CHRNA1 — 574 ClinVar variants

All ClinVar germline CHRNA1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 176 flagged for review →

24 Pathogenic · 8 Pathogenic/Likely pathogenic · 16 Likely pathogenic · 36 Conflicting · 40 Benign · 9 Benign/Likely benign · 164 Likely benign · 277 Uncertain significance

Full CHRNA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 176

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 13

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

Predictors lean, ClinVar uncertain 132

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

Predictors split 29

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

All CHRNA1 variants

Pathogenic 24

  • p.Gln59Ter Multiple submitters lethal multiple pterygium syndrome
  • c.345-63_403del Single submitter lethal multiple pterygium syndrome
  • p.Arg75fs Single submitter lethal multiple pterygium syndrome
  • p.Cys213Ter Single submitter lethal multiple pterygium syndrome
  • p.Glu282Ter Single submitter lethal multiple pterygium syndrome
  • p.Glu391Ter Single submitter lethal multiple pterygium syndrome
  • p.His45fs Single submitter lethal multiple pterygium syndrome
  • p.Ile361fs Single submitter lethal multiple pterygium syndrome
  • p.Ile98fs Single submitter lethal multiple pterygium syndrome
  • p.Lys127Ter Single submitter lethal multiple pterygium syndrome
  • p.Lys205Ter Single submitter lethal multiple pterygium syndrome
  • p.Lys360fs Single submitter lethal multiple pterygium syndrome
  • p.Trp196Ter Single submitter lethal multiple pterygium syndrome
  • p.Tyr83Ter Single submitter lethal multiple pterygium syndrome
  • c.235-353G>A No assertion criteria myasthenic syndrome, congenital, 1B, fast-channel
  • p.Asn237Lys No assertion criteria congenital myasthenic syndrome 1A
  • p.Cys148fs No assertion criteria myasthenic syndrome, congenital, 1B, fast-channel
  • p.Cys438Trp No assertion criteria congenital myasthenic syndrome 1A
  • p.Phe276Leu No assertion criteria myasthenic syndrome, congenital, 1B, fast-channel
  • p.Ser246Tyr No assertion criteria Slow-Channel Congenital Myasthenia Syndrome
  • p.Ser289Ile No assertion criteria congenital myasthenic syndrome 1A
  • p.Thr274Ile No assertion criteria congenital myasthenic syndrome 1A
  • p.Val152Leu No assertion criteria myasthenic syndrome, congenital, 1B, fast-channel
  • p.Val305Ile No assertion criteria myasthenic syndrome, congenital, 1B, fast-channel ⚠

Pathogenic/Likely pathogenic 8

  • p.Arg333Trp Multiple submitters lethal multiple pterygium syndrome
  • p.Gln131Ter Multiple submitters lethal multiple pterygium syndrome
  • p.Gly173Ser Multiple submitters myasthenic syndrome, congenital, 1B, fast-channel ⚠
  • p.Gly441Arg Multiple submitters centronuclear myopathy
  • p.Lys124Ter Multiple submitters CHRNA1-related disorders
  • p.Lys127fs Multiple submitters congenital myasthenic syndrome
  • p.Ser174fs Multiple submitters myasthenic syndrome, congenital, 1B, fast-channel
  • p.Trp106Ter No assertion criteria

