Sugi Variant

Sugi Variant/VPS53

VPS53 — 597 ClinVar variants

All ClinVar germline VPS53 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 106 flagged for review →

2 Pathogenic · 1 Pathogenic/Likely pathogenic · 13 Likely pathogenic · 5 Conflicting · 67 Benign · 7 Benign/Likely benign · 381 Likely benign · 121 Uncertain significance

Full VPS53 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 106

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 3

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors lean, ClinVar uncertain 77

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

Predictors split 26

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

All VPS53 variants

Pathogenic 2

  • p.Gln695Arg Multiple submitters pontocerebellar hypoplasia type 2E
  • p.Arg168Gln Single submitter pontocerebellar hypoplasia type 2A ⚠

Pathogenic/Likely pathogenic 1

  • c.1556+5G>A Multiple submitters pontocerebellar hypoplasia

Likely pathogenic 13

  • p.Gln101fs Multiple submitters pontocerebellar hypoplasia type 2E
  • c.168+2T>G Single submitter pontocerebellar hypoplasia type 2E
  • c.609-1G>T Single submitter pontocerebellar hypoplasia type 2E
  • c.687+1G>A Single submitter pontocerebellar hypoplasia type 2E
  • c.88-2A>G Single submitter
  • p.Arg80Ter Single submitter pontocerebellar hypoplasia type 2E
  • p.Glu267fs Single submitter pontocerebellar hypoplasia type 2E
  • p.Glu46Gly Single submitter ⚠
  • p.Ser658fs Single submitter pontocerebellar hypoplasia type 2E
  • p.Thr639fs Single submitter pontocerebellar hypoplasia type 2E
  • p.Trp280Ter Single submitter pontocerebellar hypoplasia type 2E
  • p.Arg506Ter No assertion criteria pontocerebellar hypoplasia type 2E
  • p.Pro231Leu No assertion criteria pontocerebellar hypoplasia type 2E ⚠

Conflicting classifications of pathogenicity 5

Benign 67

Benign/Likely benign 7

Likely benign 381

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

Uncertain significance 121