BEAN1 — 115 ClinVar variants
All ClinVar germline BEAN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 65 flagged for review →
3 Conflicting · 14 Benign · 1 Benign/Likely benign · 34 Likely benign · 63 Uncertain significance
Full BEAN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 65
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 3
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
Predictors lean, ClinVar uncertain 42
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- BEAN1 p.Ala156Ser Uncertain significance Multiple submitters
- BEAN1 p.Arg90Gln Uncertain significance Multiple submitters
- BEAN1 p.Ala10Thr Uncertain significance Single submitter
- BEAN1 p.Ala165Thr Uncertain significance Single submitter
- BEAN1 p.Ala222Pro Uncertain significance Single submitter
- BEAN1 p.Ala250Pro Uncertain significance Single submitter
- BEAN1 p.Arg105His Uncertain significance Single submitter
- BEAN1 p.Arg111Cys Uncertain significance Single submitter
- BEAN1 p.Arg111His Uncertain significance Single submitter
- BEAN1 p.Arg138Lys Uncertain significance Single submitter
- BEAN1 p.Arg14His Uncertain significance Single submitter
- BEAN1 p.Arg71Ser Uncertain significance Single submitter
- BEAN1 p.Arg85His Uncertain significance Single submitter
- BEAN1 p.Arg86Gln Uncertain significance Single submitter
- BEAN1 p.Arg87Cys Uncertain significance Single submitter
- BEAN1 p.Arg87His Uncertain significance Single submitter
- BEAN1 p.Arg88Gln Uncertain significance Single submitter
- BEAN1 p.Asn13His Uncertain significance Single submitter
- BEAN1 p.Asp164Gly Uncertain significance Single submitter
- BEAN1 p.Gln64Glu Uncertain significance Single submitter
- BEAN1 p.His79Arg Uncertain significance Single submitter
- BEAN1 p.His80Arg Uncertain significance Single submitter
- BEAN1 p.His89Gln Uncertain significance Single submitter
- BEAN1 p.Ile43Lys Uncertain significance Single submitter
- BEAN1 p.Ile43Val Uncertain significance Single submitter
- BEAN1 p.Leu205Pro Uncertain significance Single submitter
- BEAN1 p.Pro123His Uncertain significance Single submitter
- BEAN1 p.Pro154Gln Uncertain significance Single submitter
- BEAN1 p.Pro200Leu Uncertain significance Single submitter
- BEAN1 p.Pro232Leu Uncertain significance Single submitter
- BEAN1 p.Pro232Thr Uncertain significance Single submitter
- BEAN1 p.Ser128Phe Uncertain significance Single submitter
- BEAN1 p.Ser174Ala Uncertain significance Single submitter
- BEAN1 p.Ser241Phe Uncertain significance Single submitter
- BEAN1 p.Ser241Pro Uncertain significance Single submitter
- BEAN1 p.Ser26Leu Uncertain significance Single submitter
- BEAN1 p.Thr163Met Uncertain significance Single submitter
- BEAN1 p.Thr181Ile Uncertain significance Single submitter
- BEAN1 p.Thr207Lys Uncertain significance Single submitter
- BEAN1 p.Tyr169Cys Uncertain significance Single submitter
- BEAN1 p.Val132Leu Uncertain significance Single submitter
- BEAN1 p.Val136Met Uncertain significance Single submitter
Predictors split 20
The independent predictors disagree with each other — read with care.
- BEAN1 p.Arg60Cys Uncertain significance Single submitter
- BEAN1 p.Arg63Met Uncertain significance Single submitter
- BEAN1 p.Arg69Trp Likely benign Single submitter
- BEAN1 p.Arg71Cys Uncertain significance Single submitter
- BEAN1 p.Arg73Cys Uncertain significance Single submitter
- BEAN1 p.Arg86Trp Uncertain significance Single submitter
- BEAN1 p.Asp62Ala Uncertain significance Single submitter
- BEAN1 p.Glu118Lys Uncertain significance Single submitter
- BEAN1 p.Glu149Lys Uncertain significance Single submitter
- BEAN1 p.Ile43Thr Uncertain significance Single submitter
- BEAN1 p.Leu213His Uncertain significance Single submitter
- BEAN1 p.Leu213Pro Uncertain significance Single submitter
- BEAN1 p.Pro162Ser Uncertain significance Single submitter
- BEAN1 p.Pro214Ser Uncertain significance Single submitter
- BEAN1 p.Pro215Arg Uncertain significance Single submitter
- BEAN1 p.Pro215His Uncertain significance Single submitter
- BEAN1 p.Pro6Leu Uncertain significance Single submitter
- BEAN1 p.Ser170Leu Uncertain significance Single submitter
