Sugi Variant

Sugi Variant/SMS

SMS — 208 ClinVar variants

All ClinVar germline SMS variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 89 flagged for review →

12 Pathogenic · 2 Pathogenic/Likely pathogenic · 20 Likely pathogenic · 6 Conflicting · 26 Benign · 9 Benign/Likely benign · 37 Likely benign · 96 Uncertain significance

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

⚑ Evidence disagreements 89

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 3

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

Predictors agree, ClinVar conflicts 2

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

Predictors lean, ClinVar uncertain 59

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

Predictors split 25

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

All SMS variants

Pathogenic 12

  • p.Gly203Asp Multiple submitters syndromic X-linked intellectual disability Snyder type
  • p.Gly56Ser Multiple submitters Inborn genetic diseases ⚠
  • c.661-13A>C Single submitter syndromic X-linked intellectual disability Snyder type
  • p.Arg130Cys Single submitter syndromic X-linked intellectual disability Snyder type
  • p.Cys318Trp Single submitter syndromic X-linked intellectual disability Snyder type
  • p.Gly67Glu Single submitter syndromic X-linked intellectual disability Snyder type
  • p.Met303fs Single submitter syndromic X-linked intellectual disability Snyder type
  • c.329+5G>A No assertion criteria syndromic X-linked intellectual disability Snyder type
  • p.Gln148Arg No assertion criteria syndromic X-linked intellectual disability Snyder type
  • p.Ser302Leu No assertion criteria intellectual disability
  • p.Tyr328Cys No assertion criteria syndromic X-linked intellectual disability Snyder type
  • p.Val132Gly No assertion criteria syndromic X-linked intellectual disability Snyder type ⚠

Pathogenic/Likely pathogenic 2

Likely pathogenic 20

  • p.Ile196Thr Multiple submitters syndromic X-linked intellectual disability Snyder type
  • c.865+2T>C Single submitter syndromic X-linked intellectual disability Snyder type
  • p.Arg116Ter Single submitter SMS-related disorder
  • p.Asp137Gly Single submitter syndromic X-linked intellectual disability Snyder type
  • p.Asp222Val Single submitter
  • p.Gln148Glu Single submitter syndromic X-linked intellectual disability Snyder type
  • p.Gly117Val Single submitter ⚠
  • p.Gly203Val Single submitter syndromic X-linked intellectual disability Snyder type
  • p.Leu277Phe Single submitter
  • p.Met233Val Single submitter ⚠
  • p.Pro112Gln Single submitter syndromic X-linked intellectual disability Snyder type ⚠
  • p.Pro213Gln Single submitter Inborn genetic diseases
  • p.Pro349Thr Single submitter
  • p.Trp292Leu Single submitter
  • p.Tyr134His Single submitter
  • p.Val194Gly Single submitter Smith-Magenis syndrome
  • p.Val225Ala Single submitter syndromic X-linked intellectual disability Snyder type
  • c.661-1C>T No assertion criteria SMS-related disorder
  • p.Arg110Gly No assertion criteria syndromic X-linked intellectual disability Snyder type ⚠
  • p.Gly67Val No assertion criteria SMS-related disorder

Conflicting classifications of pathogenicity 6

  • c.661-5C>T Single submitter Inborn genetic diseases
  • p.Arg110Gln Single submitter syndromic X-linked intellectual disability Snyder type ⚠
  • p.Glu340Gly Single submitter syndromic X-linked intellectual disability Snyder type ⚠
  • p.Gly238= Single submitter Inborn genetic diseases
  • p.Ser326= Single submitter Inborn genetic diseases
  • p.Tyr51Cys Single submitter syndromic X-linked intellectual disability Snyder type ⚠

Benign 26

Benign/Likely benign 9

Likely benign 37

Uncertain significance 96