Sugi Variant

Sugi Variant/FOXC1

FOXC1 — 781 ClinVar variants

All ClinVar germline FOXC1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 343 flagged for review →

90 Pathogenic · 15 Pathogenic/Likely pathogenic · 48 Likely pathogenic · 35 Conflicting · 16 Benign · 15 Benign/Likely benign · 136 Likely benign · 426 Uncertain significance

Full FOXC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 343

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 14

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

Predictors lean, ClinVar uncertain 234

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 234

Predictors split 94

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

All FOXC1 variants

Pathogenic 90

Pathogenic/Likely pathogenic 15

  • p.Ala251fs Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ala28fs Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Arg127Leu Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Glu258Ter Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ile223fs Multiple submitters hypertelorism and tetralogy of fallot
  • p.Leu168fs Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Leu348fs Multiple submitters Axenfeld-Rieger anomaly with partially absent eye muscles, distinctive face, hydrocephaly, and skeletal abnormalities
  • p.Leu433fs Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Pro274fs Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ser131Leu Multiple submitters FOXC1-related disorders
  • p.Ser276fs Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ser82Thr Multiple submitters FOXC1-related disorders
  • p.Trp122Ter Multiple submitters FOXC1-related anterior segment dysgenesis
  • p.Tyr393Ter Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Tyr47Ter Multiple submitters Axenfeld-Rieger syndrome type 3

Likely pathogenic 48

  • p.Cys135Tyr Multiple submitters FOXC1-related disorder
  • p.Cys365fs Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ala342fs Single submitter FOXC1-related disorder
  • p.Ala419fs Single submitter FOXC1-related disorders
  • p.Ala85Val Single submitter
  • p.Arg169Trp Single submitter FOXC1-related disorders
  • p.Arg173dup Single submitter Axenfeld-Rieger syndrome type 3
  • p.Arg4fs Single submitter FOXC1-related disorders
  • p.Asn164fs Single submitter FOXC1-related disorders
  • p.Asp157Val Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gln2Ter Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gln367Ter Single submitter
  • p.Gly121Ser Single submitter Axenfeld-Rieger syndrome type 3 ⚠
  • p.Gly270fs Single submitter FOXC1-related disorders
  • p.Gly35fs Single submitter FOXC1-related disorder
  • p.Gly386fs Single submitter anterior segment dysgenesis 3
  • p.Gly410fs Single submitter
  • p.Gly59fs Single submitter Axenfeld-Rieger syndrome type 3
  • p.His128Gln Single submitter Axenfeld-Rieger syndrome type 3
  • p.Leu332fs Single submitter
  • p.Leu86Pro Single submitter FOXC1-related disorders
  • p.Lys98del Single submitter
  • p.Met1Val Single submitter FOXC1-related disorders
  • p.Phe136fs Single submitter
  • p.Phe136Ser Single submitter Axenfeld-Rieger syndrome type 3
  • p.Phe162Val Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro197fs Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro57fs Single submitter
  • p.Ser265fs Single submitter FOXC1-related disorders
  • p.Ser269fs Single submitter FOXC1-related disorders
  • p.Ser373fs Single submitter Axenfeld-Rieger syndrome type 3
  • p.Thr153fs Single submitter anterior segment dysgenesis 3
  • p.Thr368fs Single submitter
  • p.Trp152Arg Single submitter anterior segment dysgenesis 3
  • p.Trp152Cys Single submitter Axenfeld-Rieger syndrome type 3
  • p.Trp152Gly Single submitter
  • p.Tyr105Ter Single submitter Axenfeld-Rieger syndrome type 3
  • p.Tyr18Ter Single submitter
  • p.Tyr56fs Single submitter FOXC1-related disorders
  • p.Tyr5Ter Single submitter Axenfeld-Rieger syndrome type 3
  • p.Tyr81_Pro95del Single submitter Axenfeld-Rieger syndrome type 3
  • p.Tyr83His Single submitter FOXC1-related anterior segment dysgenesis
  • p.70QP[3] No assertion criteria congenital anomaly of kidney and urinary tract
  • p.Arg127Ser No assertion criteria FOXC1-related disorder
  • p.Arg173His No assertion criteria anterior segment dysgenesis
  • p.Gly380Val No assertion criteria congenital anomaly of kidney and urinary tract ⚠
  • p.Gly59Val No assertion criteria congenital anomaly of kidney and urinary tract
  • p.Ser298fs No assertion criteria FOXC1-related disorder

