SNAP25 — 255 ClinVar variants

All ClinVar germline SNAP25 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 67 flagged for review →

1 Pathogenic · 5 Pathogenic/Likely pathogenic · 19 Likely pathogenic · 10 Conflicting · 23 Benign · 2 Benign/Likely benign · 108 Likely benign · 87 Uncertain significance

Full SNAP25 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 67

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 6

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 40

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

Predictors split 19

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

All SNAP25 variants

Pathogenic 1

  • p.Gln177Ter Single submitter congenital myasthenic syndrome 18

Pathogenic/Likely pathogenic 5

  • p.Ala199Glu Multiple submitters developmental and epileptic encephalopathy, 2
  • p.Ala199Gly Multiple submitters Severe intellectual disability
  • p.Gly43Arg Multiple submitters SNAP25-related disorder
  • p.Ile67Asn Multiple submitters Inborn genetic diseases
  • p.Met71Thr Multiple submitters SNAP25-related disorder ⚠

Likely pathogenic 19

  • p.Arg198Pro Multiple submitters developmental and epileptic encephalopathy
  • p.Gln197Ter Multiple submitters neurodevelopmental disorder
  • p.Lys40Glu Multiple submitters Global developmental delay ⚠
  • p.Val48Phe Multiple submitters epilepsy with generalized tonic-clonic seizures
  • c.114_114+6del Single submitter Inborn genetic diseases
  • c.114+1G>A Single submitter
  • c.114+2T>G Single submitter developmental and epileptic encephalopathy
  • c.164-252del Single submitter presynaptic congenital myasthenic syndrome
  • c.72+1G>A Single submitter developmental and epileptic encephalopathy
  • p.Ala185Pro Single submitter congenital myasthenic syndrome 18
  • p.Arg176_Gln177insGluIleAspThrGlnAsnArg Single submitter congenital myasthenic syndrome 18
  • p.Asp166Gly Single submitter developmental and epileptic encephalopathy
  • p.Asp166Tyr Single submitter developmental and epileptic encephalopathy
  • p.Gln174Pro Single submitter developmental and epileptic encephalopathy
  • p.Ile181Asn Single submitter congenital myasthenic syndrome 18
  • p.Leu50Ser Single submitter developmental and epileptic encephalopathy
  • p.Leu57Arg Single submitter developmental and epileptic encephalopathy
  • p.Leu57Pro Single submitter congenital myasthenic syndrome 18
  • p.Lys184del Single submitter congenital myasthenic syndrome 18

Conflicting classifications of pathogenicity 10

  • p.Ala199Val Single submitter congenital myasthenic syndrome 18 ⚠
  • p.Arg30His Single submitter Inborn genetic diseases ⚠
  • p.Asp172Asn Single submitter congenital myasthenic syndrome 18 ⚠
  • p.Asp99Val Single submitter congenital myasthenic syndrome 18 ⚠
  • p.Gln174Ter Single submitter developmental and epileptic encephalopathy ⚠
  • p.Gln66Pro Single submitter developmental and epileptic encephalopathy ⚠
  • p.Ile192Thr Single submitter developmental and epileptic encephalopathy ⚠
  • p.Lys201Ter Single submitter developmental and epileptic encephalopathy ⚠
  • p.Met163Arg Single submitter congenital myasthenic syndrome 18 ⚠
  • p.Ser25Leu Single submitter congenital myasthenic syndrome 18 ⚠

Benign 23

Benign/Likely benign 2

  • c.281+16C>T Multiple submitters congenital myasthenic syndrome 18
  • p.Ala5Thr Multiple submitters congenital myasthenic syndrome 18

