SIX3 — 268 ClinVar variants

All ClinVar germline SIX3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 122 flagged for review →

20 Pathogenic · 12 Likely pathogenic · 15 Conflicting · 10 Benign · 10 Benign/Likely benign · 58 Likely benign · 143 Uncertain significance

Full SIX3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 122

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 3

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

Predicted LoF vs a conflicting call 2

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 85

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

Predictors split 32

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

All SIX3 variants

Pathogenic 20

Likely pathogenic 12

Conflicting classifications of pathogenicity 15

Benign 10

Benign/Likely benign 10

  • c.807-7C>T Multiple submitters holoprosencephaly 2
  • p.Ala240= Multiple submitters holoprosencephaly 2
  • p.Gln175= Multiple submitters holoprosencephaly 2
  • p.Gly37Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Pro116= Multiple submitters holoprosencephaly 2
  • p.Pro303= Multiple submitters holoprosencephaly 2
  • p.Pro73= Multiple submitters holoprosencephaly 2
  • p.Thr102= Multiple submitters holoprosencephaly 2
  • p.Thr98= Multiple submitters holoprosencephaly 2
  • p.Val117= Multiple submitters holoprosencephaly 2

Likely benign 58

Uncertain significance 143