Sugi Variant

Sugi Variant/LCT

LCT — 967 ClinVar variants

All ClinVar germline LCT variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 392 flagged for review →

31 Pathogenic · 3 Pathogenic/Likely pathogenic · 18 Likely pathogenic · 36 Conflicting · 49 Benign · 24 Benign/Likely benign · 392 Likely benign · 414 Uncertain significance

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

⚑ Evidence disagreements 392

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 1

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

Predictors agree, ClinVar conflicts 12

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

Predictors lean, ClinVar uncertain 318

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 318

Predictors split 61

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

All LCT variants

Pathogenic 31

Pathogenic/Likely pathogenic 3

Likely pathogenic 18

Conflicting classifications of pathogenicity 36

  • c.4664-10A>G Single submitter congenital lactase deficiency
  • p.Ala1096Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala1483Ser Single submitter congenital lactase deficiency ⚠
  • p.Ala1794Val Single submitter Inborn genetic diseases ⚠
  • p.Ala237Val Single submitter Inborn genetic diseases ⚠
  • p.Ala372= Single submitter congenital lactase deficiency
  • p.Ala961= Single submitter congenital lactase deficiency
  • p.Arg1220Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg1376Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg1587= Single submitter congenital lactase deficiency
  • p.Arg1587His Single submitter LCT-related disorder ⚠
  • p.Arg1908Cys Single submitter congenital lactase deficiency ⚠
  • p.Arg371= Single submitter congenital lactase deficiency
  • p.Asn1161= Single submitter congenital lactase deficiency
  • p.Asn1797= Single submitter congenital lactase deficiency
  • p.Asn280= Single submitter congenital lactase deficiency
  • p.Asp1478= Single submitter congenital lactase deficiency
  • p.Gln1114Arg Single submitter Inborn genetic diseases ⚠
  • p.Glu513= Single submitter congenital lactase deficiency
  • p.Gly1876Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly851Glu Single submitter Inborn genetic diseases ⚠
  • p.His1095= Single submitter congenital lactase deficiency
  • p.Ile10= Single submitter congenital lactase deficiency
  • p.Ile841Val Single submitter Inborn genetic diseases ⚠
  • p.Leu966= Single submitter congenital lactase deficiency
  • p.Pro1268= Single submitter congenital lactase deficiency
  • p.Pro1843= Single submitter congenital lactase deficiency
  • p.Ser1150= Single submitter congenital lactase deficiency
  • p.Ser1454= Single submitter congenital lactase deficiency
  • p.Thr1286Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr1408= Single submitter congenital lactase deficiency
  • p.Trp1316Ser Single submitter congenital lactase deficiency ⚠
  • p.Tyr1565= Single submitter congenital lactase deficiency
  • p.Tyr1831= Single submitter congenital lactase deficiency
  • p.Tyr1885= Single submitter congenital lactase deficiency
  • p.Val7= Single submitter congenital lactase deficiency

Benign 49

Benign/Likely benign 24

Likely benign 392

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 414

Showing the top 300 by review status; the full set is in the sitemap.