Sugi Variant

Sugi Variant/GALNT3

GALNT3 — 525 ClinVar variants

All ClinVar germline GALNT3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 176 flagged for review →

39 Pathogenic · 7 Pathogenic/Likely pathogenic · 21 Likely pathogenic · 16 Conflicting · 25 Benign · 7 Benign/Likely benign · 209 Likely benign · 201 Uncertain significance

Full GALNT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 176

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 agree, ClinVar conflicts 7

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

Predictors lean, ClinVar uncertain 132

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

Predictors split 37

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

All GALNT3 variants

Pathogenic 39

Pathogenic/Likely pathogenic 7

  • c.516-2A>G Multiple submitters GALNT3-related disorder
  • p.Arg87fs Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Gln566Ter Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Gly329Arg Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Ser50Ter Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Thr269fs Multiple submitters GALNT3-related disorder
  • p.Tyr298fs Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1

Likely pathogenic 21

Conflicting classifications of pathogenicity 16

  • c.1392+7T>G Single submitter
  • c.838+10T>C Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1
  • c.839-11G>T Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Ala127Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala197= Single submitter
  • p.Arg162Gln Single submitter GALNT3-related disorder ⚠
  • p.Arg169= Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Arg6Ter Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Asp277Glu Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1 ⚠
  • p.His17= Single submitter
  • p.Ile306= Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Leu624Phe Single submitter Inborn genetic diseases ⚠
  • p.Lys448Glu Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1 ⚠
  • p.Thr200= Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Val240Leu Single submitter Inborn genetic diseases ⚠
  • p.Val301Ile Single submitter tumoral calcinosis, hyperphosphatemic, familial, 1 ⚠

Benign 25

Benign/Likely benign 7

  • c.839-16A>C Multiple submitters
  • c.*186C>T Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Asn609= Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Gln44= Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Thr168= Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Thr299= Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1
  • p.Val223= Multiple submitters tumoral calcinosis, hyperphosphatemic, familial, 1

Likely benign 209

Uncertain significance 201