Sugi Variant

Sugi Variant/OTX2

OTX2 — 323 ClinVar variants

All ClinVar germline OTX2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 153 flagged for review →

40 Pathogenic · 4 Pathogenic/Likely pathogenic · 17 Likely pathogenic · 16 Conflicting · 5 Benign · 6 Benign/Likely benign · 63 Likely benign · 172 Uncertain significance

Full OTX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 153

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 8

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

Predictors lean, ClinVar uncertain 102

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

Predictors split 42

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

All OTX2 variants

Pathogenic 40

  • p.Arg44fs Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Arg76Ter Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ser135Leufs Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ala198fs Single submitter Anophthalmia
  • p.Ala225fs Single submitter syndromic microphthalmia type 5
  • p.Ala244fs Single submitter syndromic microphthalmia type 5
  • p.Arg97Ter Single submitter syndromic microphthalmia type 5
  • p.Asn233fs Single submitter Leber congenital amaurosis
  • p.Cys178Ter Single submitter
  • p.Gln106Ter Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gln189Ter Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gln219Ter Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gln241Ter Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gly196Ter Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gly199fs Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gly250fs Single submitter syndromic microphthalmia type 5
  • p.Ile159fs Single submitter OTX2-related disorder
  • p.Leu172fs Single submitter Anophthalmia-microphthalmia syndrome
  • p.Leu220fs Single submitter Anophthalmia-microphthalmia syndrome
  • p.Leu64fs Single submitter Anophthalmia-microphthalmia syndrome
  • p.Phe204fs Single submitter OTX2-related disorder
  • p.Thr149fs Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr261fs Single submitter syndromic microphthalmia type 5
  • p.Thr271fs Single submitter syndromic microphthalmia type 5
  • p.Thr51fs Single submitter Anophthalmia-microphthalmia syndrome
  • p.Trp160Ter Single submitter Anophthalmia-microphthalmia syndrome
  • p.Tyr183fs Single submitter Anophthalmia-microphthalmia syndrome
  • p.Tyr183Ter Single submitter Anophthalmia
  • p.Tyr187Ter Single submitter syndromic microphthalmia type 5
  • p.Ala56fs No assertion criteria OTX2-related disorder
  • p.Ala99Asp No assertion criteria Anophthalmia
  • p.Arg97Gly No assertion criteria syndromic microphthalmia type 5
  • p.Arg98Ser No assertion criteria syndromic microphthalmia type 5
  • p.Gln106fs No assertion criteria syndromic microphthalmia type 5
  • p.Lys82fs No assertion criteria syndromic microphthalmia type 5
  • p.Ser144fs No assertion criteria syndromic microphthalmia type 5
  • p.Ser146Ter No assertion criteria syndromic microphthalmia type 5
  • p.Ser164fs No assertion criteria syndromic microphthalmia type 5
  • p.Ser28fs No assertion criteria syndromic microphthalmia type 5
  • p.Tyr212fs No assertion criteria syndromic microphthalmia type 5

Pathogenic/Likely pathogenic 4

  • p.Glu87Lys Multiple submitters OTX2-related disorder
  • p.Lys122fs Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ser211Ter Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Tyr197Ter Multiple submitters OTX2-related disorder

Likely pathogenic 17

Conflicting classifications of pathogenicity 16

Benign 5

Benign/Likely benign 6

  • c.97+12C>T Multiple submitters pituitary hormone deficiency, combined, 6
  • c.97+20C>T Multiple submitters Anophthalmia-microphthalmia syndrome
  • c.*10G>A Multiple submitters syndromic microphthalmia type 5
  • p.Ala280= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Asn277= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ser153= Multiple submitters pituitary hormone deficiency, combined, 6

Likely benign 63

  • p.Ala253Thr Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ala56= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ile159= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Pro141= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Pro142= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Pro221= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ser124= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ser161= Multiple submitters Anophthalmia-microphthalmia syndrome
  • c.273+10A>T Single submitter Anophthalmia-microphthalmia syndrome
  • c.273+11T>A Single submitter Anophthalmia-microphthalmia syndrome
  • c.273+18A>T Single submitter
  • c.274-4C>T Single submitter Anophthalmia-microphthalmia syndrome
  • c.274-9C>T Single submitter
  • c.-119-238del Single submitter
  • c.*316G>A Single submitter pituitary hormone deficiency, combined, 6
  • c.*340del Single submitter
  • p.Ala119= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Ala151= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Ala155Val Single submitter
  • p.Ala190= Single submitter
  • p.Ala36Ser Single submitter Anophthalmia-microphthalmia syndrome
  • p.Ala99= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Arg117= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Arg181= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Arg55= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Arg69= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Arg76= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Asn279= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gln189= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gly137= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gly14= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gly199= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gly222= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Gly30= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Leu15= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Leu172= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Leu239= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Leu25= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Leu64= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Lys268= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Lys275= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Pro167= Single submitter
  • p.Pro27= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Pro86= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Ser161Ile Single submitter syndromic microphthalmia type 5
  • p.Ser175= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Ser291= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr123= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr19= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr248= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr271= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr289= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr42= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr54= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Thr68= Single submitter
  • p.Tyr183= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Tyr187= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Tyr193= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Tyr285= Single submitter
  • p.Val147= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Val60= Single submitter
  • p.Val90= Single submitter Anophthalmia-microphthalmia syndrome
  • p.Pro39= No assertion criteria OTX2-related disorder

Uncertain significance 172