LCAT — 342 ClinVar variants

All ClinVar germline LCAT variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 152 flagged for review →

19 Pathogenic · 5 Pathogenic/Likely pathogenic · 16 Likely pathogenic · 22 Conflicting · 5 Benign · 3 Benign/Likely benign · 128 Likely benign · 144 Uncertain significance

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

⚑ Evidence disagreements 152

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 5

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

Predictors agree, ClinVar conflicts 7

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

Predictors lean, ClinVar uncertain 99

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

Predictors split 41

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

All LCAT variants

Pathogenic 19

Pathogenic/Likely pathogenic 5

Likely pathogenic 16

Conflicting classifications of pathogenicity 22

Benign 5

Benign/Likely benign 3

Likely benign 128

  • p.Ala330= Multiple submitters Cardiovascular phenotype
  • p.Arg123= Multiple submitters Cardiovascular phenotype
  • p.Arg164= Multiple submitters Cardiovascular phenotype
  • p.Asp160= Multiple submitters Cardiovascular phenotype
  • p.Asp301= Multiple submitters Cardiovascular phenotype
  • p.Gly207= Multiple submitters Cardiovascular phenotype
  • p.Gly354= Multiple submitters Cardiovascular phenotype
  • p.His210= Multiple submitters Cardiovascular phenotype
  • p.His397= Multiple submitters Cardiovascular phenotype
  • p.Ile231= Multiple submitters Cardiovascular phenotype
  • p.Leu136= Multiple submitters Cardiovascular phenotype
  • p.Leu209= Multiple submitters Cardiovascular phenotype
  • p.Lys262= Multiple submitters Cardiovascular phenotype
  • p.Pro24= Multiple submitters Cardiovascular phenotype
  • p.Pro34= Multiple submitters Cardiovascular phenotype
  • p.Pro395= Multiple submitters Cardiovascular phenotype
  • p.Pro430= Multiple submitters Cardiovascular phenotype
  • p.Pro48= Multiple submitters Cardiovascular phenotype
  • p.Pro7= Multiple submitters Cardiovascular phenotype
  • p.Ser110= Multiple submitters Cardiovascular phenotype
  • p.Ser6= Multiple submitters Cardiovascular phenotype
  • p.Thr12= Multiple submitters Cardiovascular phenotype
  • p.Thr345= Multiple submitters Cardiovascular phenotype
  • p.Thr348= Multiple submitters Cardiovascular phenotype
  • p.Tyr157= Multiple submitters Cardiovascular phenotype
  • p.Tyr195= Multiple submitters Cardiovascular phenotype
  • p.Tyr339= Multiple submitters Cardiovascular phenotype
  • p.Tyr351= Multiple submitters Cardiovascular phenotype
  • c.154+15G>A Single submitter
  • c.154+17C>T Single submitter
  • c.154+19C>G Single submitter
  • c.311+14C>G Single submitter
  • c.312-10C>T Single submitter
  • c.312-15A>C Single submitter
  • c.312-4G>A Single submitter
  • c.312-5C>T Single submitter
  • c.427+17A>G Single submitter
  • c.428-10C>A Single submitter
  • c.428-11T>C Single submitter
  • c.428-5C>A Single submitter
  • c.523+14C>T Single submitter
  • c.523+15G>A Single submitter
  • c.523+17A>G Single submitter
  • c.523+9C>G Single submitter
  • c.524-14dup Single submitter
  • c.524-16C>T Single submitter
  • c.524-7G>T Single submitter
  • c.748+18A>G Single submitter
  • c.749-6C>A Single submitter
  • c.749-7T>C Single submitter
  • p.Ala166= Single submitter Cardiovascular phenotype
  • p.Ala185= Single submitter Cardiovascular phenotype
  • p.Ala193= Single submitter
  • p.Ala22= Single submitter Cardiovascular phenotype
  • p.Ala235= Single submitter Cardiovascular phenotype
  • p.Ala23Thr Single submitter Cardiovascular phenotype
  • p.Ala373= Single submitter Cardiovascular phenotype
