Sugi Variant

Sugi Variant/SPTBN1

SPTBN1 — 762 ClinVar variants

All ClinVar germline SPTBN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 498 flagged for review →

26 Pathogenic · 1 Pathogenic/Likely pathogenic · 48 Likely pathogenic · 6 Conflicting · 10 Benign · 5 Benign/Likely benign · 118 Likely benign · 548 Uncertain significance

Full SPTBN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 498

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 4

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

Predicted LoF vs a conflicting call 2

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 340

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 340

Predictors split 149

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

All SPTBN1 variants

Pathogenic 26

  • p.Arg1745Ter Multiple submitters developmental delay, impaired speech, and behavioral abnormalities
  • c.4997+1G>A Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • c.5961+2T>C Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Ala1373fs Single submitter Inborn genetic diseases
  • p.Arg289Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Arg610Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Arg83Ter Single submitter
  • p.Gln1285fs Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Gln2126Ter Single submitter
  • p.Glu713fs Single submitter
  • p.Glu973fs Single submitter
  • p.Gly1769fs Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Ile324fs Single submitter Inborn genetic diseases
  • p.Leu1175fs Single submitter Inborn genetic diseases
  • p.Phe618fs Single submitter
  • p.Ser1447fs Single submitter Inborn genetic diseases
  • p.Thr268Ser Single submitter SPTBN1-related disorder
  • p.Thr59Ser Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Trp1574fs Single submitter neurodevelopmental disorder
  • p.Trp182del Single submitter
  • p.Trp759fs Single submitter pervasive developmental disorder
  • p.Cys183Ter No assertion criteria developmental delay, impaired speech, and behavioral abnormalities
  • p.Glu1886Gln No assertion criteria developmental delay, impaired speech, and behavioral abnormalities ⚠
  • p.Glu892Ter No assertion criteria developmental delay, impaired speech, and behavioral abnormalities
  • p.Gly205Asp No assertion criteria developmental delay, impaired speech, and behavioral abnormalities
  • p.Leu250Arg No assertion criteria developmental delay, impaired speech, and behavioral abnormalities

Pathogenic/Likely pathogenic 1

  • p.Ala1086Thr Multiple submitters SPTBN1-related neurodevelopmental disease ⚠

Likely pathogenic 48

  • p.Arg1054Ter Multiple submitters developmental delay, impaired speech, and behavioral abnormalities
  • p.Val271Met Multiple submitters neurodevelopmental disorder
  • c.3564+1G>A Single submitter Inborn genetic diseases
  • c.3564+1G>C Single submitter
  • c.3859-2A>G Single submitter SPTBN1-related disorder
  • c.4494+1G>A Single submitter
  • c.4495-2A>T Single submitter
  • c.475-1G>A Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • c.475-1G>T Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • c.4998-607G>T Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • c.6244-1G>C Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • c.6353_6356+15del Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Ala2244Asp Single submitter ⚠
  • p.Arg107Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Arg109His Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Arg1739Ter Single submitter SPTBN1-related disorder
  • p.Arg348Pro Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Arg411Trp Single submitter
  • p.Arg477Cys Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Asp1177fs Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Gln1172Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Gln1282Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Gln1423Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Gln1528Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Gln696Ter Single submitter
  • p.Gln725fs Single submitter SPTBN1-related disorder
  • p.Gln812Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Glu131Ter Single submitter SPTBN1-related disorder
  • p.Glu1363Ter Single submitter SPTBN1-related disorder
  • p.Glu1435Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Glu1986Ter Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Glu2093Ter Single submitter
  • p.Glu254Lys Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Glu491Gln Single submitter ⚠
  • p.His196Tyr Single submitter developmental delay, impaired speech, and behavioral abnormalities ⚠
  • p.Leu1314fs Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Leu250Val Single submitter Neurodevelopmental delay
  • p.Leu251Ser Single submitter
  • p.Lys249fs Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Phe1184fs Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Phe157Leu Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Ser1388fs Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Thr59Ile Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Thr671Asn Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Trp1787Ter Single submitter SPTBN1-related disorder
  • p.Trp641Ter Single submitter neurodevelopmental disorder
  • p.Val64Phe Single submitter developmental delay, impaired speech, and behavioral abnormalities
  • p.Trp1893Ter No assertion criteria developmental delay, impaired speech, and behavioral abnormalities

Conflicting classifications of pathogenicity 6

  • c.474+1G>T Single submitter developmental delay, impaired speech, and behavioral abnormalities ⚠
  • p.Arg1003Trp Single submitter SPTBN1-related disorder ⚠
  • p.Arg1036Gln Single submitter developmental delay, impaired speech, and behavioral abnormalities ⚠
  • p.Arg1593Lys Single submitter Inborn genetic diseases ⚠
  • p.Asn873Asp Single submitter Inborn genetic diseases ⚠
  • p.Asp1912fs Single submitter Inborn genetic diseases ⚠

Benign 10

Benign/Likely benign 5

Likely benign 118

Uncertain significance 548

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