SIN3A — 813 ClinVar variants

All ClinVar germline SIN3A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 360 flagged for review →

71 Pathogenic · 9 Pathogenic/Likely pathogenic · 42 Likely pathogenic · 27 Conflicting · 24 Benign · 9 Benign/Likely benign · 252 Likely benign · 379 Uncertain significance

Full SIN3A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 360

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 3

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

Predictors agree, ClinVar conflicts 20

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

Predictors lean, ClinVar uncertain 269

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 269

Predictors split 68

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

All SIN3A variants

Pathogenic 71

  • p.Arg1140Ter Multiple submitters SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Arg471Ter Multiple submitters SIN3A-related intellectual disability syndrome
  • p.Arg537Ter Multiple submitters
  • p.Arg897Ter Multiple submitters
  • p.Lys937fs Multiple submitters SIN3A-related disorder
  • p.Tyr1105Ter Multiple submitters Inborn genetic diseases
  • c.2094-1G>T Single submitter
  • c.3384dup Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • c.366+1G>T Single submitter
  • c.473+2T>A Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • c.474-574_1408-735dup Single submitter
  • p.Ala455fs Single submitter Inborn genetic diseases
  • p.Ala847fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Arg1134fs Single submitter
  • p.Arg167fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Arg340fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Arg707Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Arg922Ter Single submitter
  • p.Asn890fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Asp845fs Single submitter
  • p.Gln1009Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln1040fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln116Ter Single submitter Inborn genetic diseases
  • p.Gln117Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln255fs Single submitter
  • p.Gln336Ter Single submitter
  • p.Gln339Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln604Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln637Ter Single submitter
  • p.Gln827fs Single submitter Inborn genetic diseases
  • p.Gln8fs Single submitter
  • p.Gln900Ter Single submitter Paediatric disorders
  • p.Gln944Ter Single submitter Inborn genetic diseases
  • p.Glu1103Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Glu375fs Single submitter
  • p.Glu526fs Single submitter Inborn genetic diseases
  • p.Glu754fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Glu836Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.His214fs Single submitter
  • p.His283fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.His731fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.His817fs Single submitter
  • p.Leu290Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Leu380fs Single submitter
  • p.Leu388fs Single submitter
  • p.Leu514Ter Single submitter
  • p.Leu876fs Single submitter
  • p.Leu876Ter Single submitter
  • p.Lys326fs Single submitter
  • p.Lys410fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Lys638Ter Single submitter
  • p.Phe507fs Single submitter
  • p.Pro222fs Single submitter
  • p.Pro88_Thr89delinsIleThrSerTer Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Ser1161fs Single submitter Inborn genetic diseases
  • p.Ser748delinsProHisTer Single submitter SIN3A-related intellectual disability syndrome
  • p.Ser977fs Single submitter Inborn genetic diseases
  • p.Ser982fs Single submitter
  • p.Trp517Ter Single submitter
  • p.Trp591Ter Single submitter
  • p.Trp892Ter Single submitter
  • p.Tyr335_Lys337delinsTer Single submitter SIN3A-related disorder
  • p.Tyr565delinsTrpAlaLeuLeuTrpArgTer Single submitter
  • p.Tyr673Ter Single submitter
  • p.Tyr979Ter Single submitter Inborn genetic diseases
  • p.Val504fs Single submitter
  • p.Val58fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Val81fs Single submitter Inborn genetic diseases
  • p.Arg1104Ter No assertion criteria SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Leu269fs No assertion criteria SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Ser587fs No assertion criteria SIN3A-related intellectual disability syndrome due to a point mutation

Pathogenic/Likely pathogenic 9

  • p.Arg553Ter Multiple submitters Inborn genetic diseases
  • p.Arg559Ter Multiple submitters SIN3A-related disorder
  • p.Arg718Ter Multiple submitters SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Arg935Ter Multiple submitters SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Asp323fs Multiple submitters SIN3A-related disorder
  • p.Gln785fs Multiple submitters SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Lys948fs Multiple submitters SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Glu985fs No assertion criteria SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Tyr1101Ter No assertion criteria

Likely pathogenic 42

  • c.1526+1G>T Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • c.1527-2A>C Single submitter
  • c.1527-2A>T Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • c.1738-1G>A Single submitter
  • c.1855-13_1874inv Single submitter
  • c.2094-1G>A Single submitter
  • c.2277+4A>G Single submitter
  • c.366+5T>C Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • c.367-2A>C Single submitter
  • c.474-1G>A Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • c.474-1G>T Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Arg616Cys Single submitter ⚠
  • p.Arg984fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Asn1158fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln1137Ter Single submitter
  • p.Gln195Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln217fs Single submitter SIN3A-related disorder
  • p.Gln255Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln426Glu Single submitter ⚠
  • p.Gln761fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Gln827Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Glu914Ter Single submitter chromosome 15q24 deletion syndrome
  • p.Gly1150fs Single submitter SIN3A-related disorder
  • p.His85delinsSerSerTer Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Ile1016fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Leu669His Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Leu669Phe Single submitter SIN3A-related intellectual disability syndrome due to a point mutation ⚠
  • p.Leu793Pro Single submitter SIN3A-related intellectual disability syndrome
  • p.Met1067_Ile1069dup Single submitter
  • p.Ser289Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Ser421fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Ser456fs Single submitter
  • p.Ser600fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Thr161Ala Single submitter
  • p.Thr629Ala Single submitter ⚠
  • p.Tyr1174Ter Single submitter SIN3A-related disorder
  • p.Tyr1262fs Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Tyr129Ter Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Tyr359Ter Single submitter neurodevelopmental disorder
  • p.Val504Asp Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Val851_Lys852insTer Single submitter SIN3A-related intellectual disability syndrome due to a point mutation
  • p.Val955fs No assertion criteria SIN3A-related disorder

Conflicting classifications of pathogenicity 27

Benign 24

Benign/Likely benign 9

Likely benign 252

Uncertain significance 379

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