Likely pathogenic 16

Conflicting classifications of pathogenicity 36

  • c.1002+9G>A Single submitter congenital myasthenic syndrome
  • c.235-323G>A Single submitter lethal multiple pterygium syndrome ⚠
  • c.-37A>G Single submitter congenital myasthenic syndrome
  • c.*411G>A Single submitter congenital myasthenic syndrome
  • c.*422G>T Single submitter congenital myasthenic syndrome
  • c.*499A>T Single submitter congenital myasthenic syndrome
  • p.Ala395Val Single submitter Inborn genetic diseases ⚠
  • p.Ala444= Single submitter congenital myasthenic syndrome
  • p.Arg107Cys Single submitter Inborn genetic diseases
  • p.Arg229His Single submitter congenital myasthenic syndrome ⚠
  • p.Arg229Leu Single submitter CHRNA1-related disorders ⚠
  • p.Arg46His Single submitter lethal multiple pterygium syndrome ⚠
  • p.Arg75His Single submitter congenital myasthenic syndrome
  • p.Asn237= Single submitter congenital myasthenic syndrome
  • p.Asp91Asn Single submitter myasthenic syndrome, congenital, 1B, fast-channel
  • p.Gln68= Single submitter
  • p.Glu22Lys Single submitter lethal multiple pterygium syndrome ⚠
  • p.Glu355Gly Single submitter lethal multiple pterygium syndrome
  • p.Gly260Trp Single submitter congenital myasthenic syndrome 1A ⚠
  • p.Gly381= Single submitter lethal multiple pterygium syndrome
  • p.Gly432Arg Single submitter congenital myasthenic syndrome ⚠
  • p.Gly94Cys Single submitter lethal multiple pterygium syndrome ⚠
  • p.Ile235= Single submitter congenital myasthenic syndrome
  • p.Ile316= Single submitter lethal multiple pterygium syndrome
  • p.Leu219= Single submitter congenital myasthenic syndrome
  • p.Leu431= Single submitter congenital myasthenic syndrome
  • p.Lys356Thr Single submitter Inborn genetic diseases
  • p.Met1Thr Single submitter congenital myasthenic syndrome
  • p.Met1Val Single submitter lethal multiple pterygium syndrome
  • p.Met380Thr Single submitter lethal multiple pterygium syndrome ⚠
  • p.Phe304= Single submitter lethal multiple pterygium syndrome
  • p.Ser246Phe Single submitter lethal multiple pterygium syndrome ⚠
  • p.Ser37= Single submitter congenital myasthenic syndrome
  • p.Thr312Asn Single submitter Inborn genetic diseases ⚠
  • p.Val226Ile Single submitter Inborn genetic diseases ⚠
  • p.Val269Phe Single submitter Inborn genetic diseases ⚠

Benign 40

Benign/Likely benign 9

  • c.189+12G>A Multiple submitters lethal multiple pterygium syndrome
  • c.190-5del Multiple submitters congenital myasthenic syndrome 1A
  • c.779-14_779-12del Multiple submitters
  • c.*218C>T Multiple submitters congenital myasthenic syndrome
  • c.*426C>A Multiple submitters congenital myasthenic syndrome
  • p.Asp215Asn Multiple submitters congenital myasthenic syndrome
  • p.Glu411Asp Multiple submitters congenital myasthenic syndrome
  • p.Pro241= Multiple submitters congenital myasthenic syndrome
  • p.Ser207= Multiple submitters lethal multiple pterygium syndrome