Likely benign 108

  • c.114+18T>C Multiple submitters congenital myasthenic syndrome 18
  • c.115-20C>G Multiple submitters congenital myasthenic syndrome 18
  • c.163+177T>G Multiple submitters
  • c.164-263C>T Multiple submitters Inborn genetic diseases
  • c.282-11C>G Multiple submitters congenital myasthenic syndrome 18
  • c.552+8C>T Multiple submitters congenital myasthenic syndrome 18
  • c.552+9G>A Multiple submitters congenital myasthenic syndrome 18
  • c.72+110G>A Multiple submitters
  • c.-34C>A Multiple submitters
  • c.-9A>G Multiple submitters
  • c.*271C>T Multiple submitters
  • p.Ala2= Multiple submitters Inborn genetic diseases
  • p.Asp122= Multiple submitters Inborn genetic diseases
  • p.Gln20= Multiple submitters congenital myasthenic syndrome 18
  • p.Gly132Ser Multiple submitters Inborn genetic diseases
  • p.Ile157= Multiple submitters congenital myasthenic syndrome 18
  • p.Ile178= Multiple submitters Inborn genetic diseases
  • p.Ser154= Multiple submitters Inborn genetic diseases
  • p.Val121= Multiple submitters congenital myasthenic syndrome 18
  • c.114+13A>G Single submitter congenital myasthenic syndrome 18
  • c.114+16A>G Single submitter congenital myasthenic syndrome 18
  • c.114+7A>G Single submitter congenital myasthenic syndrome 18
  • c.114+8G>A Single submitter congenital myasthenic syndrome 18
  • c.115-12A>G Single submitter congenital myasthenic syndrome 18
  • c.163+12T>C Single submitter congenital myasthenic syndrome 18
  • c.163+20G>A Single submitter congenital myasthenic syndrome 18
  • c.164-10G>T Single submitter congenital myasthenic syndrome 18
  • c.164-257A>C Single submitter Inborn genetic diseases
  • c.164-4T>C Single submitter congenital myasthenic syndrome 18
  • c.164-510T>C Single submitter
  • c.164-8T>A Single submitter congenital myasthenic syndrome 18
  • c.281+13T>A Single submitter congenital myasthenic syndrome 18
  • c.281+17T>C Single submitter congenital myasthenic syndrome 18
  • c.281+18G>C Single submitter congenital myasthenic syndrome 18
  • c.282-14T>C Single submitter
  • c.282-15C>G Single submitter congenital myasthenic syndrome 18
  • c.282-17C>T Single submitter congenital myasthenic syndrome 18
  • c.282-20T>A Single submitter congenital myasthenic syndrome 18
  • c.282-20T>G Single submitter congenital myasthenic syndrome 18
  • c.282-218A>G Single submitter
  • c.407+11T>A Single submitter congenital myasthenic syndrome 18
  • c.407+11T>C Single submitter congenital myasthenic syndrome 18
  • c.407+12G>A Single submitter congenital myasthenic syndrome 18
  • c.407+16C>G Single submitter congenital myasthenic syndrome 18
  • c.407+18T>C Single submitter congenital myasthenic syndrome 18
  • c.407+5_407+19dup Single submitter congenital myasthenic syndrome 18
  • c.408-11T>G Single submitter congenital myasthenic syndrome 18
  • c.408-14T>C Single submitter congenital myasthenic syndrome 18
  • c.408-18T>G Single submitter congenital myasthenic syndrome 18
  • c.408-19C>T Single submitter congenital myasthenic syndrome 18
  • c.408-8G>A Single submitter congenital myasthenic syndrome 18
  • c.408-9G>T Single submitter congenital myasthenic syndrome 18
  • c.552+12G>T Single submitter congenital myasthenic syndrome 18
  • c.552+280A>T Single submitter
  • c.553-12C>T Single submitter congenital myasthenic syndrome 18
  • c.553-13C>T Single submitter congenital myasthenic syndrome 18
  • c.553-163A>C Single submitter
  • c.553-217C>T Single submitter
  • c.72+11GA[3] Single submitter congenital myasthenic syndrome 18
  • c.72+13G>A Single submitter congenital myasthenic syndrome 18
  • c.72+7A>C Single submitter congenital myasthenic syndrome 18
  • c.73-12T>C Single submitter congenital myasthenic syndrome 18
  • c.73-16del Single submitter congenital myasthenic syndrome 18
  • c.73-5C>T Single submitter congenital myasthenic syndrome 18
  • c.73-61T>C Single submitter
  • c.73-9A>G Single submitter congenital myasthenic syndrome 18
  • c.-63-286C>T Single submitter
  • c.-6G>A Single submitter
  • c.*13G>A Single submitter
  • p.Arg135= Single submitter congenital myasthenic syndrome 18
  • p.Arg142= Single submitter congenital myasthenic syndrome 18
  • p.Arg142Ter Single submitter congenital myasthenic syndrome 18
  • p.Arg17= Single submitter congenital myasthenic syndrome 18
  • p.Arg176= Single submitter congenital myasthenic syndrome 18
  • p.Arg198= Single submitter congenital myasthenic syndrome 18
  • p.Arg31= Single submitter congenital myasthenic syndrome 18
  • p.Arg8= Single submitter Inborn genetic diseases
  • p.Asn9= Single submitter congenital myasthenic syndrome 18
  • p.Asp172= Single submitter congenital myasthenic syndrome 18
  • p.Asp23= Single submitter congenital myasthenic syndrome 18
  • p.Asp4= Single submitter congenital myasthenic syndrome 18
  • p.Asp51= Single submitter
  • p.Gln126= Single submitter congenital myasthenic syndrome 18
  • p.Gln197= Single submitter congenital myasthenic syndrome 18
  • p.Gln20_Asp23del Single submitter congenital myasthenic syndrome 18
  • p.Glu143Gln Single submitter congenital myasthenic syndrome 18
  • p.Glu55= Single submitter congenital myasthenic syndrome 18
  • p.Glu61= Single submitter congenital myasthenic syndrome 18
  • p.Glu62= Single submitter congenital myasthenic syndrome 18
  • p.Gly111= Single submitter congenital myasthenic syndrome 18
  • p.Gly111Arg Single submitter congenital myasthenic syndrome 18 ⚠
  • p.Gly131= Single submitter congenital myasthenic syndrome 18
  • p.Gly158Arg Single submitter congenital myasthenic syndrome 18
  • p.Gly43= Single submitter congenital myasthenic syndrome 18
  • p.Gly63= Single submitter congenital myasthenic syndrome 18
  • p.Ile171= Single submitter congenital myasthenic syndrome 18
  • p.Ile60= Single submitter congenital myasthenic syndrome 18
  • p.Leu165= Single submitter congenital myasthenic syndrome 18
  • p.Leu21= Single submitter congenital myasthenic syndrome 18
  • p.Leu35= Single submitter congenital myasthenic syndrome 18
  • p.Leu47= Single submitter congenital myasthenic syndrome 18
  • p.Leu50= Single submitter congenital myasthenic syndrome 18
  • p.Pro117= Single submitter congenital myasthenic syndrome 18
  • p.Ser115= Single submitter congenital myasthenic syndrome 18
  • p.Ser25= Single submitter congenital myasthenic syndrome 18
  • p.Ser28= Single submitter congenital myasthenic syndrome 18
  • p.Thr79= Single submitter
  • c.72+10G>A No assertion criteria SNAP25-related disorder

Uncertain significance 87