  • p.Ala40= Single submitter Cardiovascular phenotype
  • p.Ala428= Single submitter Cardiovascular phenotype
  • p.Arg159= Single submitter
  • p.Arg182His Single submitter Cardiovascular phenotype
  • p.Arg225= Single submitter Cardiovascular phenotype
  • p.Arg280= Single submitter Cardiovascular phenotype
  • p.Arg347His Single submitter Cardiovascular phenotype
  • p.Arg375= Single submitter Cardiovascular phenotype
  • p.Asn116= Single submitter Cardiovascular phenotype
  • p.Asn58= Single submitter
  • p.Asn71= Single submitter Cardiovascular phenotype
  • p.Asp359= Single submitter Cardiovascular phenotype
  • p.Glu179= Single submitter
  • p.Glu265= Single submitter
  • p.Glu366= Single submitter Cardiovascular phenotype
  • p.Glu79= Single submitter
  • p.Gly112= Single submitter Cardiovascular phenotype
  • p.Gly126= Single submitter Cardiovascular phenotype
  • p.Gly128= Single submitter Cardiovascular phenotype
  • p.Gly234= Single submitter Cardiovascular phenotype
  • p.Gly239= Single submitter Cardiovascular phenotype
  • p.Gly362Asp Single submitter Cardiovascular phenotype
  • p.His204= Single submitter Cardiovascular phenotype
  • p.His353= Single submitter Cardiovascular phenotype
  • p.His397Arg Single submitter Cardiovascular phenotype
  • p.Ile227= Single submitter Cardiovascular phenotype
  • p.Ile290= Single submitter Cardiovascular phenotype
  • p.Ile417= Single submitter Cardiovascular phenotype
  • p.Leu113= Single submitter Cardiovascular phenotype
  • p.Leu148= Single submitter Cardiovascular phenotype
  • p.Leu19= Single submitter Cardiovascular phenotype
  • p.Leu216= Single submitter Cardiovascular phenotype
  • p.Leu247= Single submitter Cardiovascular phenotype
  • p.Leu31= Single submitter Cardiovascular phenotype
  • p.Leu324= Single submitter Cardiovascular phenotype
  • p.Leu343= Single submitter Cardiovascular phenotype
  • p.Leu379= Single submitter Cardiovascular phenotype
  • p.Leu382Arg Single submitter Cardiovascular phenotype
  • p.Leu394= Single submitter Cardiovascular phenotype
  • p.Leu396= Single submitter Cardiovascular phenotype
  • p.Leu51= Single submitter Cardiovascular phenotype
  • p.Leu60= Single submitter
  • p.Lys197= Single submitter Cardiovascular phenotype
  • p.Lys223= Single submitter Cardiovascular phenotype
  • p.Lys264= Single submitter Cardiovascular phenotype
  • p.Phe25= Single submitter Cardiovascular phenotype
  • p.Phe306= Single submitter Cardiovascular phenotype
  • p.Phe91= Single submitter
  • p.Pro174= Single submitter Cardiovascular phenotype
  • p.Pro198= Single submitter Cardiovascular phenotype
  • p.Pro243= Single submitter
  • p.Pro284= Single submitter Cardiovascular phenotype
  • p.Pro3= Single submitter Cardiovascular phenotype
  • p.Pro356= Single submitter Cardiovascular phenotype
  • p.Pro38= Single submitter Cardiovascular phenotype
  • p.Pro4= Single submitter Cardiovascular phenotype
  • p.Pro437= Single submitter Cardiovascular phenotype
  • p.Ser138= Single submitter Cardiovascular phenotype
  • p.Ser240= Single submitter
  • p.Ser273= Single submitter Cardiovascular phenotype
  • p.Ser433= Single submitter
  • p.Thr271= Single submitter Cardiovascular phenotype
  • p.Thr358= Single submitter Cardiovascular phenotype
  • p.Thr37= Single submitter Cardiovascular phenotype
  • p.Thr377= Single submitter Cardiovascular phenotype
  • p.Thr431Ala Single submitter Cardiovascular phenotype
  • p.Tyr75= Single submitter Cardiovascular phenotype
  • p.Val105= Single submitter
  • p.Val124= Single submitter
  • p.Val149= Single submitter Cardiovascular phenotype
  • p.Val69= Single submitter Cardiovascular phenotype

Uncertain significance 144