SI — 1667 ClinVar variants

All ClinVar germline SI variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 733 flagged for review →

64 Pathogenic · 18 Pathogenic/Likely pathogenic · 77 Likely pathogenic · 92 Conflicting · 36 Benign · 26 Benign/Likely benign · 591 Likely benign · 763 Uncertain significance

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

⚑ Evidence disagreements 733

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 23

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

Predictors lean, ClinVar uncertain 376

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 376

Predictors split 333

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 333

All SI variants

Pathogenic 64

Pathogenic/Likely pathogenic 18

  • p.Arg1124Ter Multiple submitters Inborn genetic diseases
  • p.Arg1609Ter Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Asn1403fs Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Asp885fs Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Cys955Ter Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Gln1178Ter Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Gln278fs Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Gln278Ter Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Gln677fs Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Glu285Ter Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Glu613Ter Multiple submitters SI-related disorder
  • p.Glu801Ter Multiple submitters Congenital sucrose-isomaltase deficiency
  • p.His1210fs Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Leu1062_Tyr1063insTer Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Phe1366fs Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Phe637fs Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Ser982fs Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Val342fs Multiple submitters congenital sucrase-isomaltase deficiency

Likely pathogenic 77

Conflicting classifications of pathogenicity 92

  • c.1147-6T>A Single submitter congenital sucrase-isomaltase deficiency
  • c.118+10A>G Single submitter congenital sucrase-isomaltase deficiency
  • c.118+11C>T Single submitter congenital sucrase-isomaltase deficiency
  • c.1278+11A>G Single submitter congenital sucrase-isomaltase deficiency
  • c.1398+12T>C Single submitter congenital sucrase-isomaltase deficiency
  • c.1715+8C>A Single submitter congenital sucrase-isomaltase deficiency
  • c.1716-13G>A Single submitter congenital sucrase-isomaltase deficiency
  • c.2005-11C>T Single submitter congenital sucrase-isomaltase deficiency
  • c.2566-11A>G Single submitter congenital sucrase-isomaltase deficiency
  • c.2893-10G>A Single submitter congenital sucrase-isomaltase deficiency
  • c.3254+14T>G Single submitter congenital sucrase-isomaltase deficiency
  • c.3423+11A>G Single submitter congenital sucrase-isomaltase deficiency
  • c.3424-12T>C Single submitter congenital sucrase-isomaltase deficiency
  • c.373+11C>T Single submitter congenital sucrase-isomaltase deficiency
  • c.3760-7A>G Single submitter congenital sucrase-isomaltase deficiency
  • c.4062+11C>T Single submitter congenital sucrase-isomaltase deficiency
  • c.4062+17C>G Single submitter congenital sucrase-isomaltase deficiency
  • c.4540+4A>G Single submitter congenital sucrase-isomaltase deficiency
  • c.4692+12C>T Single submitter congenital sucrase-isomaltase deficiency
  • c.5108+13T>C Single submitter congenital sucrase-isomaltase deficiency
  • c.636-14C>T Single submitter congenital sucrase-isomaltase deficiency
  • c.808-14T>A Single submitter congenital sucrase-isomaltase deficiency
  • p.Ala1654Gly Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Ala404= Single submitter congenital sucrase-isomaltase deficiency
  • p.Ala893Val Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Arg1078= Single submitter congenital sucrase-isomaltase deficiency
  • p.Arg1367Gly Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Arg1768= Single submitter congenital sucrase-isomaltase deficiency
  • p.Arg434Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg52His Single submitter Inborn genetic diseases ⚠
  • p.Arg774Gly Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Asn1005Thr Single submitter Inborn genetic diseases ⚠
  • p.Asn1403= Single submitter congenital sucrase-isomaltase deficiency
  • p.Asn437= Single submitter congenital sucrase-isomaltase deficiency
  • p.Asp1261Asn Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Asp1413= Single submitter congenital sucrase-isomaltase deficiency
  • p.Asp1429Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp1623Ala Single submitter Inborn genetic diseases ⚠
  • p.Asp1801= Single submitter Inborn genetic diseases
  • p.Gln1000Pro Single submitter Inborn genetic diseases ⚠
  • p.Gln151= Single submitter congenital sucrase-isomaltase deficiency
  • p.Gln930Arg Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Gln953= Single submitter congenital sucrase-isomaltase deficiency
  • p.Glu1158Gln Single submitter Inborn genetic diseases ⚠
  • p.Glu1397= Single submitter congenital sucrase-isomaltase deficiency
  • p.Gly1073Asp Single submitter Inborn genetic diseases ⚠
  • p.Gly1302Ala Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Gly1760Asp Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Gly209= Single submitter congenital sucrase-isomaltase deficiency
  • p.Gly407Arg Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Gly515Val Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.His1598Leu Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.His1773= Single submitter congenital sucrase-isomaltase deficiency
  • p.Ile1378Ser Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Ile1756Val Single submitter Inborn genetic diseases ⚠
  • p.Ile22Thr Single submitter SI-related disorder ⚠
  • p.Ile389Asn Single submitter Inborn genetic diseases ⚠
  • p.Ile41= Single submitter congenital sucrase-isomaltase deficiency
  • p.Ile492Val Single submitter Inborn genetic diseases ⚠
  • p.Ile799Val Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Leu212= Single submitter Inborn genetic diseases
  • p.Leu321= Single submitter congenital sucrase-isomaltase deficiency
  • p.Met1196fs Single submitter congenital sucrase-isomaltase deficiency
  • p.Met119Leu Single submitter Inborn genetic diseases ⚠
  • p.Phe1745Cys Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Phe213= Single submitter congenital sucrase-isomaltase deficiency
  • p.Pro1140Ala Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Pro1324= Single submitter congenital sucrase-isomaltase deficiency
  • p.Pro267= Single submitter congenital sucrase-isomaltase deficiency
  • p.Pro348Leu Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Ser1795Leu Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Ser186Pro Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Thr1187Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr122Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr1258Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr1486= Single submitter congenital sucrase-isomaltase deficiency
  • p.Thr1574Ser Single submitter Inborn genetic diseases ⚠
  • p.Thr1606Ile Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Thr1767= Single submitter congenital sucrase-isomaltase deficiency
  • p.Thr1788Met Single submitter Inborn genetic diseases ⚠
  • p.Thr964= Single submitter congenital sucrase-isomaltase deficiency
  • p.Trp105Cys Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Tyr1243= Single submitter congenital sucrase-isomaltase deficiency
  • p.Tyr1417Ter Single submitter congenital sucrase-isomaltase deficiency
  • p.Tyr1650= Single submitter congenital sucrase-isomaltase deficiency
  • p.Tyr1789= Single submitter congenital sucrase-isomaltase deficiency
  • p.Tyr275= Single submitter congenital sucrase-isomaltase deficiency
  • p.Tyr975His Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Val1651Ile Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Val371Met Single submitter congenital sucrase-isomaltase deficiency ⚠
  • p.Val452= Single submitter congenital sucrase-isomaltase deficiency
  • p.Val577Gly Single submitter congenital sucrase-isomaltase deficiency ⚠

