CD40LG — 300 ClinVar variants

All ClinVar germline CD40LG variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 86 flagged for review →

69 Pathogenic · 5 Pathogenic/Likely pathogenic · 25 Likely pathogenic · 13 Conflicting · 30 Benign · 3 Benign/Likely benign · 76 Likely benign · 79 Uncertain significance

Full CD40LG gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 86

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 11

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

Predictors lean, ClinVar uncertain 49

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

Predictors split 24

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

All CD40LG variants

Pathogenic 69

  • c.347-2A>G Multiple submitters hyper-IgM syndrome type 1
  • p.Ala187fs Multiple submitters Inborn genetic diseases
  • p.Arg11Ter Multiple submitters hyper-IgM syndrome type 1
  • p.Cys218Ter Multiple submitters hyper-IgM syndrome type 1
  • p.Gln160Ter Multiple submitters hyper-IgM syndrome type 1
  • p.Gln220Ter Multiple submitters hyper-IgM syndrome type 1
  • p.Gln90Ter Multiple submitters hyper-IgM syndrome type 1
  • p.Thr254Met Multiple submitters hyper-IgM syndrome type 1
  • c.156+1G>A Single submitter hyper-IgM syndrome type 1
  • c.156+1G>T Single submitter hyper-IgM syndrome type 1
  • c.156+2T>C Single submitter hyper-IgM syndrome type 1
  • c.289-1G>A Single submitter hyper-IgM syndrome type 1
  • c.289-2A>C Single submitter
  • c.346+1del Single submitter
  • c.346+1G>A Single submitter hyper-IgM syndrome type 1
  • c.346+1G>T Single submitter hyper-IgM syndrome type 1
  • c.346+2T>C Single submitter hyper-IgM syndrome type 1
  • c.347-1G>A Single submitter hyper-IgM syndrome
  • c.409+1del Single submitter hyper-IgM syndrome type 1
  • c.409+1G>C Single submitter hyper-IgM syndrome type 1
  • c.409+2T>C Single submitter hyper-IgM syndrome type 1
  • p.Ala123Glu Single submitter hyper-IgM syndrome type 1
  • p.Ala141Pro Single submitter hyper-IgM syndrome type 1
  • p.Ala215fs Single submitter hyper-IgM syndrome type 1
  • p.Arg200Ter Single submitter hyper-IgM syndrome type 1
  • p.Asn157fs Single submitter hyper-IgM syndrome type 1
  • p.Asp55fs Single submitter
  • p.Cys72Ter Single submitter
  • p.Gln114fs Single submitter hyper-IgM syndrome type 1
  • p.Gln186Ter Single submitter hyper-IgM syndrome type 1
  • p.Gln221Ter Single submitter hyper-IgM syndrome type 1
  • p.Gln232Ter Single submitter hyper-IgM syndrome type 1
  • p.Gln70Ter Single submitter hyper-IgM syndrome type 1
  • p.Glu108fs Single submitter hyper-IgM syndrome type 1
  • p.Glu129fs Single submitter hyper-IgM syndrome type 1
  • p.Glu129Ter Single submitter hyper-IgM syndrome type 1
  • p.Glu56Ter Single submitter hyper-IgM syndrome type 1
  • p.Gly144fs Single submitter hyper-IgM syndrome type 1
  • p.Gly167Arg Single submitter hyper-IgM syndrome type 1
  • p.Gly199fs Single submitter hyper-IgM syndrome type 1
  • p.Gly234fs Single submitter hyper-IgM syndrome type 1
  • p.Gly257Asp Single submitter hyper-IgM syndrome type 1
  • p.Gly38fs Single submitter hyper-IgM syndrome type 1
  • p.His47fs Single submitter hyper-IgM syndrome type 1
  • p.Leu100Ter Single submitter hyper-IgM syndrome type 1
  • p.Leu155Pro Single submitter hyper-IgM syndrome type 1 ⚠
  • p.Lys102fs Single submitter hyper-IgM syndrome type 1
  • p.Lys159fs Single submitter hyper-IgM syndrome type 1
  • p.Phe253fs Single submitter hyper-IgM syndrome type 1
  • p.Pro120fs Single submitter hyper-IgM syndrome type 1
  • p.Ser128fs Single submitter hyper-IgM syndrome type 1
  • p.Ser12fs Single submitter hyper-IgM syndrome type 1
  • p.Ser213fs Single submitter
  • p.Ser39Ter Single submitter hyper-IgM syndrome type 1
  • p.Thr134fs Single submitter hyper-IgM syndrome type 1
  • p.Thr15fs Single submitter hyper-IgM syndrome type 1
  • p.Trp140Arg Single submitter hyper-IgM syndrome type 1
  • p.Trp140Cys Single submitter hyper-IgM syndrome type 1
  • p.Tyr146Ter Single submitter hyper-IgM syndrome type 1
  • p.Tyr170fs Single submitter hyper-IgM syndrome type 1
  • p.Tyr170Ter Single submitter hyper-IgM syndrome type 1
  • p.Tyr45fs Single submitter hyper-IgM syndrome type 1
  • p.Tyr5Ter Single submitter hyper-IgM syndrome type 1
  • c.412_419del No assertion criteria hyper-IgM syndrome type 1
  • p.Ala235Pro No assertion criteria hyper-IgM syndrome type 1
  • p.Arg77fs No assertion criteria hyper-IgM syndrome type 1
  • p.Gly227Val No assertion criteria hyper-IgM syndrome type 1
  • p.Trp140Ter No assertion criteria hyper-IgM syndrome type 1
  • p.Val64fs No assertion criteria hyper-IgM syndrome type 1

