Sugi Variant

Sugi Variant/HOXA2

HOXA2 — 107 ClinVar variants

All ClinVar germline HOXA2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 57 flagged for review →

5 Pathogenic · 3 Likely pathogenic · 2 Conflicting · 3 Benign · 12 Likely benign · 82 Uncertain significance

Full HOXA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 57

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 45

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

Predictors split 10

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

All HOXA2 variants

Pathogenic 5

  • p.Gln186Lys No assertion criteria bilateral microtia-deafness-cleft palate syndrome
  • p.Gln235Ter No assertion criteria MICROTIA WITH OR WITHOUT HEARING IMPAIRMENT
  • p.Glu224Ter No assertion criteria MICROTIA WITHOUT HEARING IMPAIRMENT
  • p.Glu229fs No assertion criteria HOXA2-related disorder
  • p.Gly79fs No assertion criteria bilateral microtia-deafness-cleft palate syndrome

Likely pathogenic 3

  • p.Pro84fs Single submitter hearing loss disorder
  • p.Ser271fs Single submitter Monogenic hearing loss
  • p.Gln91Ter No assertion criteria HOXA2-related disorder

Conflicting classifications of pathogenicity 2

  • p.Thr118Ala Single submitter Inborn genetic diseases ⚠
  • p.Val327Ile Single submitter bilateral microtia-deafness-cleft palate syndrome ⚠

Benign 3

Likely benign 12

Uncertain significance 82