Sugi Variant

Sugi Variant/CDH2

CDH2 — 1093 ClinVar variants

All ClinVar germline CDH2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 571 flagged for review →

8 Pathogenic · 5 Pathogenic/Likely pathogenic · 11 Likely pathogenic · 30 Conflicting · 36 Benign · 19 Benign/Likely benign · 382 Likely benign · 602 Uncertain significance

Full CDH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 571

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 4

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 3

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 323

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 323

Predictors split 227

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 227

All CDH2 variants

Pathogenic 8

  • p.Tyr676Cys Multiple submitters CDH2-related disorder
  • c.1159-1G>A Single submitter arrhythmogenic right ventricular dysplasia, familial, 14
  • c.1344+1G>C Single submitter
  • p.Cys613Trp Single submitter corpus callosum, agenesis of
  • p.Asn601Thr No assertion criteria Axon pathfinding, cardiac, ocular and genital defects
  • p.Asp597Tyr No assertion criteria agenesis of corpus callosum, cardiac, ocular, and genital syndrome
  • p.Gln229Pro No assertion criteria arrhythmogenic right ventricular dysplasia, familial, 14 ⚠
  • p.Val162Asp No assertion criteria agenesis of corpus callosum, cardiac, ocular, and genital syndrome

Pathogenic/Likely pathogenic 5

  • c.1344+1G>A Multiple submitters arrhythmogenic right ventricular dysplasia, familial, 14
  • c.702+1G>A Multiple submitters agenesis of corpus callosum, cardiac, ocular, and genital syndrome
  • p.Asp597Asn No assertion criteria agenesis of corpus callosum, cardiac, ocular, and genital syndrome
  • p.Asp627Gly No assertion criteria Syndromic neurodevelopmental disorder
  • p.Leu855fs No assertion criteria agenesis of corpus callosum, cardiac, ocular, and genital syndrome

Likely pathogenic 11

  • c.1344+5G>A Single submitter
  • c.172+2T>C Single submitter
  • c.702+2dup Single submitter agenesis of corpus callosum, cardiac, ocular, and genital syndrome
  • p.Ala602Gly Single submitter auditory neuropathy ⚠
  • p.Asn692Ser Single submitter arteriovenous malformations of the brain ⚠
  • p.Asp353Asn Single submitter corpus callosum, agenesis of
  • p.Asp441Tyr Single submitter ⚠
  • p.Asp627His Single submitter agenesis of corpus callosum, cardiac, ocular, and genital syndrome
  • p.His150Tyr Single submitter attention deficit-hyperactivity disorder 8 ⚠
  • p.Leu856fs Single submitter agenesis of corpus callosum, cardiac, ocular, and genital syndrome
  • p.Trp115Ter Single submitter

Conflicting classifications of pathogenicity 30

Benign 36

Benign/Likely benign 19

  • c.172+6A>C Multiple submitters
  • c.173-22589C>T Multiple submitters
  • c.702+6A>T Multiple submitters arrhythmogenic right ventricular dysplasia, familial, 14
  • c.848-4C>G Multiple submitters
  • p.Ala118Thr Multiple submitters
  • p.Ala21Thr Multiple submitters
  • p.Ala30= Multiple submitters Inborn genetic diseases
  • p.Ala368= Multiple submitters Inborn genetic diseases
  • p.Ala512= Multiple submitters Inborn genetic diseases
  • p.Arg173= Multiple submitters Inborn genetic diseases
  • p.Arg232= Multiple submitters Inborn genetic diseases
  • p.Asn845Ser Multiple submitters
  • p.Asp295= Multiple submitters arrhythmogenic right ventricular dysplasia, familial, 14
  • p.Cys63= Multiple submitters Inborn genetic diseases
  • p.Ile450= Multiple submitters Inborn genetic diseases
  • p.Lys47= Multiple submitters Inborn genetic diseases
  • p.Pro469= Multiple submitters Inborn genetic diseases
  • p.Ser92= Multiple submitters Inborn genetic diseases
  • p.Thr371= Multiple submitters Inborn genetic diseases

Likely benign 382

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

Uncertain significance 602

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