ZIC2 — 478 ClinVar variants

All ClinVar germline ZIC2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 205 flagged for review →

32 Pathogenic · 23 Likely pathogenic · 8 Conflicting · 15 Benign · 5 Benign/Likely benign · 147 Likely benign · 248 Uncertain significance

Full ZIC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 205

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 135

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

Predictors split 66

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

All ZIC2 variants

Pathogenic 32

Likely pathogenic 23

Conflicting classifications of pathogenicity 8

Benign 15

Benign/Likely benign 5

  • p.Asn176= Multiple submitters holoprosencephaly 5
  • p.Gly182= Multiple submitters holoprosencephaly 5
  • p.Gly518= Multiple submitters holoprosencephaly 5
  • p.His239del Multiple submitters holoprosencephaly 5
  • p.His239dup Multiple submitters holoprosencephaly 5

Likely benign 147

  • c.1240-96A>G Multiple submitters
  • p.Ala153= Multiple submitters holoprosencephaly 5
  • p.Ala18= Multiple submitters holoprosencephaly 5
  • p.Ala94= Multiple submitters holoprosencephaly 5
  • p.Arg309= Multiple submitters holoprosencephaly 5
  • p.Gln209= Multiple submitters holoprosencephaly 5
  • p.Gly140= Multiple submitters holoprosencephaly 5
  • p.Gly498= Multiple submitters holoprosencephaly 5
  • p.Gly499= Multiple submitters holoprosencephaly 5
  • p.Gly507= Multiple submitters holoprosencephaly 5
  • p.Gly65= Multiple submitters holoprosencephaly 5
  • p.His166Arg Multiple submitters holoprosencephaly 5
  • p.Ile257= Multiple submitters holoprosencephaly 5
  • p.Leu181= Multiple submitters holoprosencephaly 5
  • p.Pro163= Multiple submitters holoprosencephaly 5
  • p.Pro184= Multiple submitters holoprosencephaly 5
  • p.Pro295= Multiple submitters holoprosencephaly 5
  • p.Ser430= Multiple submitters holoprosencephaly 5
  • p.Ser449= Multiple submitters holoprosencephaly 5
  • c.1075+15G>A Single submitter holoprosencephaly 5
  • c.1075+18C>T Single submitter holoprosencephaly 5
  • c.1076-17A>G Single submitter holoprosencephaly 5
  • c.1076-18G>A Single submitter holoprosencephaly 5
  • c.1076-18G>T Single submitter holoprosencephaly 5
  • c.1076-19C>T Single submitter holoprosencephaly 5
  • c.1076-8G>A Single submitter holoprosencephaly 5
  • c.1239+11G>C Single submitter holoprosencephaly 5
  • c.1239+12G>A Single submitter holoprosencephaly 5
  • c.1239+7C>T Single submitter holoprosencephaly 5
  • c.1239+8C>T Single submitter
  • c.1239+9G>A Single submitter holoprosencephaly 5
  • c.1239+9G>T Single submitter holoprosencephaly 5
  • c.1240-10T>C Single submitter holoprosencephaly 5
  • c.1240-11T>C Single submitter holoprosencephaly 5
  • c.*166_*170dup Single submitter
  • p.Ala207Thr Single submitter Inborn genetic diseases
  • p.Ala229= Single submitter holoprosencephaly 5
  • p.Ala26= Single submitter holoprosencephaly 5
  • p.Ala33= Single submitter holoprosencephaly 5
  • p.Ala33del Single submitter
  • p.Ala44= Single submitter holoprosencephaly 5
  • p.Ala445= Single submitter holoprosencephaly 5
  • p.Ala473= Single submitter holoprosencephaly 5
  • p.Ala502= Single submitter holoprosencephaly 5
  • p.Ala91= Single submitter holoprosencephaly 5
  • p.Ala92= Single submitter holoprosencephaly 5
  • p.Ala95= Single submitter holoprosencephaly 5
  • p.Arg19= Single submitter holoprosencephaly 5
  • p.Arg201= Single submitter holoprosencephaly 5
  • p.Arg248= Single submitter holoprosencephaly 5
  • p.Arg373= Single submitter holoprosencephaly 5
  • p.Arg409= Single submitter holoprosencephaly 5
  • p.Asn220= Single submitter holoprosencephaly 5
  • p.Asn268= Single submitter holoprosencephaly 5
  • p.Asn452= Single submitter holoprosencephaly 5
  • p.Asp152= Single submitter holoprosencephaly 5
  • p.Asp37= Single submitter holoprosencephaly 5
  • p.Cys370= Single submitter holoprosencephaly 5
  • p.Gln172= Single submitter holoprosencephaly 5
  • p.Gln254= Single submitter holoprosencephaly 5
  • p.Gln265= Single submitter holoprosencephaly 5
  • p.Gln36Glu Single submitter holoprosencephaly 5
  • p.Glu34= Single submitter holoprosencephaly 5