Pathogenic/Likely pathogenic 5

  • c.158_161del Multiple submitters hyper-IgM syndrome type 1
  • c.346+5G>A Multiple submitters hyper-IgM syndrome type 1
  • p.Gln174Ter Multiple submitters hyper-IgM syndrome type 1
  • p.His125Tyr Multiple submitters hyper-IgM syndrome type 1
  • p.Met36Arg Multiple submitters hyper-IgM syndrome type 1

Likely pathogenic 25

Conflicting classifications of pathogenicity 13

Benign 30

  • c.410-13T>C Multiple submitters hyper-IgM syndrome type 1
  • p.Arg181Gln Multiple submitters hyper-IgM syndrome type 1
  • p.Leu27= Multiple submitters hyper-IgM syndrome type 1
  • p.Leu50= Multiple submitters hyper-IgM syndrome type 1
  • p.Val228= Multiple submitters hyper-IgM syndrome type 1
  • c.156+17G>A Single submitter hyper-IgM syndrome type 1
  • c.157-277G>A Single submitter
  • c.288+188dup Single submitter
  • c.288+20del Single submitter hyper-IgM syndrome type 1
  • c.289-327T>C Single submitter
  • c.409+17C>T Single submitter hyper-IgM syndrome type 1
  • p.Ala13= Single submitter hyper-IgM syndrome type 1
  • p.Ala130Thr Single submitter hyper-IgM syndrome type 1
  • p.Ala173Val Single submitter hyper-IgM syndrome type 1 ⚠
  • p.Arg200= Single submitter hyper-IgM syndrome type 1
  • p.Asn151Lys Single submitter hyper-IgM syndrome type 1
  • p.Gly199Ser Single submitter hyper-IgM syndrome type 1 ⚠
  • p.Gly38= Single submitter hyper-IgM syndrome type 1
  • p.Ile2= Single submitter hyper-IgM syndrome type 1
  • p.Pro10= Single submitter hyper-IgM syndrome type 1
  • p.Pro233Leu Single submitter hyper-IgM syndrome type 1
  • p.Ser197Ala Single submitter hyper-IgM syndrome type 1
  • p.Ser214= Single submitter hyper-IgM syndrome type 1
  • p.Ser236= Single submitter hyper-IgM syndrome type 1
  • p.Thr105= Single submitter hyper-IgM syndrome type 1
  • p.Thr105Met Single submitter hyper-IgM syndrome type 1
  • p.Thr68= Single submitter hyper-IgM syndrome type 1
  • p.Val163Ile Single submitter hyper-IgM syndrome type 1 ⚠
  • p.Val247= Single submitter hyper-IgM syndrome type 1
  • p.Val64Ala Single submitter hyper-IgM syndrome type 1

Benign/Likely benign 3

  • p.Arg11Gln Multiple submitters hyper-IgM syndrome type 1
  • p.Gly219Arg Multiple submitters hyper-IgM syndrome type 1
  • p.Phe201Leu Multiple submitters hyper-IgM syndrome type 1

