Sugi Variant

Sugi Variant/CSNK2A1

CSNK2A1 — 269 ClinVar variants

All ClinVar germline CSNK2A1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 72 flagged for review →

34 Pathogenic · 16 Pathogenic/Likely pathogenic · 34 Likely pathogenic · 7 Conflicting · 25 Benign · 5 Benign/Likely benign · 59 Likely benign · 89 Uncertain significance

Full CSNK2A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 72

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 5

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

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 53

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

Predictors split 13

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

All CSNK2A1 variants

Pathogenic 34

  • p.Arg191Gln Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Arg280Ter Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Asp156Glu Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Lys76fs Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Ser51Arg Multiple submitters Okur-Chung neurodevelopmental syndrome
  • c.102-2A>G Single submitter
  • c.213+1G>T Single submitter
  • c.214-1G>A Single submitter
  • c.426+1G>T Single submitter
  • p.Arg21Ter Single submitter
  • p.Arg278Ter Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Arg43Ter Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Arg47Gly Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Asp156Gly Single submitter
  • p.Asp156His Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Asp175Asn Single submitter
  • p.Asp308fs Single submitter
  • p.Gln126fs Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Glu180Lys Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Glu32fs Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Leu128Ter Single submitter Inborn genetic diseases
  • p.Leu85fs Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Met1Val Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Phe197Val Single submitter
  • p.Ser194Phe Single submitter
  • p.Ser277fs Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Ser51Ile Single submitter
  • p.Trp33Ter Single submitter CSNK2A1-related disorder
  • p.Tyr182Ter Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Tyr261Ter Single submitter Inborn genetic diseases
  • c.824+2T>C No assertion criteria Okur-Chung neurodevelopmental syndrome
  • p.Asp175Gly No assertion criteria Okur-Chung neurodevelopmental syndrome
  • p.Trp176Arg No assertion criteria
  • p.Tyr50Ser No assertion criteria Okur-Chung neurodevelopmental syndrome

Pathogenic/Likely pathogenic 16

  • p.Arg134Ter Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Arg306Ter Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Arg312Gln Multiple submitters
  • p.Arg312Trp Multiple submitters Inborn genetic diseases
  • p.Arg333Ter Multiple submitters CSNK2A1-related neurodevelopmental syndrome
  • p.Arg47Gln Multiple submitters Inborn genetic diseases
  • p.Arg47Ter Multiple submitters CSNK2A1-related disorder
  • p.Asp175Ala Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Glu27Lys Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Gly177Asp Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Gly177Ser Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Gly48Ser Multiple submitters CSNK2A1-related disorder
  • p.His160Arg Multiple submitters CSNK2A1-related disorder
  • p.Lys198Arg Multiple submitters CSNK2A1-related disorder
  • p.Ser51Asn Multiple submitters Okur-Chung neurodevelopmental syndrome
  • p.Tyr50Cys Multiple submitters CSNK2A1-related disorder

Likely pathogenic 34

  • p.Arg107Ter Multiple submitters Okur-Chung neurodevelopmental syndrome
  • c.101+1G>T Single submitter Okur-Chung neurodevelopmental syndrome
  • c.367-1G>A Single submitter Okur-Chung neurodevelopmental syndrome
  • c.723+1G>C Single submitter
  • p.Ala110fs Single submitter
  • p.Ala223Glu Single submitter CSNK2A1-related disorder
  • p.Arg172Ter Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Arg195Pro Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Arg47Pro Single submitter Inborn genetic diseases
  • p.Asn161Asp Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Asp175Val Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Gln207Ter Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Gln290Ter Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Glu52Lys Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Glu81Ala Single submitter
  • p.Gly177Ala Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Gly235Val Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Gly48Asp Single submitter Okur-Chung neurodevelopmental syndrome
  • p.His18fs Single submitter
  • p.His286fs Single submitter Okur-Chung neurodevelopmental syndrome
  • p.His29fs Single submitter
  • p.Lys158Asn Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Phe233Ser Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Ser194Pro Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Ser343fs Single submitter
  • p.Ser51Pro Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Trp216Arg Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Trp24Ter Single submitter
  • p.Tyr209Cys Single submitter Inborn genetic diseases
  • p.Tyr307Ter Single submitter
  • p.Tyr323fs Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Tyr39Ter Single submitter Okur-Chung neurodevelopmental syndrome
  • p.Val192Ile Single submitter CSNK2A1-related disorder
  • p.Asp156Tyr No assertion criteria Okur-Chung neurodevelopmental syndrome

Conflicting classifications of pathogenicity 7

Benign 25

Benign/Likely benign 5

Likely benign 59

Uncertain significance 89