MEIS2 — 238 ClinVar variants

All ClinVar germline MEIS2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 90 flagged for review →

19 Pathogenic · 3 Pathogenic/Likely pathogenic · 24 Likely pathogenic · 4 Conflicting · 8 Benign · 6 Benign/Likely benign · 59 Likely benign · 115 Uncertain significance

Full MEIS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 90

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 3

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

Predictors lean, ClinVar uncertain 65

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

Predictors split 22

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

All MEIS2 variants

Pathogenic 19

  • p.Arg174Ter Multiple submitters MEIS2-related disorder
  • c.977+1G>A Single submitter
  • c.977+2T>G Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg276fs Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg331Gly Single submitter
  • p.Arg331Lys Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Asp266delinsSerPheThrTrpTyrArgTer Single submitter cleft lip/palate
  • p.Gln152Ter Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gln251Ter Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gln297Ter Single submitter
  • p.Glu142Ter Single submitter
  • p.His41fs Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Phe171fs Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Pro302Arg Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Trp218Ter Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Val36fs Single submitter
  • c.639+1G>A No assertion criteria cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.978-2A>G No assertion criteria
  • p.Ser204Ter No assertion criteria cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies

Pathogenic/Likely pathogenic 3

  • p.Arg219Ter Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg333del Multiple submitters Inborn genetic diseases
  • p.Leu312fs Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies

Likely pathogenic 24

  • p.Ala260fs Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.387+1G>C Single submitter MEIS2-related disorder
  • c.388-1G>A Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.640-1G>C Single submitter MEIS2-related disorder
  • c.754+2T>C Single submitter
  • p.Ala293Pro Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg332Gly Single submitter
  • p.Arg333Lys Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg333Ser Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg344Ter Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Asn329Ser Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gln322Leu Single submitter
  • p.Gly239fs Single submitter
  • p.His57fs Single submitter syndromic intellectual disability
  • p.Pro302Leu Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Pro337_Met338delinsLeu Single submitter cleft palate
  • p.Ser342Ter Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Tyr303Asn Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Tyr303Cys Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Val323Gly Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Val69fs Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg174_Tyr175insTer No assertion criteria cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Asn325Asp No assertion criteria cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gln322Glu No assertion criteria cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies

Conflicting classifications of pathogenicity 4

  • p.Glu306Lys Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Gly254Cys Single submitter Inborn genetic diseases ⚠
  • p.Met377Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro270Leu Single submitter Inborn genetic diseases ⚠

Benign 8

  • c.1147+359A>G Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.388-17CT[2] Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.755-20642A>G Single submitter
  • p.Ala68Ser Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gln477= Single submitter
  • p.Gly194Ser Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.His240Arg Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Pro235Leu Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠

Benign/Likely benign 6

  • c.13-19C>A Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Asp169= Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.His421Arg Multiple submitters
  • p.Leu210= Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Leu8= Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ser244= Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies

Likely benign 59

  • c.754+7G>C Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Asn40= Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Glu201= Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.His157= Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Met472Thr Multiple submitters Inborn genetic diseases
  • p.Pro20= Multiple submitters
  • c.1147+17C>T Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.1147+18G>A Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.12+18A>G Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.13-19C>G Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.13-226TC[22] Single submitter
  • c.245+13C>T Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.245+15dup Single submitter
  • c.246-17G>C Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.387+8C>T Single submitter
  • c.438+16C>T Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.489+20C>A Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.490-16A>G Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.490-7G>A Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.900+12T>C Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ala109= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ala2= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ala260= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ala313= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ala55= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ala68= Single submitter
  • p.Ala79= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg219= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg276His Single submitter
  • p.Asp193= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Asp6Glu Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gln355= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gln418= Single submitter
  • p.Gly110= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gly12= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gly13= Single submitter
  • p.Gly205= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gly389Ala Single submitter Inborn genetic diseases
  • p.His165= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.His441= Single submitter Inborn genetic diseases
  • p.His50= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ile185= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Leu187= Single submitter
  • p.Leu299= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Lys309= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Met438Val Single submitter Inborn genetic diseases
  • p.Met472Ile Single submitter Inborn genetic diseases
  • p.Pro215Arg Single submitter Inborn genetic diseases
  • p.Pro270= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Pro30= Single submitter
  • p.Pro32= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Pro35= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ser216= Single submitter
  • p.Ser229= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ser305= Single submitter
  • p.Tyr51= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Val471= Single submitter
  • p.Arg75= No assertion criteria MEIS2-related disorder
  • p.Asp271= No assertion criteria MEIS2-related disorder

