Sugi Variant

Sugi Variant/CSGALNACT1

CSGALNACT1 — 364 ClinVar variants

All ClinVar germline CSGALNACT1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 191 flagged for review →

11 Pathogenic · 5 Likely pathogenic · 5 Conflicting · 30 Benign · 5 Benign/Likely benign · 121 Likely benign · 187 Uncertain significance

Full CSGALNACT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 191

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 3

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 120

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

Predictors split 67

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

All CSGALNACT1 variants

Pathogenic 11

Likely pathogenic 5

  • p.Asn264Ser Multiple submitters skeletal dysplasia, mild, with joint laxity and advanced bone age ⚠
  • c.1228-6_1230del Single submitter
  • p.Asp432Tyr Single submitter skeletal dysplasia, mild, with joint laxity and advanced bone age
  • p.Gln290Ter Single submitter skeletal dysplasia, mild, with joint laxity and advanced bone age
  • p.Glu211del Single submitter skeletal dysplasia, mild, with joint laxity and advanced bone age

Conflicting classifications of pathogenicity 5

Benign 30

Benign/Likely benign 5

  • p.Arg521Pro Multiple submitters ⚠
  • p.Phe473Tyr Multiple submitters skeletal dysplasia, mild, with joint laxity and advanced bone age ⚠
  • p.Thr261= Multiple submitters skeletal dysplasia, mild, with joint laxity and advanced bone age
  • p.Val133Met Multiple submitters skeletal dysplasia, mild, with joint laxity and advanced bone age
  • p.Val137Ile Multiple submitters skeletal dysplasia, mild, with joint laxity and advanced bone age

Likely benign 121

Uncertain significance 187