EBF3 — 382 ClinVar variants

All ClinVar germline EBF3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 143 flagged for review →

56 Pathogenic · 8 Pathogenic/Likely pathogenic · 51 Likely pathogenic · 7 Conflicting · 7 Benign · 5 Benign/Likely benign · 76 Likely benign · 172 Uncertain significance

Full EBF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 143

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 4

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 91

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 46

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

All EBF3 variants

Pathogenic 56

  • c.486-1G>A Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Ala279fs Multiple submitters Paediatric disorders
  • p.Arg152Gly Multiple submitters Inborn genetic diseases
  • p.Arg163Gln Multiple submitters Inborn genetic diseases
  • p.Arg163Leu Multiple submitters Hypotonia
  • p.Arg206Ter Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Arg312Ter Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.His157Tyr Multiple submitters
  • p.Pro177Leu Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Thr477fs Multiple submitters Inborn genetic diseases
  • p.Tyr116Ter Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Tyr391Ter Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • c.1128+1G>C Single submitter hypotonia, ataxia, and delayed development syndrome
  • c.1128+1G>T Single submitter hypotonia, ataxia, and delayed development syndrome
  • c.1372+1G>A Single submitter
  • c.289_291+1del Single submitter Inborn genetic diseases
  • c.291+1G>A Single submitter
  • c.291+2del Single submitter hypotonia, ataxia, and delayed development syndrome
  • c.292-2A>G Single submitter
  • c.554+4A>C Single submitter
  • c.636+1G>A Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Arg152Leu Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Arg51Ter Single submitter
  • p.Asn237del Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Cys198Tyr Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Gln113fs Single submitter Inborn genetic diseases
  • p.Gln124Ter Single submitter
  • p.Gln196Arg Single submitter
  • p.Gln212Ter Single submitter Inborn genetic diseases
  • p.Gln361Ter Single submitter Inborn genetic diseases
  • p.Gln421fs Single submitter
  • p.Gln57fs Single submitter
  • p.Gln78Ter Single submitter autism spectrum disorder
  • p.Gln80fs Single submitter
  • p.Glu175fs Single submitter
  • p.Glu55Ter Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Gly171Asp Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Leu114Ter Single submitter
  • p.Leu154Gln Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Lys146Glu Single submitter
  • p.Lys193Asn Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Lys97fs Single submitter
  • p.Met134fs Single submitter Inborn genetic diseases
  • p.Phe186_Phe187insTer Single submitter
  • p.Pro180fs Single submitter Inborn genetic diseases
  • p.Pro81fs Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Ser29Ter Single submitter
  • p.Ser449Ter Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Trp30Ter Single submitter
  • p.Tyr141fs Single submitter
  • p.Val566fs Single submitter
  • p.Val82fs Single submitter
  • p.Cys161Ser No assertion criteria hypotonia, ataxia, and delayed development syndrome
  • p.Glu94fs No assertion criteria vesicoureteral reflux
  • p.His157_Ile159dup No assertion criteria
  • p.Met208fs No assertion criteria hypotonia, ataxia, and delayed development syndrome

Pathogenic/Likely pathogenic 8

  • c.485+2_485+8del Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Arg163Trp Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Arg209Gln Multiple submitters Inborn genetic diseases
  • p.Arg209Trp Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Arg404Ter Multiple submitters EBF3-related disorder
  • p.Arg63Gln Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Arg63Trp Multiple submitters hypotonia, ataxia, and delayed development syndrome ⚠
  • p.Tyr141Cys Multiple submitters hypotonia, ataxia, and delayed development syndrome

Likely pathogenic 51

  • c.555-2A>G Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Asn197Asp Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • p.Gly143Asp Multiple submitters hypotonia, ataxia, and delayed development syndrome
  • c.1194+1G>C Single submitter EBF3-related disorder
  • c.1373-2A>C Single submitter hypotonia, ataxia, and delayed development syndrome
  • c.1561+3_1561+6del Single submitter
  • c.356-2A>G Single submitter Inborn genetic diseases
  • c.486-12A>G Single submitter hypotonia, ataxia, and delayed development syndrome
  • c.554+1del Single submitter
  • p.Ala384Val Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Arg129Pro Single submitter Inborn genetic diseases
  • p.Arg152Cys Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Arg152Pro Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Arg163Pro Single submitter EBF3-related disorder
  • p.Arg185Ser Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Arg312Gln Single submitter
  • p.Asn287fs Single submitter
  • p.Asn40fs Single submitter EBF3-related disorder
  • p.Asn66Asp Single submitter Inborn genetic diseases
  • p.Asp222fs Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Cys161Arg Single submitter EBF3-related disorder
  • p.Cys164Gly Single submitter Inborn genetic diseases
  • p.Cys164Ser Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Cys170Tyr Single submitter
  • p.Gln453Ter Single submitter
  • p.Glu175Ter Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.His109Pro Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.His157Gln Single submitter
  • p.His395fs Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Ile183fs Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Leu154fs Single submitter Hhypotonia, ataxia, and delayed development syndrome
  • p.Leu192del Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Leu328His Single submitter Inborn genetic diseases
  • p.Leu62Phe Single submitter
  • p.Lys193Glu Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Lys239Arg Single submitter ⚠
  • p.Lys64Thr Single submitter
  • p.Met208Leu Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Met232fs Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Met232Lys Single submitter EBF3-related disorder
  • p.Pro317fs Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Ser169Gly Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Ser229Leu Single submitter Inborn genetic diseases
  • p.Thr122fs Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Thr327delinsSerLysTer Single submitter
  • p.Thr485fs Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Val219Ala Single submitter hypotonia, ataxia, and delayed development syndrome
  • p.Val234Ala Single submitter hypotonia, ataxia, and delayed development syndrome
  • c.412-2A>T No assertion criteria hypotonia, ataxia, and delayed development syndrome
  • p.Arg163Gly No assertion criteria hypotonia, ataxia, and delayed development syndrome
  • p.Asn105fs No assertion criteria hypotonia, ataxia, and delayed development syndrome

Conflicting classifications of pathogenicity 7

Benign 7

Benign/Likely benign 5

Likely benign 76

Uncertain significance 172