Sugi Variant

Sugi Variant/LIPA

LIPA — 746 ClinVar variants

All ClinVar germline LIPA variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 213 flagged for review →

49 Pathogenic · 22 Pathogenic/Likely pathogenic · 80 Likely pathogenic · 45 Conflicting · 36 Benign · 11 Benign/Likely benign · 261 Likely benign · 242 Uncertain significance

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

⚑ Evidence disagreements 213

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 19

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

Predictors lean, ClinVar uncertain 147

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

Predictors split 45

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

All LIPA variants

Pathogenic 49

Pathogenic/Likely pathogenic 22

  • c.111+1G>A Multiple submitters cholesteryl ester storage disease
  • p.Asn268fs Multiple submitters cholesteryl ester storage disease
  • p.Asn98Lys Multiple submitters Wolman disease
  • p.Asp345Asn Multiple submitters Wolman disease
  • p.Gln298= Multiple submitters LIPA-related disorder
  • p.Gln298His Multiple submitters lysosomal acid lipase deficiency ⚠
  • p.Gln85Arg Multiple submitters Wolman disease
  • p.Gln85Lys Multiple submitters cholesteryl ester storage disease
  • p.Glu232Ter Multiple submitters Wolman disease
  • p.His129Arg Multiple submitters lysosomal acid lipase deficiency
  • p.His129Pro Multiple submitters cholesteryl ester storage disease
  • p.Leu152Pro Multiple submitters lysosomal acid lipase deficiency
  • p.Leu356Ter Multiple submitters lysosomal acid lipase deficiency
  • p.Leu394fs Multiple submitters Wolman disease
  • p.Met117fs Multiple submitters Wolman disease
  • p.Ser103Arg Multiple submitters Wolman disease
  • p.Ser174Phe Multiple submitters cholesteryl ester storage disease
  • p.Ser297fs Multiple submitters Wolman disease
  • p.Thr327fs Multiple submitters lysosomal acid lipase deficiency
  • p.Trp310Ter Multiple submitters lysosomal acid lipase deficiency
  • p.Trp44Ter Multiple submitters Wolman disease
  • p.Trp15Ter No assertion criteria

