Sugi Variant

Sugi Variant/GCM2

GCM2 — 300 ClinVar variants

All ClinVar germline GCM2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 147 flagged for review →

8 Pathogenic · 13 Likely pathogenic · 11 Conflicting · 27 Benign · 12 Benign/Likely benign · 54 Likely benign · 175 Uncertain significance

Full GCM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 147

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 6

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

Predictors lean, ClinVar uncertain 128

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

Predictors split 12

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

All GCM2 variants

Pathogenic 8

  • p.Arg47Leu Multiple submitters GCM2-related disorder
  • p.Tyr136Ter Multiple submitters hypoparathyroidism, familial isolated, 2
  • c.456+2dup Single submitter
  • p.Glu8Ter Single submitter familial hypoparathyroidism
  • p.Tyr368Ter Single submitter
  • p.His465fs No assertion criteria hypoparathyroidism, familial isolated, 2
  • p.Ile298fs No assertion criteria hypoparathyroidism, familial isolated, 2
  • p.Pro467fs No assertion criteria hypoparathyroidism, familial isolated, 2

Likely pathogenic 13

  • c.90+2T>G Multiple submitters familial hypoparathyroidism
  • p.Arg67Cys Multiple submitters hyperparathyroidism 4
  • p.Arg367fs Single submitter hypoparathyroidism, familial isolated, 2
  • p.Arg39Ter Single submitter
  • p.Arg406Ter Single submitter hypoparathyroidism, familial isolated, 2
  • p.Arg67Gly Single submitter hypoparathyroidism, familial isolated, 2
  • p.Arg67Ser Single submitter hypoparathyroidism, familial isolated, 2
  • p.Asn502Asp Single submitter ⚠
  • p.Cys366Ter Single submitter hypoparathyroidism, familial isolated, 2
  • p.Gln350Ter Single submitter hypoparathyroidism, familial isolated, 2
  • p.Ile383Thr Single submitter hyperparathyroidism 4 ⚠
  • p.Met1Val Single submitter hyperparathyroidism 4
  • p.Ser285fs Single submitter hypoparathyroidism, familial isolated, 2

Conflicting classifications of pathogenicity 11

  • c.344-7T>C Single submitter familial hypoparathyroidism
  • c.90+12G>C Single submitter familial hypoparathyroidism
  • c.91-7C>T Single submitter familial hypoparathyroidism
  • p.Arg47Cys Single submitter hyperparathyroidism 4 ⚠
  • p.Glu8Lys Single submitter hypoparathyroidism, familial isolated, 2 ⚠
  • p.Gly229= Single submitter familial hypoparathyroidism
  • p.Gly63Ser Single submitter hypoparathyroidism, familial isolated, 2 ⚠
  • p.His465= Single submitter familial hypoparathyroidism
  • p.Met448Val Single submitter hypoparathyroidism, familial isolated, 2 ⚠
  • p.Thr370Met Single submitter hyperparathyroidism 4 ⚠
  • p.Tyr394Ser Single submitter familial hypoparathyroidism ⚠

Benign 27

Benign/Likely benign 12

Likely benign 54

Uncertain significance 175