Sugi Variant

Sugi Variant/LNPK

LNPK — 71 ClinVar variants

All ClinVar germline LNPK variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 12 flagged for review →

12 Pathogenic · 1 Pathogenic/Likely pathogenic · 5 Likely pathogenic · 2 Conflicting · 4 Benign · 1 Benign/Likely benign · 28 Likely benign · 18 Uncertain significance

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

⚑ Evidence disagreements 12

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 1

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

Predictors lean, ClinVar uncertain 7

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

Predictors split 4

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

All LNPK variants

Pathogenic 12

  • c.1054+1G>C Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Arg297Ter Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • c.1054+1G>T No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • c.316+4dup No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • c.357+1G>A No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • c.-62-1G>T No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Arg251Ter No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Arg7Ter No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Ile119fs No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Leu120fs No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Lys145fs No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Pro243fs No assertion criteria neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum

Pathogenic/Likely pathogenic 1

  • p.Pro208fs Multiple submitters neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum

Likely pathogenic 5

  • p.Cys301fs Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Glu121Ter Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Leu134fs Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Pro197fs Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Ser143Ter Single submitter LNPK-related disorder

Conflicting classifications of pathogenicity 2

Benign 4

Benign/Likely benign 1

Likely benign 28

Uncertain significance 18

  • p.Arg167His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg253Ter Multiple submitters neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • c.317-1_317delinsTT Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • c.317-4073T>C Single submitter
  • c.707-328C>G Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • c.-98dup Single submitter
  • p.Ala156Glu Single submitter ⚠
  • p.Ala160Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala299Val Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum ⚠
  • p.Arg311Gly Single submitter ⚠
  • p.Asn35fs Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Gln269Arg Single submitter LNPK-related disorder
  • p.Ile370Met Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum ⚠
  • p.Leu237His Single submitter ⚠
  • p.Met285Ile Single submitter ⚠
  • p.Phe98del Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum
  • p.Pro228Ser Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum ⚠
  • p.Pro67Leu Single submitter neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum ⚠