Sugi Variant

Sugi Variant/VPS16

VPS16 — 283 ClinVar variants

All ClinVar germline VPS16 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 181 flagged for review →

12 Pathogenic · 2 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 4 Conflicting · 16 Benign · 29 Likely benign · 211 Uncertain significance

Full VPS16 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 181

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 1

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 139

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

Predictors split 39

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

All VPS16 variants

Pathogenic 12

Pathogenic/Likely pathogenic 2

Likely pathogenic 9

Conflicting classifications of pathogenicity 4

Benign 16

Likely benign 29

Uncertain significance 211