Sugi Variant

Sugi Variant/SETD1A

SETD1A — 903 ClinVar variants

All ClinVar germline SETD1A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 486 flagged for review →

37 Pathogenic · 3 Pathogenic/Likely pathogenic · 37 Likely pathogenic · 33 Conflicting · 7 Benign · 6 Benign/Likely benign · 240 Likely benign · 540 Uncertain significance

Full SETD1A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 486

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 19

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 341

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 341

Predictors split 122

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

All SETD1A variants

Pathogenic 37

  • c.4582-2_4582-1del Multiple submitters epilepsy, early-onset, with or without developmental delay
  • c.518-2A>G Multiple submitters schizophrenia
  • p.Arg668Ter Multiple submitters epilepsy, early-onset, with or without developmental delay
  • p.Pro644fs Multiple submitters Inborn genetic diseases
  • p.Tyr646Ter Multiple submitters schizophrenia
  • p.Ala1142fs Single submitter Inborn genetic diseases
  • p.Ala148fs Single submitter
  • p.Ala725fs Single submitter schizophrenia
  • p.Arg1236Ter Single submitter
  • p.Arg461fs Single submitter Inborn genetic diseases
  • p.Arg72fs Single submitter Inborn genetic diseases
  • p.Asp112fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Asp73fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Gln1540Ter Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Gln735fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Gln737Ter Single submitter schizophrenia
  • p.Glu1278fs Single submitter Inborn genetic diseases
  • p.Glu1319fs Single submitter Inborn genetic diseases
  • p.Glu982Ter Single submitter SETD1A-related disorder
  • p.Leu1212fs Single submitter Inborn genetic diseases
  • p.Pro1404fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Pro435fs Single submitter
  • p.Pro92fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Pro942fs Single submitter neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
  • p.Ser1058fs Single submitter Inborn genetic diseases
  • p.Ser411fs Single submitter
  • p.Ser430fs Single submitter epilepsy, early-onset, with or without developmental delay
  • p.Ser52fs Single submitter Inborn genetic diseases
  • p.Thr1454fs Single submitter SETD1A-related disorder
  • p.Thr421fs Single submitter neurodevelopmental disorder
  • p.Tyr425fs Single submitter schizophrenia
  • p.Ala339fs No assertion criteria neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Arg253Ter No assertion criteria schizophrenia
  • p.Gln269Arg No assertion criteria epilepsy, early-onset, with or without developmental delay
  • p.Gly1369Arg No assertion criteria epilepsy, early-onset, with or without developmental delay ⚠
  • p.Gly535fs No assertion criteria neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Tyr1499Asp No assertion criteria neurodevelopmental disorder with speech impairment and dysmorphic facies

Pathogenic/Likely pathogenic 3

  • p.Arg1571Ter Multiple submitters neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Arg176Ter Multiple submitters neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Arg990Ter Multiple submitters epilepsy, early-onset, with or without developmental delay

Likely pathogenic 37

  • p.Arg913Cys Multiple submitters epilepsy, early-onset, with or without developmental delay ⚠
  • c.151-2A>G Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • c.1720-1G>A Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • c.-15-1G>A Single submitter
  • p.Ala1323fs Single submitter SETD1A-related disorder
  • p.Ala148Thr Single submitter
  • p.Ala777fs Single submitter intellectual disability
  • p.Arg889Trp Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies ⚠
  • p.Cys1697Arg Single submitter SETD1A-related disorder
  • p.Gln16Ter Single submitter epilepsy, early-onset, with or without developmental delay
  • p.Gln377Ter Single submitter
  • p.Gln3Ter Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Gln838Ter Single submitter epilepsy, early-onset, with or without developmental delay
  • p.Glu1002fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Glu1345Ter Single submitter SETD1A-related disorder
  • p.Glu1592Lys Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Glu181Ter Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Glu416fs Single submitter
  • p.Glu857Ter Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Gly206fs Single submitter SETD1A-related disorder
  • p.Gly674Ter Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Leu759fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Lys835= Single submitter
  • p.Pro1182fs Single submitter
  • p.Pro543fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Pro609fs Single submitter SETD1A-related disorder
  • p.Pro649fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Pro654fs Single submitter SETD1A-related disorder
  • p.Ser1033fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Ser290Ile Single submitter
  • p.Thr1681Ile Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Thr322fs Single submitter SETD1A-related disorder
  • p.Tyr1415Ter Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Tyr1510Ter Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Tyr382fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Tyr412fs Single submitter neurodevelopmental disorder with speech impairment and dysmorphic facies
  • p.Val994fs Single submitter autism spectrum disorder

Conflicting classifications of pathogenicity 33

Benign 7

Benign/Likely benign 6

Likely benign 240

Uncertain significance 540

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