SLC46A1 — 390 ClinVar variants

All ClinVar germline SLC46A1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 144 flagged for review →

17 Pathogenic · 1 Pathogenic/Likely pathogenic · 5 Likely pathogenic · 18 Conflicting · 26 Benign · 6 Benign/Likely benign · 116 Likely benign · 201 Uncertain significance

Full SLC46A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 144

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 11

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 34

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

All SLC46A1 variants

Pathogenic 17

Pathogenic/Likely pathogenic 1

Likely pathogenic 5

Conflicting classifications of pathogenicity 18

Benign 26

  • c.1082-114T>C Multiple submitters
  • c.1082-89G>A Multiple submitters
  • c.1322+249= Multiple submitters
  • c.*1407C>T Multiple submitters hereditary folate malabsorption
  • c.*2853G>A Multiple submitters hereditary folate malabsorption
  • c.*3009= Multiple submitters hereditary folate malabsorption
  • c.*3062C>A Multiple submitters hereditary folate malabsorption
  • c.*3266G>A Multiple submitters hereditary folate malabsorption
  • c.*3785T>C Multiple submitters hereditary folate malabsorption
  • c.*3947G>A Multiple submitters hereditary folate malabsorption
  • c.*4030C>T Multiple submitters hereditary folate malabsorption
  • c.*4780C>T Multiple submitters hereditary folate malabsorption
  • c.*4884G>T Multiple submitters hereditary folate malabsorption
  • c.*928A>G Multiple submitters hereditary folate malabsorption
  • p.Ile409= Multiple submitters
  • c.*1243A>G Single submitter hereditary folate malabsorption
  • c.*1774A>G Single submitter hereditary folate malabsorption
  • c.*2217A>G Single submitter hereditary folate malabsorption
  • c.*2248T>C Single submitter hereditary folate malabsorption
  • c.*2746G>A Single submitter hereditary folate malabsorption
  • c.*2843G>A Single submitter hereditary folate malabsorption
  • c.*2968C>T Single submitter hereditary folate malabsorption
  • c.*4584C>T Single submitter hereditary folate malabsorption
  • c.*671C>T Single submitter hereditary folate malabsorption
  • c.*692A>T Single submitter hereditary folate malabsorption
  • c.*729G>A Single submitter hereditary folate malabsorption

Benign/Likely benign 6

  • c.228+17G>A Multiple submitters
  • p.Arg63Ser Multiple submitters hereditary folate malabsorption
  • p.Lys302= Multiple submitters hereditary folate malabsorption
  • p.Pro456Ser Multiple submitters
  • p.Thr295Ala Multiple submitters hereditary folate malabsorption
  • p.Val252= Multiple submitters hereditary folate malabsorption

Likely benign 116

Uncertain significance 201