Sugi Variant

Sugi Variant/NEK9

NEK9 — 212 ClinVar variants

All ClinVar germline NEK9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 118 flagged for review →

10 Pathogenic · 12 Likely pathogenic · 3 Conflicting · 32 Benign · 2 Benign/Likely benign · 24 Likely benign · 129 Uncertain significance

Full NEK9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 118

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 lean, ClinVar uncertain 97

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

Predictors split 20

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

All NEK9 variants

Pathogenic 10

Likely pathogenic 12

Conflicting classifications of pathogenicity 3

  • c.1840+2T>C Single submitter NEK9-related lethal skeletal dysplasia
  • c.762+10C>T Single submitter arthrogryposis, Perthes disease, and upward gaze palsy
  • p.Thr744= Single submitter arthrogryposis, Perthes disease, and upward gaze palsy

Benign 32

Benign/Likely benign 2

Likely benign 24

Uncertain significance 129