Sugi Variant

Sugi Variant/STXBP1

STXBP1 — 1200 ClinVar variants

All ClinVar germline STXBP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 278 flagged for review →

233 Pathogenic · 30 Pathogenic/Likely pathogenic · 121 Likely pathogenic · 53 Conflicting · 69 Benign · 31 Benign/Likely benign · 365 Likely benign · 298 Uncertain significance

Full STXBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 278

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 2

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

Predictors agree, ClinVar conflicts 31

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

Predictors lean, ClinVar uncertain 170

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 170

Predictors split 75

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

All STXBP1 variants

Pathogenic 233

Pathogenic/Likely pathogenic 30

  • c.1029+1G>A Multiple submitters Inborn genetic diseases
  • c.1030-2A>G Multiple submitters developmental and epileptic encephalopathy, 4
  • c.1110+2T>G Multiple submitters developmental and epileptic encephalopathy, 4
  • c.1461+1G>T Multiple submitters developmental and epileptic encephalopathy, 4
  • c.325+2_325+3del Multiple submitters developmental and epileptic encephalopathy, 4
  • c.326-1G>T Multiple submitters developmental and epileptic encephalopathy
  • c.579-1G>A Multiple submitters developmental and epileptic encephalopathy, 4
  • c.87+1G>A Multiple submitters early-infantile DEE
  • p.Arg292Cys Multiple submitters early-infantile DEE
  • p.Arg292His Multiple submitters Inborn genetic diseases
  • p.Arg406Cys Multiple submitters early-infantile DEE
  • p.Arg406His Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Arg406Leu Multiple submitters STXBP1-related disorder
  • p.Arg551His Multiple submitters Inborn genetic diseases
  • p.Arg551Ser Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Asp49fs Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Cys354Tyr Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Cys552Tyr Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Gln250Arg Multiple submitters Inborn genetic diseases
  • p.Glu283Lys Multiple submitters early-infantile DEE
  • p.Gly543Glu Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Leu281Pro Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Leu87fs Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Pro139Leu Multiple submitters early-infantile DEE ⚠
  • p.Pro187Leu Multiple submitters developmental and epileptic encephalopathy, 4
  • p.Pro335Ser Multiple submitters early-infantile DEE
  • p.Ser42Pro Multiple submitters early-infantile DEE
  • p.Tyr145Cys Multiple submitters early-infantile DEE
  • p.Tyr266Ter Multiple submitters early-infantile DEE
  • p.Tyr402Ter Multiple submitters developmental and epileptic encephalopathy, 4

