Sugi Variant

Sugi Variant/MSX2

MSX2 — 253 ClinVar variants

All ClinVar germline MSX2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 96 flagged for review →

8 Pathogenic · 1 Pathogenic/Likely pathogenic · 5 Likely pathogenic · 4 Conflicting · 35 Benign · 8 Benign/Likely benign · 58 Likely benign · 134 Uncertain significance

Full MSX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 96

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 2

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

Predictors lean, ClinVar uncertain 78

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

Predictors split 16

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

All MSX2 variants

Pathogenic 8

Pathogenic/Likely pathogenic 1

  • p.Gln153Ter Multiple submitters Cranium bifidum occultum

Likely pathogenic 5

Conflicting classifications of pathogenicity 4

Benign 35

Benign/Likely benign 8

  • c.-17C>G Multiple submitters parietal foramina 1
  • p.Gly17Ser Multiple submitters Cranium bifidum occultum
  • p.Pro241= Multiple submitters Cranium bifidum occultum
  • p.Pro4= Multiple submitters Cranium bifidum occultum
  • p.Val252= Multiple submitters Cranium bifidum occultum
  • c.-42C>T Single submitter parietal foramina 1
  • c.*1206T>C Single submitter parietal foramina 1
  • p.Lys105Asn Single submitter parietal foramina 1 ⚠

Likely benign 58

Uncertain significance 134