Likely benign 164

  • c.1242+10G>A Multiple submitters lethal multiple pterygium syndrome
  • c.189+16T>A Multiple submitters lethal multiple pterygium syndrome
  • c.235-358T>C Multiple submitters
  • c.344+74G>A Multiple submitters
  • c.345-130C>T Multiple submitters
  • c.345-98C>T Multiple submitters
  • c.44-118G>A Multiple submitters
  • c.778+201G>A Multiple submitters
  • c.778+316C>G Multiple submitters
  • c.779-124C>T Multiple submitters
  • c.-8G>A Multiple submitters
  • p.Asp172= Multiple submitters lethal multiple pterygium syndrome
  • p.Ile440= Multiple submitters lethal multiple pterygium syndrome
  • p.Leu265= Multiple submitters lethal multiple pterygium syndrome
  • p.Lys124= Multiple submitters lethal multiple pterygium syndrome
  • p.Phe245= Multiple submitters lethal multiple pterygium syndrome
  • p.Ser182= Multiple submitters lethal multiple pterygium syndrome
  • p.Thr137= Multiple submitters lethal multiple pterygium syndrome
  • p.Tyr171= Multiple submitters lethal multiple pterygium syndrome
  • p.Val175= Multiple submitters lethal multiple pterygium syndrome
  • c.1002+10G>C Single submitter lethal multiple pterygium syndrome
  • c.1002+120C>T Single submitter
  • c.1002+14C>G Single submitter lethal multiple pterygium syndrome
  • c.1002+14C>T Single submitter lethal multiple pterygium syndrome
  • c.1002+17C>G Single submitter lethal multiple pterygium syndrome
  • c.1003-12_1003-8del Single submitter lethal multiple pterygium syndrome
  • c.1003-12T>A Single submitter lethal multiple pterygium syndrome
  • c.1003-6T>C Single submitter lethal multiple pterygium syndrome
  • c.1003-8T>C Single submitter lethal multiple pterygium syndrome
  • c.1003-9T>A Single submitter lethal multiple pterygium syndrome
  • c.1003-9T>C Single submitter lethal multiple pterygium syndrome
  • c.1242+11T>A Single submitter lethal multiple pterygium syndrome
  • c.1242+17G>A Single submitter lethal multiple pterygium syndrome
  • c.1243-7C>T Single submitter lethal multiple pterygium syndrome
  • c.189+18G>A Single submitter lethal multiple pterygium syndrome
  • c.189+7_189+8insCCT Single submitter lethal multiple pterygium syndrome
  • c.190-11T>G Single submitter lethal multiple pterygium syndrome
  • c.190-12T>A Single submitter lethal multiple pterygium syndrome
  • c.190-18C>T Single submitter lethal multiple pterygium syndrome
  • c.234+33T>C Single submitter
  • c.235-14G>A Single submitter lethal multiple pterygium syndrome
  • c.235-18G>A Single submitter lethal multiple pterygium syndrome
  • c.235-19T>C Single submitter lethal multiple pterygium syndrome
  • c.235-20C>T Single submitter lethal multiple pterygium syndrome
  • c.235-518C>G Single submitter
  • c.235-8G>T Single submitter lethal multiple pterygium syndrome
  • c.235-9dup Single submitter lethal multiple pterygium syndrome
  • c.344+12G>C Single submitter lethal multiple pterygium syndrome
  • c.344+14A>G Single submitter lethal multiple pterygium syndrome
  • c.344+15T>C Single submitter lethal multiple pterygium syndrome
  • c.344+17G>C Single submitter lethal multiple pterygium syndrome
  • c.345-10C>T Single submitter lethal multiple pterygium syndrome
  • c.345-14T>A Single submitter lethal multiple pterygium syndrome
  • c.345-19T>A Single submitter lethal multiple pterygium syndrome
  • c.345-7del Single submitter lethal multiple pterygium syndrome
  • c.43+11G>A Single submitter lethal multiple pterygium syndrome
  • c.43+13G>T Single submitter
  • c.43+20G>T Single submitter lethal multiple pterygium syndrome
  • c.44-10G>A Single submitter
  • c.44-10G>T Single submitter lethal multiple pterygium syndrome
  • c.44-5C>G Single submitter lethal multiple pterygium syndrome
  • c.44-9C>A Single submitter lethal multiple pterygium syndrome
  • c.540+16A>C Single submitter lethal multiple pterygium syndrome
  • c.540+17T>A Single submitter lethal multiple pterygium syndrome
  • c.540+7G>A Single submitter lethal multiple pterygium syndrome
  • c.541-12T>C Single submitter lethal multiple pterygium syndrome
  • c.541-13C>T Single submitter lethal multiple pterygium syndrome
  • c.541-15del Single submitter lethal multiple pterygium syndrome
  • c.541-17del Single submitter lethal multiple pterygium syndrome
  • c.541-20A>C Single submitter lethal multiple pterygium syndrome
  • c.778+145C>T Single submitter
  • c.778+18G>A Single submitter lethal multiple pterygium syndrome
  • c.779-12_779-11del Single submitter lethal multiple pterygium syndrome
  • c.779-13_779-11del Single submitter lethal multiple pterygium syndrome
  • c.779-15_779-12del Single submitter
  • c.779-28dup Single submitter
  • c.779-5T>C Single submitter lethal multiple pterygium syndrome
  • c.-13G>A Single submitter
  • c.-17A>C Single submitter
  • p.Ala290= Single submitter lethal multiple pterygium syndrome
  • p.Ala416= Single submitter lethal multiple pterygium syndrome
  • p.Ala423= Single submitter lethal multiple pterygium syndrome
  • p.Arg40= Single submitter lethal multiple pterygium syndrome
  • p.Asn179Ser Single submitter lethal multiple pterygium syndrome
  • p.Asn413= Single submitter
