SMARCA2 — 1575 ClinVar variants

All ClinVar germline SMARCA2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 477 flagged for review →

46 Pathogenic · 13 Pathogenic/Likely pathogenic · 62 Likely pathogenic · 62 Conflicting · 194 Benign · 88 Benign/Likely benign · 544 Likely benign · 566 Uncertain significance

Full SMARCA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 477

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 1

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 328

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 328

Predictors split 117

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

All SMARCA2 variants

Pathogenic 46

  • p.Ala1160Gly Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg1105Cys Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg1105His Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg1159Gly Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg525Cys Multiple submitters blepharophimosis-impaired intellectual development syndrome
  • p.Arg855Gln Multiple submitters SMARCA2-related BAFopathy
  • p.Glu852Lys Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gly1129Asp Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Pro883Leu Multiple submitters SMARCA2-related BAFopathy
  • p.Ala1128Pro Single submitter
  • p.Ala1156Thr Single submitter
  • p.Ala1219Pro Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg1105Gly Single submitter
  • p.Arg1162Ser Single submitter
  • p.Arg937Cys Single submitter blepharophimosis-impaired intellectual development syndrome
  • p.Asn1149Ser Single submitter
  • p.Asp1147Ala Single submitter
  • p.Gln1074Glu Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gln1155Pro Single submitter
  • p.Glu852Gln Single submitter SMARCA2-related BAFopathy
  • p.Gly1098Ser Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gly752Ala Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gly853Asp Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Ile779Leu Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Leu1217Pro Single submitter
  • p.Leu529Val Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Leu753His Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Leu753Phe Single submitter
  • p.Leu946Phe Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Lys755Arg Single submitter
  • p.Pro883Ala Single submitter
  • p.Pro883Ser Single submitter
  • p.Ser1146Arg Single submitter
  • p.Thr1100Pro Single submitter
  • p.Thr829Ile Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Thr880Ile Single submitter
  • p.Val1198Gly Single submitter Inborn genetic diseases
  • p.Arg1159Leu No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg855Gly No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.Asp1158Val No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gly1132Asp No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gly1202Cys No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gly881Val No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.His854Leu No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.His939Tyr No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.Trp795Arg No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome

Pathogenic/Likely pathogenic 13

  • p.Ala1138Pro Multiple submitters Inborn genetic diseases
  • p.Ala1201Glu Multiple submitters neurodevelopmental disorder
  • p.Ala1201Val Multiple submitters Developmental delay
  • p.Arg1105Pro Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg1159Gln Multiple submitters SMARCA2-related BAFopathy
  • p.Arg1162Cys Multiple submitters SMARCA2-related disorder
  • p.Arg1162His Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg505Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg525His Multiple submitters blepharophimosis-impaired intellectual development syndrome
  • p.Arg937His Multiple submitters SMARCA2-related BAFopathy
  • p.Asp534Tyr Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Ser783Leu Multiple submitters SMARCA2-related BAFopathy
  • p.Arg937Leu No assertion criteria blepharophimosis-impaired intellectual development syndrome

Likely pathogenic 62

  • p.Asp534Gly Multiple submitters blepharophimosis-impaired intellectual development syndrome
  • p.Ile518Thr Multiple submitters SMARCA2-related disorder
  • p.Pro883Gln Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Ser783Trp Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Thr1321Met Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • c.3457-2A>T Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • c.(-37+1_-36-1 Single submitter blepharophimosis-impaired intellectual development syndrome
  • p.Ala1156Gly Single submitter Autosomal dominant epilepsy
  • p.Ala1160Asp Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg1068Ter Single submitter
  • p.Arg1105Leu Single submitter
  • p.Arg1162Gly Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg1213Trp Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg1342Trp Single submitter
  • p.Arg420Cys Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg811Gly Single submitter Neurodevelopmental delay
  • p.Arg844Gln Single submitter intellectual disability-sparse hair-brachydactyly syndrome ⚠
  • p.Asn1007Lys Single submitter
  • p.Asp534His Single submitter
  • p.Asp851Asn Single submitter
  • p.Gln1136Arg Single submitter SMARCA2-related disorder
  • p.Gln1152His Single submitter ⚠
  • p.Gln1165Lys Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gln1196Pro Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gln1200Pro Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gln957Arg Single submitter blepharophimosis-impaired intellectual development syndrome ⚠
  • p.Glu464Lys Single submitter blepharophimosis-impaired intellectual development syndrome ⚠
  • p.Glu929Val Single submitter intellectual disability
  • p.Gly1130_Leu1131insGly Single submitter
  • p.Gly1164Arg Single submitter
  • p.Gly513Asp Single submitter intellectual disability
  • p.Gly752Arg Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.His1151Tyr Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.His1161Arg Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.His1161Gln Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Lys951Asn Single submitter
  • p.Met1079Thr Single submitter
  • p.Met1242Lys Single submitter SMARCA2-related disorder
  • p.Phe1204Leu Single submitter
  • p.Phe913Leu Single submitter Inborn genetic diseases
  • p.Phe945Cys Single submitter
  • p.Pro158fs Single submitter
  • p.Pro625Leu Single submitter blepharophimosis-impaired intellectual development syndrome
  • p.Pro781Arg Single submitter intellectual disability
  • p.Pro944Gln Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Ser1208Cys Single submitter intellectual disability
  • p.Ser263Thr Single submitter pituitary stalk interruption syndrome ⚠
  • p.Thr989Arg Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Thr989Lys Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Trp1283Arg Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Trp1283Cys Single submitter Neurodevelopmental delay
  • p.Trp912Cys Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Tyr1489Cys Single submitter blepharophimosis-impaired intellectual development syndrome
  • p.Tyr514His Single submitter
  • p.Tyr776His Single submitter Inborn genetic diseases
  • p.Val1141Met Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Val1169Ala Single submitter intellectual disability-sparse hair-brachydactyly syndrome
  • p.Asp1147Glu No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.Asp510Gly No assertion criteria blepharophimosis - intellectual disability syndrome
  • p.Asp851Gly No assertion criteria intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gly1034Asp No assertion criteria SMARCA2-related disorder
  • p.Gly513Val No assertion criteria intellectual disability