Likely pathogenic 121

  • p.Cys110Arg Multiple submitters early-infantile DEE
  • p.Ile485Asn Multiple submitters STXBP1-related disorder
  • p.Leu287Pro Multiple submitters STXBP1-related disorder
  • p.Pro480Ser Multiple submitters early-infantile DEE ⚠
  • p.Trp288Arg Multiple submitters developmental and epileptic encephalopathy, 4
  • c.1110+1G>A Single submitter early-infantile DEE
  • c.1110+3A>C Single submitter developmental and epileptic encephalopathy, 4
  • c.1111-10_1111-6delinsG Single submitter cerebellar ataxia
  • c.1250-2A>G Single submitter early-infantile DEE
  • c.1359+5G>C Single submitter developmental and epileptic encephalopathy, 4
  • c.1360-2A>C Single submitter early-infantile DEE
  • c.1360-2A>T Single submitter early-infantile DEE
  • c.1547+1G>A Single submitter infantile spasms
  • c.1547+2T>C Single submitter STXBP1-related disorder
  • c.1547+2T>G Single submitter developmental and epileptic encephalopathy, 4
  • c.170-1G>A Single submitter developmental and epileptic encephalopathy, 4
  • c.170-3_325+2del Single submitter generalized epilepsy with febrile seizures plus, type 9
  • c.218_246+22del Single submitter early-infantile DEE
  • c.325+2T>A Single submitter developmental and epileptic encephalopathy
  • c.326-1G>C Single submitter developmental and epileptic encephalopathy, 4
  • c.429+2T>G Single submitter developmental and epileptic encephalopathy, 4
  • c.578+3A>T Single submitter developmental and epileptic encephalopathy, 4
  • c.578+49A>G Single submitter Inborn genetic diseases
  • c.664-1G>A Single submitter
  • c.902+4A>G Single submitter infantile epilepsy syndrome
  • c.963+3A>C Single submitter
  • p.Ala102del Single submitter developmental and epileptic encephalopathy, 4
  • p.Ala251Thr Single submitter STXBP1-related disorder
  • p.Ala297Ser Single submitter
  • p.Ala297Val Single submitter
  • p.Ala517Ser Single submitter ⚠
  • p.Ala553Pro Single submitter developmental and epileptic encephalopathy, 4
  • p.Arg292Pro Single submitter developmental and epileptic encephalopathy, 4
  • p.Arg325_Met330del Single submitter intellectual disability
  • p.Arg406Pro Single submitter early-infantile DEE
  • p.Arg406Ser Single submitter STXBP1-related disorder
  • p.Arg464Gly Single submitter developmental and epileptic encephalopathy, 4
  • p.Arg477fs Single submitter developmental and epileptic encephalopathy, 4
  • p.Arg65Ter Single submitter intellectual disability
  • p.Asn548Asp Single submitter infantile epilepsy syndrome ⚠
  • p.Asp151fs Single submitter developmental and epileptic encephalopathy, 4
  • p.Asp207Gly Single submitter developmental and epileptic encephalopathy, 4 ⚠
  • p.Asp234Gly Single submitter developmental and epileptic encephalopathy, 4
  • p.Asp262Tyr Single submitter developmental and epileptic encephalopathy, 4
  • p.Asp262Val Single submitter developmental and epileptic encephalopathy, 4
  • p.Asp90Gly Single submitter
  • p.Cys354Gly Single submitter early-infantile DEE
  • p.Cys354Phe Single submitter developmental and epileptic encephalopathy, 4
  • p.Cys552Phe Single submitter STXBP1-related disorder
  • p.Gln250Glu Single submitter developmental and epileptic encephalopathy, 4 ⚠
  • p.Gln336fs Single submitter STXBP1-related disorder
  • p.Glu185del Single submitter developmental and epileptic encephalopathy, 4
  • p.Glu185Gly Single submitter intellectual disability
  • p.Glu246Gln Single submitter
  • p.Glu369Lys Single submitter
  • p.Glu603Asp Single submitter developmental and epileptic encephalopathy
  • p.Gly236Asp Single submitter ⚠
  • p.Gly236Val Single submitter developmental and epileptic encephalopathy, 4
  • p.Gly417Ser Single submitter STXBP1-related disorder ⚠
  • p.Gly543fs Single submitter STXBP1-related disorder
  • p.Gly544Ser Single submitter developmental and epileptic encephalopathy, 4
  • p.His103Pro Single submitter developmental and epileptic encephalopathy, 4
  • p.His245Leu Single submitter STXBP1-related disorder
  • p.His347Asp Single submitter early-infantile DEE
  • p.His571fs Single submitter STXBP1-related disorder
  • p.Ile232Asn Single submitter
  • p.Ile418Phe Single submitter
  • p.Ile439Asn Single submitter early-infantile DEE
  • p.Ile439Phe Single submitter
  • p.Ile55Thr Single submitter
  • p.Leu118fs Single submitter STXBP1-related disorder
  • p.Leu138Pro Single submitter STXBP1-related disorder
  • p.Leu179His Single submitter
  • p.Leu231fs Single submitter developmental and epileptic encephalopathy, 4
  • p.Leu256Pro Single submitter
  • p.Leu257dup Single submitter
  • p.Leu291Pro Single submitter
  • p.Leu31Pro Single submitter developmental and epileptic encephalopathy, 4
  • p.Leu341Pro Single submitter
  • p.Leu348Pro Single submitter developmental and epileptic encephalopathy, 4
  • p.Leu36Ter Single submitter developmental and epileptic encephalopathy, 4
  • p.Leu41Gln Single submitter developmental and epileptic encephalopathy, 4
  • p.Leu426Arg Single submitter developmental and epileptic encephalopathy, 4
  • p.Leu87His Single submitter developmental and epileptic encephalopathy, 4
  • p.Lys184del Single submitter developmental and epileptic encephalopathy, 4
  • p.Lys332fs Single submitter developmental and epileptic encephalopathy, 4
  • p.Lys46Glu Single submitter Inborn genetic diseases
  • p.Met252Val Single submitter early-infantile DEE
  • p.Met316fs Single submitter developmental and epileptic encephalopathy, 4
  • p.Pro79Leu Single submitter developmental and epileptic encephalopathy, 4
  • p.Ser241Phe Single submitter developmental and epileptic encephalopathy, 4
  • p.Ser241Thr Single submitter ⚠
  • p.Ser241Tyr Single submitter
  • p.Ser306fs Single submitter
  • p.Ser313fs Single submitter developmental and epileptic encephalopathy, 4
  • p.Ser37_Met38insTer Single submitter
  • p.Ser42Cys Single submitter developmental and epileptic encephalopathy, 4
  • p.Ser569Phe Single submitter non-syndromic intellectual disability
  • p.Ser86fs Single submitter developmental and epileptic encephalopathy, 4
  • p.Thr129Pro Single submitter early-infantile DEE
  • p.Thr512fs Single submitter developmental and epileptic encephalopathy, 4
  • p.Thr570Ala Single submitter
  • p.Thr570Ile Single submitter
  • p.Thr581_Leu582insTer Single submitter intellectual disability
  • p.Trp288_Ile289delinsLeuVal Single submitter early-infantile DEE
  • p.Tyr145His Single submitter developmental and epileptic encephalopathy, 4
  • p.Tyr186Ter Single submitter STXBP1-related disorder
  • p.Tyr554Ser Single submitter developmental and epileptic encephalopathy, 4
  • p.Tyr554Ter Single submitter developmental and epileptic encephalopathy, 4
  • p.Tyr75Cys Single submitter early-infantile DEE
  • p.Tyr99Cys Single submitter developmental and epileptic encephalopathy, 4
  • p.Val30Met Single submitter early-infantile DEE ⚠
  • p.Val33Glu Single submitter early-infantile DEE
  • p.Arg406Gly No assertion criteria Epileptic encephalopathy
  • p.Glu491del No assertion criteria infantile epilepsy syndrome
  • p.His498fs No assertion criteria developmental and epileptic encephalopathy, 4
  • p.Leu231dup No assertion criteria infantile epilepsy syndrome
  • p.Met486Arg No assertion criteria developmental and epileptic encephalopathy, 4
  • p.Ser42Tyr No assertion criteria infantile epilepsy syndrome
  • p.Thr361Ile No assertion criteria Epileptic encephalopathy ⚠
  • p.Tyr358fs No assertion criteria Severe intellectual deficiency

Conflicting classifications of pathogenicity 53

Benign 69

Benign/Likely benign 31

Likely benign 365

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

Uncertain significance 298