  • p.Asp109= Single submitter lethal multiple pterygium syndrome
  • p.Asp90= Single submitter lethal multiple pterygium syndrome
  • p.Cys213= Single submitter lethal multiple pterygium syndrome
  • p.Cys438= Single submitter lethal multiple pterygium syndrome
  • p.Gln357= Single submitter lethal multiple pterygium syndrome
  • p.Gln47= Single submitter lethal multiple pterygium syndrome
  • p.Glu195= Single submitter lethal multiple pterygium syndrome
  • p.Glu200= Single submitter lethal multiple pterygium syndrome
  • p.Glu404= Single submitter lethal multiple pterygium syndrome
  • p.Glu418= Single submitter lethal multiple pterygium syndrome
  • p.Gly250= Single submitter lethal multiple pterygium syndrome
  • p.Gly260= Single submitter lethal multiple pterygium syndrome
  • p.Gly376= Single submitter lethal multiple pterygium syndrome
  • p.Gly398= Single submitter lethal multiple pterygium syndrome
  • p.Gly93= Single submitter lethal multiple pterygium syndrome
  • p.His206= Single submitter lethal multiple pterygium syndrome
  • p.His224= Single submitter lethal multiple pterygium syndrome
  • p.His428= Single submitter lethal multiple pterygium syndrome
  • p.Ile151= Single submitter lethal multiple pterygium syndrome
  • p.Ile239= Single submitter lethal multiple pterygium syndrome
  • p.Ile267= Single submitter lethal multiple pterygium syndrome
  • p.Ile280= Single submitter lethal multiple pterygium syndrome
  • p.Ile309= Single submitter lethal multiple pterygium syndrome
  • p.Ile314= Single submitter lethal multiple pterygium syndrome
  • p.Ile361= Single submitter lethal multiple pterygium syndrome
  • p.Ile387= Single submitter lethal multiple pterygium syndrome
  • p.Ile396= Single submitter lethal multiple pterygium syndrome
  • p.Ile402= Single submitter lethal multiple pterygium syndrome
  • p.Ile69= Single submitter lethal multiple pterygium syndrome
  • p.Leu110= Single submitter lethal multiple pterygium syndrome
  • p.Leu129= Single submitter lethal multiple pterygium syndrome
  • p.Leu17= Single submitter lethal multiple pterygium syndrome
  • p.Leu187= Single submitter lethal multiple pterygium syndrome
  • p.Leu255= Single submitter lethal multiple pterygium syndrome
  • p.Leu271= Single submitter lethal multiple pterygium syndrome
  • p.Leu299= Single submitter lethal multiple pterygium syndrome
  • p.Leu443= Single submitter lethal multiple pterygium syndrome
  • p.Leu6= Single submitter lethal multiple pterygium syndrome
  • p.Leu85= Single submitter lethal multiple pterygium syndrome
  • p.Lys356= Single submitter lethal multiple pterygium syndrome
  • p.Lys96= Single submitter lethal multiple pterygium syndrome
  • p.Phe225= Single submitter lethal multiple pterygium syndrome
  • p.Phe276= Single submitter lethal multiple pterygium syndrome
  • p.Pro101= Single submitter lethal multiple pterygium syndrome
  • p.Pro108= Single submitter lethal multiple pterygium syndrome
  • p.Pro214= Single submitter lethal multiple pterygium syndrome
  • p.Pro217= Single submitter lethal multiple pterygium syndrome
  • p.Pro292= Single submitter lethal multiple pterygium syndrome
  • p.Pro379= Single submitter lethal multiple pterygium syndrome
  • p.Pro390= Single submitter lethal multiple pterygium syndrome
  • p.Pro5= Single submitter
  • p.Ser193= Single submitter lethal multiple pterygium syndrome
  • p.Ser21= Single submitter lethal multiple pterygium syndrome
  • p.Ser246= Single submitter lethal multiple pterygium syndrome
  • p.Ser288= Single submitter lethal multiple pterygium syndrome
  • p.Ser308= Single submitter lethal multiple pterygium syndrome
  • p.Ser384= Single submitter lethal multiple pterygium syndrome
  • p.Thr133= Single submitter lethal multiple pterygium syndrome
  • p.Thr153= Single submitter lethal multiple pterygium syndrome
  • p.Thr170= Single submitter lethal multiple pterygium syndrome
  • p.Thr216= Single submitter lethal multiple pterygium syndrome
  • p.Thr25= Single submitter lethal multiple pterygium syndrome
  • p.Thr287= Single submitter lethal multiple pterygium syndrome
  • p.Thr301= Single submitter lethal multiple pterygium syndrome
  • p.Thr318= Single submitter lethal multiple pterygium syndrome
  • p.Thr325= Single submitter lethal multiple pterygium syndrome
  • p.Thr405= Single submitter lethal multiple pterygium syndrome
  • p.Thr442= Single submitter lethal multiple pterygium syndrome
  • p.Thr52= Single submitter lethal multiple pterygium syndrome
  • p.Tyr218= Single submitter lethal multiple pterygium syndrome
  • p.Tyr223= Single submitter lethal multiple pterygium syndrome
  • p.Tyr421= Single submitter lethal multiple pterygium syndrome
  • p.Tyr92= Single submitter
  • p.Val197= Single submitter lethal multiple pterygium syndrome
  • p.Val236= Single submitter lethal multiple pterygium syndrome
  • p.Val315= Single submitter lethal multiple pterygium syndrome
  • p.Val48= Single submitter lethal multiple pterygium syndrome
  • c.-9C>T No assertion criteria CHRNA1-related disorder
  • p.Val152= No assertion criteria CHRNA1-related disorder

Uncertain significance 277