Sugi Variant

Sugi Variant/DLL3

DLL3 — 626 ClinVar variants

All ClinVar germline DLL3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 223 flagged for review →

30 Pathogenic · 6 Pathogenic/Likely pathogenic · 15 Likely pathogenic · 18 Conflicting · 29 Benign · 11 Benign/Likely benign · 286 Likely benign · 231 Uncertain significance

Full DLL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 223

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 3

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

Predictors lean, ClinVar uncertain 121

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

Predictors split 98

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

All DLL3 variants

Pathogenic 30

Pathogenic/Likely pathogenic 6

  • p.Ala317fs Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Cys207Ter Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Cys379Tyr Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Gln346Ter Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Gly504Asp Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Ile123fs Multiple submitters spondylocostal dysostosis 1, autosomal recessive

Likely pathogenic 15

  • c.652+1G>T Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Cys178Ter Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • c.1093+1G>A Single submitter
  • c.652+1G>C Single submitter
  • c.652+2T>A Single submitter
  • p.Ala81fs Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Asp425fs Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Cys362Ter Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Cys400Ter Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Cys438Ser Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Met460Lys Single submitter ⚠
  • p.Pro43fs Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Pro481fs Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Trp158Ter Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Val183fs Single submitter spondylocostal dysostosis 1, autosomal recessive

Conflicting classifications of pathogenicity 18

  • c.1674-9C>T Single submitter spondylocostal dysostosis 1, autosomal recessive
  • c.1758+57C>T Single submitter spondylocostal dysostosis 1, autosomal recessive
  • c.352-15C>T Single submitter syndactyly
  • c.652+15C>T Single submitter syndactyly
  • p.Ala434= Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Arg177= Single submitter
  • p.Arg238Gln Single submitter Inborn genetic diseases ⚠
  • p.Asn323= Single submitter syndactyly
  • p.Asn546= Single submitter
  • p.Gly269Arg Single submitter syndactyly ⚠
  • p.Gly313= Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Pro226Arg Single submitter Inborn genetic diseases ⚠
  • p.Pro541= Single submitter syndactyly
  • p.Ser51= Single submitter syndactyly
  • p.Thr188= Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Tyr305= Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Val311= Single submitter spondylocostal dysostosis 1, autosomal recessive
  • p.Val328Phe Single submitter syndactyly ⚠

Benign 29

Benign/Likely benign 11

  • c.1674-10C>T Multiple submitters syndactyly
  • c.409+19G>T Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Ala462Thr Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Arg436His Multiple submitters spondylocostal dysostosis 1, autosomal recessive ⚠
  • p.Arg463Leu Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Glu130= Multiple submitters syndactyly
  • p.Leu142Gln Multiple submitters syndactyly ⚠
  • p.Leu21= Multiple submitters syndactyly
  • p.Leu54Ile Multiple submitters syndactyly ⚠
  • p.Pro181= Multiple submitters spondylocostal dysostosis 1, autosomal recessive
  • p.Ser521Phe Multiple submitters syndactyly ⚠

Likely benign 286

Uncertain significance 231