Sugi Variant

Sugi Variant/PI4KA

PI4KA — 451 ClinVar variants

All ClinVar germline PI4KA variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 146 flagged for review →

20 Pathogenic · 1 Pathogenic/Likely pathogenic · 28 Likely pathogenic · 4 Conflicting · 107 Benign · 10 Benign/Likely benign · 122 Likely benign · 159 Uncertain significance

Full PI4KA gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 146

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 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 1

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

Predictors lean, ClinVar uncertain 89

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

Predictors split 54

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

All PI4KA variants

Pathogenic 20

  • p.Thr2053fs Multiple submitters spastic paraplegia 84, autosomal recessive
  • c.1071+1G>A Single submitter
  • c.2575-1G>A Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Arg566Ter Single submitter
  • p.Glu1820del Single submitter spastic paraplegia 84, autosomal recessive
  • p.Leu993fs Single submitter PI4KA-related disorder
  • p.Pro875fs Single submitter
  • p.Ser1092Ter Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Ser361fs Single submitter
  • p.Thr1720Ile Single submitter spastic paraplegia 84, autosomal recessive ⚠
  • p.Tyr197Ter Single submitter PI4KA-related disorder
  • p.Val110fs Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Ala1198Thr No assertion criteria polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis ⚠
  • p.Arg2022fs No assertion criteria polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Arg796Ter No assertion criteria polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Gln1191Ter No assertion criteria polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Gly1925Glu No assertion criteria polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Leu777Pro No assertion criteria polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Pro876fs No assertion criteria polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Tyr1623Asp No assertion criteria gastrointestinal defects and immunodeficiency syndrome 2

Pathogenic/Likely pathogenic 1

Likely pathogenic 28

  • p.Arg618Ter Multiple submitters spastic paraplegia 84, autosomal recessive
  • p.Glu1152Lys Multiple submitters polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Pro1992Ser Multiple submitters polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis ⚠
  • c.2802_2863-40del Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • c.2988-2A>G Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • c.3900+1G>A Single submitter
  • c.4160+1G>A Single submitter spastic paraplegia 84, autosomal recessive
  • c.4488+1G>T Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • c.5923+1G>C Single submitter
  • p.Ala1945Thr Single submitter
  • p.Arg1326Cys Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis ⚠
  • p.Arg1401fs Single submitter spastic paraplegia 84, autosomal recessive
  • p.Arg192Ter Single submitter spastic paraplegia 84, autosomal recessive
  • p.Arg1941Ter Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Arg746Ter Single submitter PI4KA-related disorder
  • p.Arg796fs Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Asp1788Tyr Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Asp653fs Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Cys1288fs Single submitter
  • p.Cys918fs Single submitter PI4KA-related disorder
  • p.Gln1187Ter Single submitter
  • p.Gln436Ter Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Glu1307Ter Single submitter PI4KA-related disorder
  • p.Glu563Ter Single submitter PI4KA-related disorder
  • p.His1097fs Single submitter gastrointestinal defects and immunodeficiency syndrome 2
  • p.Leu1084Pro Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Phe1386Val Single submitter spastic paraplegia 84, autosomal recessive ⚠
  • p.Thr1634fs Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis

Conflicting classifications of pathogenicity 4

  • p.Leu1558= Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Ser802= Single submitter
  • p.Tyr1456= Single submitter polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • p.Val1556Met Single submitter spastic paraplegia 84, autosomal recessive ⚠

Benign 107

Benign/Likely benign 10

Likely benign 122

Uncertain significance 159