Conflicting classifications of pathogenicity 35

Benign 16

Benign/Likely benign 15

  • c.-418_-417del Multiple submitters
  • p.Ala213= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ala31_Ala33del Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ala493_Ala495del Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Arg141= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Cys550= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gln72= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gly307= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gly455_Gly456del Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gly456del Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Leu168= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Leu191= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Leu485= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Pro69= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ser445Arg Multiple submitters Axenfeld-Rieger syndrome type 3 ⚠

Likely benign 136

  • c.-244C>T Multiple submitters anterior segment dysgenesis 3
  • c.*576A>C Multiple submitters
  • p.Ala3= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ala415= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ala495del Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Arg281= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Asn129= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Asp117= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Asp481= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gly391= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gly453= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gly454_Gly456del Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gly455_Gly456dup Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Gly525= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.His484= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ile344= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Leu240= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Leu397= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Pro236= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Pro282= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ser125= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ser262= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ser358= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Ser8= Multiple submitters
  • p.Thr38= Multiple submitters Axenfeld-Rieger syndrome type 3
  • p.Tyr353= Multiple submitters Axenfeld-Rieger syndrome type 3
  • c.-419C>A Single submitter
  • c.-421C>G Single submitter
  • c.-422C>T Single submitter
  • c.-431G>C Single submitter
  • c.-433C>G Single submitter
  • c.-434_-433insGGGGGGGGGG Single submitter
  • c.*547G>A Single submitter
  • p.Ala243Ser Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala244= Single submitter
  • p.Ala245= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala251= Single submitter
  • p.Ala252= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala288= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala291= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala296= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala30= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala325= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala371= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala384= Single submitter
  • p.Ala390= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala419= Single submitter
  • p.Ala486= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ala53= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Arg188= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Asn124= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Asn312= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Asn396= Single submitter
  • p.Asn503= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Asp178= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Asp261= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Asp426= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Asp75= Single submitter
  • p.Cys365= Single submitter
  • p.Gln120= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gln477His Single submitter Axenfeld-Rieger syndrome type 3
  • p.Glu184= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Glu54= Single submitter
  • p.Gly103= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly147= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly231= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly331= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly343= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly35= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly379= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly386= Single submitter
  • p.Gly406= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly410= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly420= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly454= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly454_Gly456dup Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly460= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Gly65= Single submitter Axenfeld-Rieger syndrome type 3
  • p.His190= Single submitter Axenfeld-Rieger syndrome type 3
  • p.His462= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ile126= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ile84= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ile87= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Leu189= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Leu246= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Leu350= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Leu428= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Leu433= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Lys144= Single submitter
  • p.Lys148= Single submitter
  • p.Lys181= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Lys98= Single submitter
  • p.Phe114= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Phe546= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro156= Single submitter
  • p.Pro197= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro202= Single submitter
  • p.Pro220= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro273= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro297= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro302= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro346= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Pro66= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser166= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser235= Single submitter
  • p.Ser268= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser269= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser305= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser339= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser340= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser359= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser363= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser442= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser443= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser48= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser506= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser543= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser551Gly Single submitter
  • p.Ser6= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser82= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Ser9= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Thr100= Single submitter
  • p.Thr228= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Thr542= Single submitter
  • p.Thr88= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Tyr151= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Tyr151Phe Single submitter anterior segment dysgenesis 3 ⚠
  • p.Tyr64= Single submitter Axenfeld-Rieger syndrome type 3
  • p.Tyr67_Pro71del Single submitter anterior segment dysgenesis 3
  • p.Val310= Single submitter Axenfeld-Rieger syndrome type 3
  • c.-435C>G No assertion criteria FOXC1-related disorder
  • c.-437C>G No assertion criteria FOXC1-related disorder
  • p.Ala381_Gly385del No assertion criteria FOXC1-related disorder
  • p.Gly287= No assertion criteria FOXC1-related disorder
  • p.Gly380= No assertion criteria FOXC1-related disorder
  • p.Phe533= No assertion criteria FOXC1-related disorder

Uncertain significance 426

Showing the top 300 by review status; the full set is in the sitemap.