Pathogenic/Likely pathogenic 3

  • c.2439+1G>A Multiple submitters autism, susceptibility to, 17
  • p.Leu1726fs Multiple submitters Inborn genetic diseases
  • p.Leu201fs Multiple submitters neurodevelopmental disorder

Likely pathogenic 24

Conflicting classifications of pathogenicity 24

Benign 15

Benign/Likely benign 9

Likely benign 184

Uncertain significance 238