Conflicting classifications of pathogenicity 62

Benign 194

Benign/Likely benign 88

  • c.1347+19T>G Multiple submitters
  • c.1522-19G>A Multiple submitters
  • c.1746+10C>T Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • c.1877+19G>A Multiple submitters
  • c.226-20A>G Multiple submitters
  • c.2348+3A>G Multiple submitters Inborn genetic diseases
  • c.2349-15T>A Multiple submitters
  • c.2349-3T>C Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • c.2526+13A>G Multiple submitters
  • c.3125+21del Multiple submitters
  • c.3125+5A>G Multiple submitters
  • c.3126-17C>T Multiple submitters
  • c.3126-9dup Multiple submitters
  • c.3685-6C>A Multiple submitters Inborn genetic diseases
  • c.4200-4G>A Multiple submitters Inborn genetic diseases
  • c.4200-5C>T Multiple submitters Inborn genetic diseases
  • c.4360-14A>T Multiple submitters
  • c.4360-16C>G Multiple submitters
  • c.4594+16C>T Multiple submitters
  • c.4595-7G>C Multiple submitters blepharophimosis-impaired intellectual development syndrome
  • c.4737+13G>A Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • c.4737+18G>A Multiple submitters
  • c.791-7C>T Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Ala1064Val Multiple submitters Inborn genetic diseases ⚠
  • p.Ala282Thr Multiple submitters Inborn genetic diseases
  • p.Ala630= Multiple submitters Inborn genetic diseases
  • p.Arg1170= Multiple submitters
  • p.Arg1246Gln Multiple submitters Inborn genetic diseases
  • p.Arg1549Gln Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Arg559= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Asp1313= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Asp1360Glu Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Asp1573Asn Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Asp1577= Multiple submitters Inborn genetic diseases
  • p.Asp1588Glu Multiple submitters Inborn genetic diseases
  • p.Asp82= Multiple submitters blepharophimosis-impaired intellectual development syndrome
  • p.Gln222= Multiple submitters Inborn genetic diseases
  • p.Gln223= Multiple submitters Inborn genetic diseases
  • p.Gln226Pro Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gln227Pro Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gln230Pro Multiple submitters Inborn genetic diseases
  • p.Gln232Pro Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gln234_Gln238del Multiple submitters Inborn genetic diseases
  • p.Gln236= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Gln236_Gln238del Multiple submitters Inborn genetic diseases
  • p.Gln237_Gln238del Multiple submitters Inborn genetic diseases
  • p.Gln474= Multiple submitters Inborn genetic diseases
  • p.Gln654= Multiple submitters Inborn genetic diseases
  • p.Gln911= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Glu1053= Multiple submitters Inborn genetic diseases
  • p.Glu360= Multiple submitters Inborn genetic diseases
  • p.Gly1416Ala Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.His1032Tyr Multiple submitters Inborn genetic diseases
  • p.His1459= Multiple submitters
  • p.Ile1493= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Ile77= Multiple submitters Inborn genetic diseases
  • p.Leu1094= Multiple submitters Inborn genetic diseases
  • p.Leu1185= Multiple submitters Inborn genetic diseases
  • p.Leu215= Multiple submitters
  • p.Leu319= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Leu476= Multiple submitters
  • p.Leu661= Multiple submitters
  • p.Met70Ile Multiple submitters Inborn genetic diseases
  • p.Pro1115Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Pro11Ser Multiple submitters Inborn genetic diseases
  • p.Pro1281= Multiple submitters Inborn genetic diseases
  • p.Pro153= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Pro161= Multiple submitters
  • p.Pro17= Multiple submitters Inborn genetic diseases
  • p.Pro171= Multiple submitters Inborn genetic diseases
  • p.Pro199= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Pro239Leu Multiple submitters Inborn genetic diseases
  • p.Pro33Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Pro579= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Ser1146= Multiple submitters Inborn genetic diseases
  • p.Ser1419= Multiple submitters Inborn genetic diseases
  • p.Ser1528= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Thr1480= Multiple submitters Inborn genetic diseases
  • p.Thr1587= Multiple submitters Inborn genetic diseases
  • p.Thr374= Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Thr422= Multiple submitters Inborn genetic diseases
  • p.Thr602= Multiple submitters Inborn genetic diseases
  • p.Tyr693Cys Multiple submitters
  • p.Val1403Met Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Val1406= Multiple submitters
  • p.Val1567Leu Multiple submitters intellectual disability-sparse hair-brachydactyly syndrome
  • p.Val712= Multiple submitters Inborn genetic diseases
  • p.Val924= Multiple submitters

Likely benign 544

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

Uncertain significance 566

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