Uncertain significance 115

  • c.1147+347del Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Arg192_Asp193delinsSerLeu Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Asp169Asn Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Asp6Ala Multiple submitters Inborn genetic diseases ⚠
  • p.His447Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Ile33Val Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Leu154Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Pro416Arg Multiple submitters cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • c.1036+4A>G Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.1147+344A>G Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.1147+355G>T Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.1147+356G>A Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.1147+378G>T Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.1147+5G>C Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.1148-1G>T Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.387+6G>C Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.388-3C>G Single submitter
  • c.438+5G>T Single submitter
  • c.490-8C>A Single submitter
  • c.640-29G>A Single submitter Inborn genetic diseases
  • c.755-11878A>G Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • c.901-7229_901-3516del Single submitter
  • c.977+4A>T Single submitter
  • p.Ala109Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala21Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala382Val Single submitter ⚠
  • p.Ala437Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala476Val Single submitter Inborn genetic diseases ⚠
  • p.Ala63Thr Single submitter ⚠
  • p.Ala72Thr Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Ala79Gly Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Ala90Ser Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Arg174Gly Single submitter ⚠
  • p.Arg192Gly Single submitter ⚠
  • p.Arg192Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg344Gln Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Arg380Gln Single submitter Inborn genetic diseases ⚠
  • p.Asn145Ser Single submitter ⚠
  • p.Asn247Asp Single submitter Inborn genetic diseases ⚠
  • p.Asn329Lys Single submitter ⚠
  • p.Asn70Lys Single submitter ⚠
  • p.Asp112Asn Single submitter ⚠
  • p.Asp193His Single submitter Inborn genetic diseases ⚠
  • p.Asp193Val Single submitter Inborn genetic diseases ⚠
  • p.Asp212Gly Single submitter ⚠
  • p.Asp372fs Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Asp390Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp473Ala Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Gln129= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gln149Arg Single submitter ⚠
  • p.Gln149Glu Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Gln149Pro Single submitter ⚠
  • p.Gln394Arg Single submitter Inborn genetic diseases ⚠
  • p.Gln455His Single submitter Inborn genetic diseases ⚠
  • p.Gly13Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly13Glu Single submitter ⚠
  • p.Gly18Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly194= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Gly239Ala Single submitter
  • p.Gly245Arg Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Gly317Glu Single submitter ⚠
  • p.Gly373Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly442Arg Single submitter Inborn genetic diseases
  • p.Gly469Arg Single submitter Inborn genetic diseases
  • p.His157Arg Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.His173Tyr Single submitter Inborn genetic diseases ⚠
  • p.His228Arg Single submitter Inborn genetic diseases ⚠
  • p.His301Gln Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.His37Gln Single submitter Inborn genetic diseases ⚠
  • p.His37Leu Single submitter Inborn genetic diseases ⚠
  • p.His415Leu Single submitter ⚠
  • p.His41Asn Single submitter Inborn genetic diseases ⚠
  • p.His46Gln Single submitter ⚠
  • p.Ile123Phe Single submitter ⚠
  • p.Ile185Val Single submitter Inborn genetic diseases ⚠
  • p.Leu203Ile Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Leu348fs Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Leu429Ser Single submitter Inborn genetic diseases ⚠
  • p.Leu45Val Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Leu91Pro Single submitter ⚠
  • p.Lys197Arg Single submitter Inborn genetic diseases ⚠
  • p.Lys285= Single submitter MEIS2-related disorder
  • p.Lys309Asn Single submitter ⚠
  • p.Lys74Gln Single submitter Inborn genetic diseases ⚠
  • p.Met425fs Single submitter Inborn genetic diseases
  • p.Met425Val Single submitter Inborn genetic diseases ⚠
  • p.Pro103Leu Single submitter ⚠
  • p.Pro103Thr Single submitter Inborn genetic diseases ⚠
  • p.Pro302Thr Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Pro35Ser Single submitter ⚠
  • p.Pro365Ser Single submitter ⚠
  • p.Pro44= Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Pro56Gln Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Ser198Leu Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Ser204Ala Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Ser216Tyr Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Ser217del Single submitter Inborn genetic diseases
  • p.Ser226Ala Single submitter Inborn genetic diseases ⚠
  • p.Ser236Cys Single submitter ⚠
  • p.Ser248Gly Single submitter Inborn genetic diseases ⚠
  • p.Ser258Asn Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies
  • p.Ser258Gly Single submitter ⚠
  • p.Ser354Asn Single submitter ⚠
  • p.Ser386Asn Single submitter Inborn genetic diseases ⚠
  • p.Ser453Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser67Cys Single submitter Inborn genetic diseases ⚠
  • p.Thr451Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr48Ala Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Trp294Arg Single submitter cardiac malformation, cleft lip/palate, microcephaly, and digital anomalies ⚠
  • p.Tyr5Ter Single submitter MEIS2-related disorder
  • p.Tyr81Phe Single submitter ⚠
  • p.Val17Ala Single submitter Inborn genetic diseases ⚠
  • p.Val188Phe Single submitter Inborn genetic diseases ⚠
  • p.Pro409Leu No assertion criteria MEIS2-related disorder ⚠
  • p.Ser138Pro No assertion criteria MEIS2-related disorder ⚠