FOXL2 — 300 ClinVar variants

All ClinVar germline FOXL2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 93 flagged for review →

108 Pathogenic · 6 Pathogenic/Likely pathogenic · 48 Likely pathogenic · 3 Conflicting · 12 Benign · 4 Benign/Likely benign · 23 Likely benign · 96 Uncertain significance

Full FOXL2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 93

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 lean, ClinVar uncertain 76

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

All FOXL2 variants

Pathogenic 108

  • p.Ala225_Ala234dup Multiple submitters FOXL2-related disorders
  • p.Ala234_Gly235insAlaAlaAlaAlaAlaAlaAlaAlaAlaAla Multiple submitters FOXL2-related disorders
  • p.Gln196Ter Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Gln219Ter Multiple submitters FOXL2-related disorders
  • p.Gly269fs Multiple submitters FOXL2-related disorders
  • p.Leu75Phe Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro317fs Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Trp204Ter Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala179fs Single submitter Inborn genetic diseases
  • p.Ala183fs Single submitter
  • p.Ala221fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala225_Leu376delinsTrpAlaGlyAspAlaGlyAlaProGluArgAspGluProSerArgLysArgAlaGluArgGlnLeuGlnAlaArgGlyValGlnGlyHisArgGlyGlnGlyGlyGluHisArgArgThr Single submitter
  • p.Ala225fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala227fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala229fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala234delinsGluArgLeuGlnGlnLeuArgLeuGlnProPro Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala283fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala304fs Single submitter
  • p.Ala328fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala66Glu Single submitter
  • p.Arg117fs Single submitter
  • p.Arg260fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Asn126_Gly235del Single submitter
  • p.Cys218fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Gln321fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Gln53Ter Single submitter
  • p.Gln99Ter Single submitter
  • p.Glu139Ter Single submitter
  • p.Glu69Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Gly171fs Single submitter
  • p.Gly250fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.His104Asn Single submitter
  • p.His159fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.His298fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.His311fs Single submitter Inborn genetic diseases
  • p.His312fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ile113fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ile84fs Single submitter
  • p.Ile84Thr Single submitter
  • p.Leu15fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Leu277fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Lys114Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Lys124fs Single submitter
  • p.Lys193fs Single submitter
  • p.Lys93Ter Single submitter
  • p.Lys95_Lys96delinsAsnTer Single submitter
  • p.Lys95Ter Single submitter
  • p.Phe345fs Single submitter
  • p.Phe90Ser Single submitter
  • p.Pro157fs Single submitter
  • p.Pro18fs Single submitter FOXL2-related disorders
  • p.Pro207fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro251fs Single submitter
  • p.Pro257fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro284fs Single submitter
  • p.Pro285fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro286fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro294fs Single submitter
  • p.Pro305fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro307fs Single submitter FOXL2-related disorders
  • p.Pro309fs Single submitter blepharophimosis
  • p.Pro46fs Single submitter
  • p.Pro51fs Single submitter
  • p.Pro89fs Single submitter
  • p.Ser203Ter Single submitter
  • p.Ser211Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ser217Cys Single submitter FOXL2-related disorders
  • p.Ser254Ter Single submitter
  • p.Ser365fs Single submitter
  • p.Ser58Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Thr338fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Trp98Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr194Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr274Ter Single submitter premature ovarian failure 3
  • p.Tyr57Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr59Ter Single submitter
  • p.Tyr5Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr83Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr91Ter Single submitter
  • p.Ala221[(15_24 No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala224fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala234_Gly235insAlaAlaAlaAlaAla No assertion criteria BLEPHAROPHIMOSIS, PTOSIS, AND EPICANTHUS INVERSUS, TYPE I
  • p.Ala316fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala330fs No assertion criteria premature ovarian failure 3
  • p.Ala334fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Asp184fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Cys134fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Cys176fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Gln262Ter No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Glu19Ter No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Glu69Lys No assertion criteria BLEPHAROPHIMOSIS, PTOSIS, AND EPICANTHUS INVERSUS, TYPE II
  • p.Glu7fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Gly35fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Gly368fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.His291fs No assertion criteria Genetic non-acquired premature ovarian failure
  • p.Ile84Ser No assertion criteria FOXL2-related disorder
  • p.Leu130fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Lys164Ter No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Lys48_Ser58delinsAlaLeu No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Lys54Glu No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro156fs No assertion criteria premature ovarian failure 3
  • p.Pro281fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Thr329fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Trp128Ter No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr127_Trp128insTer No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr127Ter No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr258fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr59fs No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome

Pathogenic/Likely pathogenic 6

  • p.Asp131fs Multiple submitters FOXL2-related disorders
  • p.Met65Val Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro287fs Multiple submitters FOXL2-related disorders
  • p.Ser217Phe Multiple submitters FOXL2-related disorders
  • p.Thr259fs Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr215Cys Multiple submitters FOXL2-related disorder ⚠

Likely pathogenic 48

  • p.Arg349Gly Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome ⚠
  • p.Met65Ile Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ser107Gly Multiple submitters blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala14fs Single submitter
  • p.Ala225_Ala234del Single submitter premature ovarian failure 3
  • p.Ala234_Gly235insAlaAlaAlaAlaAlaAlaAlaAlaAlaAlaAla Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ala315fs Single submitter
  • p.Ala66fs Single submitter FOXL2-related disorders
  • p.Arg154fs Single submitter
  • p.Asn275fs Single submitter
  • p.Gln208Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Glu118_Arg123del Single submitter
  • p.Glu72Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.His104Arg Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.His104Tyr Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ile63Leu Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Leu106Phe Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Leu77Pro Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Lys114Glu Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Lys124Glu Single submitter
  • p.Met149_Lys150delinsIleTer Single submitter FOXL2-related disorders
  • p.Phe112Cys Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Phe199fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Phe90Leu Single submitter
  • p.Pro281Thr Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome ⚠
  • p.Pro292fs Single submitter FOXL2-related disorders
  • p.Pro310fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro318fs Single submitter
  • p.Pro341fs Single submitter
  • p.Ser101Arg Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ser273Ter Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ser4fs Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ser58Leu Single submitter FOXL2-related disorders
  • p.Trp128Gly Single submitter FOXL2-related disorders
  • p.Trp98Arg Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr186fs Single submitter
  • p.Val60_Ala64dup Single submitter FOXL2-related disorders
  • p.Asn100Asp No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Gly185Arg No assertion criteria Genetic non-acquired premature ovarian failure ⚠
  • p.Ile113del No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ile63Asn No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Phe88Ile No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro89Arg No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Pro89Gln No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Ser263Arg No assertion criteria Genetic non-acquired premature ovarian failure ⚠
  • p.Ser58Trp No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr57Asn No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome
  • p.Tyr59Asp No assertion criteria blepharophimosis, ptosis, and epicanthus inversus syndrome

Conflicting classifications of pathogenicity 3

  • p.Ala234del Single submitter premature ovarian failure 3
  • p.Gly187Asp Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome ⚠
  • p.Tyr258Asn Single submitter blepharophimosis, ptosis, and epicanthus inversus syndrome ⚠

Benign 12

Benign/Likely benign 4

Likely benign 23

Uncertain significance 96