- BEAN1 p.Tyr141Asp Uncertain significance Single submitter
-
BEAN1 p.His30Gln
Benign
No assertion criteria
spinocerebellar ataxia type 31
All BEAN1 variants
Conflicting classifications of pathogenicity 3
- p.Arg66Gln Single submitter ⚠
- p.Arg69Gln Single submitter ⚠
- p.Thr135Met Single submitter ⚠
Benign 14
- c.152-2507_152-2506dup Single submitter
- c.152-2525A>C Single submitter
- c.152-2535A>C Single submitter
- c.152-2540A>C Single submitter
- c.152-2545A>C Single submitter
- c.152-2550A>C Single submitter
- c.152-2555A>C Single submitter
- c.152-2560A>C Single submitter
- c.25+244G>A Single submitter
- c.25+9842C>T Single submitter
- p.73RHH[1] Single submitter
- c.289+10C>T No assertion criteria BEAN1-related disorder
- c.*97C>T No assertion criteria BEAN1-related disorder
- p.His30Gln No assertion criteria spinocerebellar ataxia type 31 ⚠
Benign/Likely benign 1
- p.Arg76Ser Multiple submitters
Likely benign 34
- p.Arg108His Multiple submitters
- p.Pro167= Multiple submitters
- p.Tyr216= Multiple submitters
- p.Tyr96= Multiple submitters
- c.152-2505_152-2503del Single submitter
- c.152-2530A>C Single submitter
- c.440+14A>G Single submitter
- c.441-16G>A Single submitter
- c.-22G>A Single submitter
- c.*100G>A Single submitter
- c.*148C>T Single submitter
- c.*224G>A Single submitter
- c.*225G>A Single submitter
- c.*253G>A Single submitter
- c.*263G>A Single submitter
- c.*268G>A Single submitter
- c.*288C>A Single submitter
- c.*349C>T Single submitter
- p.Ala134Thr Single submitter
- p.Arg11Ter Single submitter
- p.Arg192Gln Single submitter
- p.Arg69Trp Single submitter ⚠
- p.Asp129= Single submitter
- p.Asp164= Single submitter
- p.Gly130Arg Single submitter
- p.Gly187Ser Single submitter
- p.Pro232= Single submitter
- p.Ser26= Single submitter
- p.Ser98Leu Single submitter
- p.Ter260Cys Single submitter
- p.Thr207= Single submitter
- p.Val161= Single submitter
- c.*1G>C No assertion criteria BEAN1-related disorder
- p.Cys220= No assertion criteria BEAN1-related disorder
Uncertain significance 63
- p.Ala156Ser Multiple submitters ⚠
- p.Arg90Gln Multiple submitters ⚠
- p.Ala10Thr Single submitter ⚠
- p.Ala165Thr Single submitter ⚠
- p.Ala222Pro Single submitter ⚠
- p.Ala250Pro Single submitter ⚠
- p.Arg105His Single submitter ⚠
- p.Arg111Cys Single submitter ⚠
- p.Arg111His Single submitter ⚠
- p.Arg138Lys Single submitter ⚠
- p.Arg14His Single submitter ⚠
- p.Arg60Cys Single submitter ⚠
- p.Arg63Met Single submitter ⚠
- p.Arg71Cys Single submitter ⚠
- p.Arg71Ser Single submitter ⚠
- p.Arg73Cys Single submitter ⚠
- p.Arg85His Single submitter ⚠
- p.Arg86Gln Single submitter ⚠
- p.Arg86Trp Single submitter ⚠
- p.Arg87Cys Single submitter ⚠
- p.Arg87His Single submitter ⚠
- p.Arg88Gln Single submitter ⚠
- p.Asn13His Single submitter ⚠
- p.Asp164Gly Single submitter ⚠
- p.Asp62Ala Single submitter ⚠
- p.Gln64Glu Single submitter ⚠
- p.Glu118Lys Single submitter ⚠
- p.Glu149Lys Single submitter ⚠
- p.His79Arg Single submitter ⚠
- p.His80Arg Single submitter ⚠
- p.His89Gln Single submitter ⚠
- p.Ile43Lys Single submitter ⚠
- p.Ile43Thr Single submitter ⚠
- p.Ile43Val Single submitter ⚠
- p.Leu205Pro Single submitter ⚠
- p.Leu213His Single submitter ⚠
- p.Leu213Pro Single submitter ⚠
- p.Pro123His Single submitter ⚠
- p.Pro154Gln Single submitter ⚠
- p.Pro162Ser Single submitter ⚠
- p.Pro200Leu Single submitter ⚠
- p.Pro214Ser Single submitter ⚠
- p.Pro215Arg Single submitter ⚠
- p.Pro215His Single submitter ⚠
- p.Pro232Leu Single submitter ⚠
- p.Pro232Thr Single submitter ⚠
- p.Pro6Leu Single submitter ⚠
- p.Ser128Phe Single submitter ⚠
- p.Ser170Leu Single submitter ⚠
- p.Ser174Ala Single submitter ⚠
- p.Ser241Phe Single submitter ⚠
- p.Ser241Pro Single submitter ⚠
- p.Ser26Leu Single submitter ⚠
- p.Thr163Met Single submitter ⚠
- p.Thr181Ile Single submitter ⚠
- p.Thr207Lys Single submitter ⚠
- p.Tyr141Asp Single submitter ⚠
- p.Tyr169Cys Single submitter ⚠
- p.Tyr63= Single submitter
- p.Val132Leu Single submitter ⚠
- p.Val136Met Single submitter ⚠
- p.Arg71His No assertion criteria
- p.Gly80= No assertion criteria