Benign 36

Benign/Likely benign 26

  • c.119-11dup Multiple submitters congenital sucrase-isomaltase deficiency
  • c.2244+14G>A Multiple submitters congenital sucrase-isomaltase deficiency
  • c.2301+20T>G Multiple submitters congenital sucrase-isomaltase deficiency
  • c.2737-11del Multiple submitters congenital sucrase-isomaltase deficiency
  • c.2737-12_2737-11del Multiple submitters congenital sucrase-isomaltase deficiency
  • c.2737-23dup Multiple submitters congenital sucrase-isomaltase deficiency
  • c.3634-5del Multiple submitters congenital sucrase-isomaltase deficiency
  • c.374-11del Multiple submitters congenital sucrase-isomaltase deficiency
  • c.374-11dup Multiple submitters congenital sucrase-isomaltase deficiency
  • c.4268-14T>C Multiple submitters congenital sucrase-isomaltase deficiency
  • c.4541-18T>G Multiple submitters congenital sucrase-isomaltase deficiency
  • c.483+4C>T Multiple submitters congenital sucrase-isomaltase deficiency
  • c.4841+9A>G Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Arg963= Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Asn406= Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Leu502= Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Lys1473Arg Multiple submitters Inborn genetic diseases
  • p.Pro173Ala Multiple submitters congenital sucrase-isomaltase deficiency ⚠
  • p.Ser200Gly Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Thr1342= Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Thr1348= Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Thr1425= Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Thr1802Ser Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Thr231Ser Multiple submitters congenital sucrase-isomaltase deficiency ⚠
  • p.Tyr781= Multiple submitters congenital sucrase-isomaltase deficiency
  • p.Val1667Ile Multiple submitters congenital sucrase-isomaltase deficiency

Likely benign 591

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

Uncertain significance 763

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