GATAD2B — 643 ClinVar variants

All ClinVar germline GATAD2B variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 269 flagged for review →

77 Pathogenic · 6 Pathogenic/Likely pathogenic · 30 Likely pathogenic · 20 Conflicting · 31 Benign · 9 Benign/Likely benign · 192 Likely benign · 278 Uncertain significance

Full GATAD2B gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 269

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 13

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

Predicted LoF vs a conflicting call 1

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 190

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 190

Predictors split 62

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

All GATAD2B variants

Pathogenic 77

  • p.Arg116Ter Multiple submitters Paediatric disorders
  • p.Arg174Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Arg179Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln190fs Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln192Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln219Ter Multiple submitters
  • p.Gln220Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln274fs Multiple submitters Inborn genetic diseases
  • p.Gln325Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln470Ter Multiple submitters Inborn genetic diseases
  • p.Gln477Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln67Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Glu144fs Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gly218fs Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.His216fs Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Pro307fs Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Pro370fs Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • c.1216+2T>C Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • c.1217-2A>G Single submitter
  • c.1419+1G>A Single submitter intellectual disability
  • c.335+1G>A Single submitter
  • c.335+1G>T Single submitter
  • c.335+2T>G Single submitter
  • c.465+2T>C Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • c.466-1G>C Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • c.730-2A>G Single submitter
  • p.Ala39fs Single submitter intellectual disability
  • p.Ala92fs Single submitter Inborn genetic diseases
  • p.Arg460fs Single submitter
  • p.Arg51fs Single submitter GATAD2B-related disorder
  • p.Arg84fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Cys441Arg Single submitter
  • p.Cys444fs Single submitter
  • p.Gln163Ter Single submitter
  • p.Gln188fs Single submitter
  • p.Gln219fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln232Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln237Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln243Ter Single submitter Inborn genetic diseases
  • p.Gln274Ter Single submitter
  • p.Gln299Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln349Ter Single submitter
  • p.Gln359Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln399fs Single submitter
  • p.Gln470fs Single submitter
  • p.Gln471Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln482Ter Single submitter Inborn genetic diseases
  • p.Glu152fs Single submitter Inborn genetic diseases
  • p.Glu177_Leu180del Single submitter
  • p.Glu472fs Single submitter
  • p.Glu476Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Glu62fs Single submitter
  • p.Glu77Ter Single submitter Inborn genetic diseases
  • p.Gly406Arg Single submitter ⚠
  • p.His245fs Single submitter
  • p.His61fs Single submitter
  • p.Ile166fs Single submitter
  • p.Leu173fs Single submitter
  • p.Leu364fs Single submitter Inborn genetic diseases
  • p.Lys224fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Lys362fs Single submitter
  • p.Met259fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Met40fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ser108fs Single submitter
  • p.Ser122Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ser348Ter Single submitter
  • p.Ser411fs Single submitter
  • p.Ser411Ter Single submitter Inborn genetic diseases
  • p.Thr328fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Tyr298fs Single submitter
  • c.1217-633_1419+490del No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ala421fs No assertion criteria
  • p.Cys420Arg No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Glu472Ter No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Leu180Pro No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Leu28fs No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Lys184fs No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome

Pathogenic/Likely pathogenic 6

  • c.1217-399C>T Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Arg414Gln Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome ⚠
  • p.Arg478Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln473Ter Multiple submitters GATAD2B-related disorder
  • p.Gln480Ter Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ser400fs Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome

Likely pathogenic 30

  • c.597+1G>A Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • c.1419+1G>C Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • c.1419+1G>T Single submitter Inborn genetic diseases
  • c.730-1G>T Single submitter Inborn genetic diseases
  • p.Arg141fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Arg228fs Single submitter
  • p.Arg24Ter Single submitter Inborn genetic diseases
  • p.Arg31Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Asn131fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Asn205fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Asp130fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln299fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln359fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln482His Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome ⚠
  • p.Gln513Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Glu115Ter Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Glu176fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Glu442Ter Single submitter GATAD2B-related disorder
  • p.Gly327fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ile316Met Single submitter ⚠
  • p.Leu128fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Leu469fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Lys97fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ser139fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ter594Gln Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Trp431Ter Single submitter GATAD2B-related disorder
  • p.Val401fs Single submitter severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • c.598-1G>A No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Gln481Ter No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Lys52fs No assertion criteria severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome

Conflicting classifications of pathogenicity 20

Benign 31

Benign/Likely benign 9

  • c.729+10C>G Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ala346= Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ala410Gly Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ala490Val Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Asn80= Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Pro226Ala Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ser139Gly Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Ser340= Multiple submitters severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome
  • p.Thr312Ala Multiple submitters

Likely benign 192

Uncertain significance 278