Sugi Variant

Sugi Variant/CNOT2

CNOT2 — 69 ClinVar variants

All ClinVar germline CNOT2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 50 flagged for review →

3 Pathogenic · 4 Likely pathogenic · 1 Conflicting · 9 Likely benign · 52 Uncertain significance

Full CNOT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 50

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, 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 35

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

Predictors split 14

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

All CNOT2 variants

Pathogenic 3

  • p.Leu68fs Single submitter
  • p.Ser228Ter Single submitter Inborn genetic diseases
  • p.Lys316Ter No assertion criteria intellectual developmental disorder with nasal speech, dysmorphic facies, and variable skeletal anomalies

Likely pathogenic 4

  • c.49-2A>G Single submitter ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder
  • p.Gln457fs Single submitter intellectual developmental disorder with nasal speech, dysmorphic facies, and variable skeletal anomalies
  • p.His526fs Single submitter intellectual developmental disorder with nasal speech, dysmorphic facies, and variable skeletal anomalies
  • p.Ter541LeuextTer? Single submitter neurodevelopmental disorder

Conflicting classifications of pathogenicity 1

Likely benign 9

Uncertain significance 52