Likely pathogenic 80

  • c.230-2del Multiple submitters Wolman disease
  • c.675+2T>G Multiple submitters Wolman disease
  • c.822+1G>A Multiple submitters Wolman disease
  • c.823-2A>G Multiple submitters lysosomal acid lipase deficiency
  • p.Ala307Asp Multiple submitters Cardiovascular phenotype
  • p.Gln291Ter Multiple submitters cholesteryl ester storage disease
  • p.His295Tyr Multiple submitters Wolman disease
  • p.Leu294Ser Multiple submitters cholesteryl ester storage disease ⚠
  • p.Leu357Pro Multiple submitters cholesteryl ester storage disease
  • p.Pro78_Val81delinsAlaThrAlaSerTer Multiple submitters cholesteryl ester storage disease
  • p.Ser126Phe Multiple submitters cholesteryl ester storage disease
  • p.Ser289Cys Multiple submitters lysosomal acid lipase deficiency
  • p.Thr288Ile Multiple submitters lysosomal acid lipase deficiency
  • p.Trp95Arg Multiple submitters Wolman disease
  • p.Val206dup Multiple submitters Wolman disease
  • c.112-1G>C Single submitter Wolman disease
  • c.229+3A>C Single submitter cholesteryl ester storage disease
  • c.230-1G>T Single submitter lysosomal acid lipase deficiency
  • c.428+2T>C Single submitter Wolman disease
  • c.429-2A>T Single submitter lysosomal acid lipase deficiency
  • c.538+5G>A Single submitter Wolman disease
  • c.822+1G>T Single submitter Wolman disease
  • c.823-1G>A Single submitter Wolman disease
  • c.894+1G>T Single submitter cholesteryl ester storage disease
  • p.Ala111fs Single submitter lysosomal acid lipase deficiency
  • p.Ala204fs Single submitter cholesteryl ester storage disease
  • p.Arg276Ter Single submitter lysosomal acid lipase deficiency
  • p.Asn119Ser Single submitter lysosomal acid lipase deficiency
  • p.Asn271His Single submitter cholesteryl ester storage disease
  • p.Asn72fs Single submitter cholesteryl ester storage disease
  • p.Asp114Tyr Single submitter Wolman disease
  • p.Asp145Glu Single submitter lysosomal acid lipase deficiency ⚠
  • p.Asp309fs Single submitter cholesteryl ester storage disease
  • p.Asp382Val Single submitter Wolman disease
  • p.Asp57Val Single submitter lysosomal acid lipase deficiency
  • p.Gln175Pro Single submitter lysosomal acid lipase deficiency
  • p.Gln236Ter Single submitter cholesteryl ester storage disease
  • p.Gln291Glu Single submitter lysosomal acid lipase deficiency ⚠
  • p.Gln359Ter Single submitter lysosomal acid lipase deficiency
  • p.Glu269Ter Single submitter lysosomal acid lipase deficiency
  • p.Glu50Gly Single submitter lysosomal acid lipase deficiency ⚠
  • p.Glu54Ter Single submitter lysosomal acid lipase deficiency
  • p.Gly105fs Single submitter lysosomal acid lipase deficiency
  • p.Gly229Ter Single submitter lysosomal acid lipase deficiency
  • p.Gly342Trp Single submitter lysosomal acid lipase deficiency
  • p.Gly342Val Single submitter lysosomal acid lipase deficiency
  • p.Gly343dup Single submitter Wolman disease
  • p.Gly77fs Single submitter cholesteryl ester storage disease
  • p.His222fs Single submitter cholesteryl ester storage disease
  • p.His295Asn Single submitter cholesteryl ester storage disease
  • p.His295Pro Single submitter Wolman disease
  • p.Ile107fs Single submitter cholesteryl ester storage disease
  • p.Ile182fs Single submitter lysosomal acid lipase deficiency
  • p.Ile360Asn Single submitter lysosomal acid lipase deficiency
  • p.Leu12fs Single submitter cholesteryl ester storage disease
  • p.Leu160fs Single submitter lysosomal acid lipase deficiency
  • p.Leu272Ter Single submitter lysosomal acid lipase deficiency
  • p.Leu294fs Single submitter lysosomal acid lipase deficiency
  • p.Lys128fs Single submitter lysosomal acid lipase deficiency
  • p.Lys149fs Single submitter lysosomal acid lipase deficiency
  • p.Lys231fs Single submitter lysosomal acid lipase deficiency
  • p.Lys76Ter Single submitter lysosomal acid lipase deficiency
  • p.Phe106fs Single submitter cholesteryl ester storage disease
  • p.Phe106Ile Single submitter lysosomal acid lipase deficiency
  • p.Phe139Leu Single submitter lysosomal acid lipase deficiency
  • p.Pro202Leu Single submitter lysosomal acid lipase deficiency
  • p.Ser174fs Single submitter lysosomal acid lipase deficiency
  • p.Thr55fs Single submitter lysosomal acid lipase deficiency
  • p.Trp125Ter Single submitter LIPA-related disorder
  • p.Trp140fs Single submitter lysosomal acid lipase deficiency
  • p.Trp385Ter Single submitter Wolman disease
  • p.Tyr324Ter Single submitter lysosomal acid lipase deficiency
  • p.Tyr388Cys Single submitter lysosomal acid lipase deficiency
  • p.Val53Gly Single submitter lysosomal acid lipase deficiency
  • c.111+2T>G No assertion criteria cholesteryl ester storage disease
  • c.676-2A>G No assertion criteria cholesteryl ester storage disease
  • c.894+2T>C No assertion criteria cholesteryl ester storage disease
  • p.His374Gln No assertion criteria Wolman disease
  • p.Thr177fs No assertion criteria LIPA-related disorder
  • p.Tyr320Ter No assertion criteria cholesteryl ester storage disease

Conflicting classifications of pathogenicity 45

Benign 36

Benign/Likely benign 11

Likely benign 261

Uncertain significance 242