Sugi Variant

Sugi Variant/PITX2

PITX2 — 268 ClinVar variants

All ClinVar germline PITX2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 54 flagged for review →

50 Pathogenic · 8 Pathogenic/Likely pathogenic · 20 Likely pathogenic · 15 Conflicting · 23 Benign · 13 Benign/Likely benign · 39 Likely benign · 100 Uncertain significance

Full PITX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 54

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 4

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

Predictors lean, ClinVar uncertain 31

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

Predictors split 19

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

All PITX2 variants

Pathogenic 50

  • c.411+1G>A Multiple submitters Axenfeld-Rieger syndrome type 1
  • c.412-11A>G Multiple submitters anterior segment dysgenesis 4
  • p.Arg122His Multiple submitters PITX2-related disorder
  • p.Arg150fs Multiple submitters Axenfeld-Rieger syndrome type 1
  • p.Gln172fs Multiple submitters anterior segment dysgenesis 4
  • c.206-1G>A Single submitter
  • c.411+2T>G Single submitter Axenfeld-Rieger syndrome type 1
  • c.412-1G>A Single submitter Axenfeld-Rieger syndrome type 1
  • p.Ala126Pro Single submitter Axenfeld-Rieger syndrome type 1
  • p.Ala272fs Single submitter
  • p.Arg143Pro Single submitter Axenfeld-Rieger syndrome type 1
  • p.Asn168fs Single submitter Axenfeld-Rieger syndrome type 1
  • p.Asn222fs Single submitter Axenfeld-Rieger syndrome type 1
  • p.Asp175fs Single submitter Axenfeld-Rieger syndrome type 1
  • p.Cys159Ter Single submitter Axenfeld-Rieger syndrome type 1
  • p.Gln103Ter Single submitter Rieger anomaly
  • p.Gln74Ter Single submitter Axenfeld-Rieger syndrome type 1
  • p.Glu106Ter Single submitter Axenfeld-Rieger syndrome type 1
  • p.Glu84Ter Single submitter anterior segment dysgenesis 4
  • p.His98fs Single submitter Axenfeld-Rieger syndrome type 1
  • p.Ile125fs Single submitter Axenfeld-Rieger syndrome type 1
  • p.Leu212fs Single submitter
  • p.Lys89fs Single submitter anterior segment dysgenesis 4
  • p.Pro117Arg Single submitter Axenfeld-Rieger syndrome type 1
  • p.Pro117fs Single submitter Axenfeld-Rieger syndrome
  • p.Pro202fs Single submitter anterior segment dysgenesis 4
  • p.Pro265fs Single submitter Axenfeld-Rieger syndrome type 1
  • p.Pro86fs Single submitter anterior segment dysgenesis 4
  • p.Ser101fs Single submitter Axenfeld-Rieger syndrome type 1
  • p.Ser290fs Single submitter Axenfeld-Rieger syndrome type 1
  • p.Thr239_Gly240insCysProGlnGlnTer Single submitter Axenfeld-Rieger syndrome type 1
  • p.Trp128Ter Single submitter Axenfeld-Rieger syndrome type 1
  • p.Trp139Cys Single submitter Axenfeld-Rieger syndrome type 1
  • p.Trp186Ter Single submitter Axenfeld-Rieger syndrome type 1
  • p.Tyr174_Asp175delinsTer Single submitter Axenfeld-Rieger syndrome type 1
  • p.Tyr178Ter Single submitter Axenfeld-Rieger syndrome type 1
  • p.Val264fs Single submitter Axenfeld-Rieger syndrome type 1
  • c.411+5G>C No assertion criteria Axenfeld-Rieger syndrome type 1
  • c.412-2A>T No assertion criteria ANTERIOR SEGMENT DYSGENESIS 4, PETERS ANOMALY SUBTYPE
  • p.Arg115fs No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Arg137Trp No assertion criteria anterior segment dysgenesis
  • p.Cys269Ter No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Gln103_Leu104insThrHisPheThrSerGlnGln No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Leu107Gln No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Lys141Glu No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Pro117Leu No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Ser262fs No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Thr121Pro No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Thr239fs No assertion criteria Axenfeld-Rieger syndrome type 1
  • p.Val136Leu No assertion criteria Axenfeld-Rieger syndrome type 1

Pathogenic/Likely pathogenic 8

  • c.412-2A>G Multiple submitters anterior segment dysgenesis 4
  • p.Arg115His Multiple submitters anterior segment dysgenesis 4
  • p.Arg144Pro Multiple submitters Inborn genetic diseases
  • p.Arg144Trp Multiple submitters Axenfeld-Rieger syndrome type 1
  • p.Arg96Trp Multiple submitters anterior segment dysgenesis 4
  • p.Trp139Ser Multiple submitters Axenfeld-Rieger syndrome type 1
  • p.Tyr174Ter Multiple submitters Axenfeld-Rieger syndrome type 1
  • p.Tyr280fs Multiple submitters Axenfeld-Rieger anomaly with partially absent eye muscles, distinctive face, hydrocephaly, and skeletal abnormalities

Likely pathogenic 20

Conflicting classifications of pathogenicity 15

  • c.-1385+12T>C Single submitter Peters anomaly
  • c.-1532C>A Single submitter Peters anomaly
  • c.-211G>A Single submitter Peters anomaly
  • c.-429C>G Single submitter anterior segment dysgenesis 4
  • c.-793C>A Single submitter Peters anomaly
  • c.-79G>A Single submitter Axenfeld-Rieger syndrome type 1
  • c.-967C>T Single submitter Axenfeld-Rieger syndrome type 1
  • c.*340A>G Single submitter Peters anomaly
  • p.Arg144Gln Single submitter anterior segment dysgenesis 4 ⚠
  • p.Arg91= Single submitter anterior segment dysgenesis 4
  • p.Gln75Pro Single submitter anterior segment dysgenesis 4 ⚠
  • p.Leu288= Single submitter Peters anomaly
  • p.Met207Val Single submitter PITX2-related disorder ⚠
  • p.Phe111Ser Single submitter anterior segment dysgenesis 4 ⚠
  • p.Ser213= Single submitter Axenfeld-Rieger syndrome type 1

Benign 23

Benign/Likely benign 13

  • c.206-9C>T Multiple submitters anterior segment dysgenesis 4
  • c.46+8C>G Multiple submitters anterior segment dysgenesis 4
  • c.-392G>T Multiple submitters Peters anomaly
  • c.*471G>A Multiple submitters Peters anomaly
  • p.Ala188Thr Multiple submitters Axenfeld-Rieger syndrome type 1
  • p.Ala21= Multiple submitters
  • p.Pro273= Multiple submitters cataract
  • p.Ser206= Multiple submitters PITX2-Related Eye Abnormalities
  • c.-1024G>A Single submitter Peters anomaly
  • c.-1111C>G Single submitter PITX2-Related Eye Abnormalities
  • c.-1311G>T Single submitter anterior segment dysgenesis 4
  • c.-1335C>A Single submitter Axenfeld-Rieger syndrome type 1
  • c.-362C>G Single submitter Axenfeld-Rieger syndrome type 1

Likely benign 39

Uncertain significance 100