Sugi Variant

Sugi Variant/XRCC4

XRCC4 — 183 ClinVar variants

All ClinVar germline XRCC4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 80 flagged for review →

10 Pathogenic · 5 Pathogenic/Likely pathogenic · 6 Likely pathogenic · 2 Conflicting · 12 Benign · 6 Benign/Likely benign · 52 Likely benign · 90 Uncertain significance

Full XRCC4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 80

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 1

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

Predictors lean, ClinVar uncertain 69

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

Predictors split 8

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

All XRCC4 variants

Pathogenic 10

  • p.Arg225Ter Multiple submitters short stature, microcephaly, and endocrine dysfunction
  • p.Ala287fs Single submitter
  • p.Ala60fs Single submitter
  • p.Arg161Gln Single submitter XRCC4-related disorder ⚠
  • p.Arg275Ter Single submitter short stature, microcephaly, and endocrine dysfunction
  • p.Glu13Ter Single submitter short stature, microcephaly, and endocrine dysfunction
  • p.Leu151fs Single submitter
  • p.Lys65fs Single submitter
  • c.-10-1G>T No assertion criteria short stature, microcephaly, and endocrine dysfunction
  • p.Asp82Glu No assertion criteria short stature, microcephaly, and endocrine dysfunction ⚠

Pathogenic/Likely pathogenic 5

  • p.Arg161Ter Multiple submitters XRCC4-related disorder
  • p.Arg205Ter Multiple submitters short stature, microcephaly, and endocrine dysfunction
  • p.His9fs Multiple submitters XRCC4-related disorder
  • p.Ser12fs Multiple submitters short stature, microcephaly, and endocrine dysfunction
  • p.Trp43Arg Multiple submitters short stature, microcephaly, and endocrine dysfunction

Likely pathogenic 6

  • c.140-2A>G Multiple submitters short stature, microcephaly, and endocrine dysfunction
  • p.Lys210Ter Multiple submitters short stature, microcephaly, and endocrine dysfunction
  • c.-10-1G>C Single submitter short stature, microcephaly, and endocrine dysfunction
  • p.Asp254fs Single submitter short stature, microcephaly, and endocrine dysfunction
  • p.Glu149Ter Single submitter short stature, microcephaly, and endocrine dysfunction
  • p.Ser89fs Single submitter short stature, microcephaly, and endocrine dysfunction

Conflicting classifications of pathogenicity 2

  • c.894-13T>G Single submitter short stature, microcephaly, and endocrine dysfunction
  • p.Lys187Asn Single submitter short stature, microcephaly, and endocrine dysfunction ⚠

Benign 12

Benign/Likely benign 6

Likely benign 52

Uncertain significance 90