  • p.Glu368= Single submitter holoprosencephaly 5
  • p.Glu529= Single submitter holoprosencephaly 5
  • p.Gly110= Single submitter holoprosencephaly 5
  • p.Gly125= Single submitter
  • p.Gly13= Single submitter
  • p.Gly133= Single submitter holoprosencephaly 5
  • p.Gly144= Single submitter holoprosencephaly 5
  • p.Gly155= Single submitter holoprosencephaly 5
  • p.Gly185= Single submitter holoprosencephaly 5
  • p.Gly293= Single submitter holoprosencephaly 5
  • p.Gly479= Single submitter holoprosencephaly 5
  • p.Gly48= Single submitter holoprosencephaly 5
  • p.Gly483= Single submitter holoprosencephaly 5
  • p.Gly500= Single submitter holoprosencephaly 5
  • p.Gly511= Single submitter holoprosencephaly 5
  • p.Gly512= Single submitter holoprosencephaly 5
  • p.Gly522= Single submitter holoprosencephaly 5
  • p.Gly87= Single submitter holoprosencephaly 5
  • p.Gly99= Single submitter holoprosencephaly 5
  • p.His147= Single submitter holoprosencephaly 5
  • p.His150= Single submitter holoprosencephaly 5
  • p.His169= Single submitter holoprosencephaly 5
  • p.His237= Single submitter holoprosencephaly 5
  • p.Ile324= Single submitter holoprosencephaly 5
  • p.Leu120= Single submitter holoprosencephaly 5
  • p.Leu138= Single submitter holoprosencephaly 5
  • p.Leu146= Single submitter
  • p.Leu158= Single submitter holoprosencephaly 5
  • p.Leu175= Single submitter holoprosencephaly 5
  • p.Leu2= Single submitter holoprosencephaly 5
  • p.Leu350= Single submitter holoprosencephaly 5
  • p.Leu440= Single submitter holoprosencephaly 5
  • p.Lys270= Single submitter holoprosencephaly 5
  • p.Lys271= Single submitter holoprosencephaly 5
  • p.Lys319= Single submitter holoprosencephaly 5
  • p.Lys382= Single submitter holoprosencephaly 5
  • p.Phe17= Single submitter holoprosencephaly 5
  • p.Phe374= Single submitter holoprosencephaly 5
  • p.Phe9= Single submitter holoprosencephaly 5
  • p.Pro10= Single submitter holoprosencephaly 5
  • p.Pro100= Single submitter holoprosencephaly 5
  • p.Pro112= Single submitter holoprosencephaly 5
  • p.Pro131= Single submitter holoprosencephaly 5
  • p.Pro160= Single submitter holoprosencephaly 5
  • p.Pro216= Single submitter
  • p.Pro362= Single submitter holoprosencephaly 5
  • p.Pro419= Single submitter holoprosencephaly 5
  • p.Pro443= Single submitter holoprosencephaly 5
  • p.Pro64= Single submitter holoprosencephaly 5
  • p.Ser272= Single submitter holoprosencephaly 5
  • p.Ser347= Single submitter holoprosencephaly 5
  • p.Ser389= Single submitter holoprosencephaly 5
  • p.Ser401= Single submitter holoprosencephaly 5
  • p.Ser407= Single submitter holoprosencephaly 5
  • p.Ser417= Single submitter holoprosencephaly 5
  • p.Ser434= Single submitter holoprosencephaly 5
  • p.Ser435fs Single submitter
  • p.Ser454= Single submitter holoprosencephaly 5
  • p.Ser493= Single submitter holoprosencephaly 5
  • p.Ser521= Single submitter holoprosencephaly 5
  • p.Ser524= Single submitter holoprosencephaly 5
  • p.Ser70= Single submitter holoprosencephaly 5
  • p.Ser75= Single submitter holoprosencephaly 5
  • p.Thr116= Single submitter holoprosencephaly 5
  • p.Thr202= Single submitter holoprosencephaly 5
  • p.Thr285= Single submitter holoprosencephaly 5
  • p.Thr356= Single submitter holoprosencephaly 5
  • p.Thr388= Single submitter holoprosencephaly 5
  • p.Thr403= Single submitter holoprosencephaly 5
  • p.Thr436= Single submitter holoprosencephaly 5
  • p.Thr436fs Single submitter
  • p.Tyr205= Single submitter holoprosencephaly 5
  • p.Tyr214= Single submitter holoprosencephaly 5
  • p.Tyr402fs Single submitter holoprosencephaly 5
  • p.Val14= Single submitter holoprosencephaly 5
  • p.Val174= Single submitter holoprosencephaly 5
  • p.Val292= Single submitter holoprosencephaly 5
  • p.Val386= Single submitter
  • p.Val471= Single submitter holoprosencephaly 5
  • p.Ala93= No assertion criteria ZIC2-related disorder
  • p.Gly421= No assertion criteria ZIC2-related disorder
  • p.Leu210= No assertion criteria ZIC2-related disorder
  • p.Phe139= No assertion criteria ZIC2-related disorder
  • p.Tyr531= No assertion criteria ZIC2-related disorder

Uncertain significance 248