Likely benign 76

  • p.Leu231= Multiple submitters hyper-IgM syndrome type 1
  • c.156+11C>A Single submitter hyper-IgM syndrome type 1
  • c.156+12C>T Single submitter hyper-IgM syndrome type 1
  • c.156+18C>T Single submitter hyper-IgM syndrome type 1
  • c.156+19C>T Single submitter hyper-IgM syndrome type 1
  • c.156+7T>A Single submitter hyper-IgM syndrome type 1
  • c.157-15G>C Single submitter hyper-IgM syndrome type 1
  • c.157-16T>C Single submitter hyper-IgM syndrome type 1
  • c.157-19C>T Single submitter hyper-IgM syndrome type 1
  • c.288+9C>T Single submitter hyper-IgM syndrome type 1
  • c.289-14G>C Single submitter hyper-IgM syndrome type 1
  • c.289-14G>T Single submitter hyper-IgM syndrome type 1
  • c.289-17A>G Single submitter hyper-IgM syndrome type 1
  • c.289-18C>A Single submitter hyper-IgM syndrome type 1
  • c.289-18C>T Single submitter hyper-IgM syndrome type 1
  • c.289-19G>A Single submitter hyper-IgM syndrome type 1
  • c.289-19G>T Single submitter hyper-IgM syndrome type 1
  • c.289-27G>T Single submitter hyper-IgM syndrome type 1
  • c.289-7A>G Single submitter hyper-IgM syndrome type 1
  • c.346+12A>G Single submitter hyper-IgM syndrome type 1
  • c.346+14T>A Single submitter hyper-IgM syndrome type 1
  • c.346+16G>T Single submitter hyper-IgM syndrome type 1
  • c.346+17C>T Single submitter hyper-IgM syndrome type 1
  • c.346+5_346+11dup Single submitter hyper-IgM syndrome type 1
  • c.347-12G>A Single submitter hyper-IgM syndrome type 1
  • c.347-14T>C Single submitter hyper-IgM syndrome type 1
  • c.347-18T>A Single submitter hyper-IgM syndrome type 1
  • c.347-18T>C Single submitter hyper-IgM syndrome type 1
  • c.347-6T>A Single submitter hyper-IgM syndrome type 1
  • c.409+10A>C Single submitter hyper-IgM syndrome type 1
  • c.409+12A>G Single submitter hyper-IgM syndrome type 1
  • c.409+14C>T Single submitter hyper-IgM syndrome type 1
  • c.410-15C>G Single submitter hyper-IgM syndrome type 1
  • c.410-5A>G Single submitter hyper-IgM syndrome type 1
  • c.410-7G>A Single submitter hyper-IgM syndrome type 1
  • p.Ala123= Single submitter hyper-IgM syndrome type 1
  • p.Ala173= Single submitter hyper-IgM syndrome type 1
  • p.Arg11= Single submitter hyper-IgM syndrome type 1
  • p.Arg207= Single submitter hyper-IgM syndrome type 1
  • p.Asn109Lys Single submitter hyper-IgM syndrome type 1
  • p.Asn157= Single submitter hyper-IgM syndrome type 1
  • p.Asn240= Single submitter hyper-IgM syndrome type 1
  • p.Asn83= Single submitter hyper-IgM syndrome type 1
  • p.Asp55= Single submitter hyper-IgM syndrome type 1
  • p.Cys218= Single submitter hyper-IgM syndrome type 1
  • p.Gln139= Single submitter hyper-IgM syndrome type 1
  • p.Gln220= Single submitter hyper-IgM syndrome type 1
  • p.Gln90= Single submitter hyper-IgM syndrome type 1
  • p.Glu104= Single submitter hyper-IgM syndrome type 1
  • p.Glu129= Single submitter hyper-IgM syndrome type 1
  • p.Gly199= Single submitter hyper-IgM syndrome type 1
  • p.Gly250= Single submitter hyper-IgM syndrome type 1
  • p.His125= Single submitter hyper-IgM syndrome type 1
  • p.His249= Single submitter hyper-IgM syndrome type 1
  • p.His60= Single submitter hyper-IgM syndrome type 1
  • p.Leu168= Single submitter hyper-IgM syndrome type 1
  • p.Leu17= Single submitter hyper-IgM syndrome type 1
  • p.Leu206= Single submitter hyper-IgM syndrome type 1
  • p.Leu225= Single submitter hyper-IgM syndrome type 1
  • p.Leu79= Single submitter hyper-IgM syndrome type 1
  • p.Lys88= Single submitter hyper-IgM syndrome type 1
  • p.Phe189= Single submitter hyper-IgM syndrome type 1
  • p.Phe201= Single submitter hyper-IgM syndrome type 1
  • p.Phe256= Single submitter hyper-IgM syndrome type 1
  • p.Pro120= Single submitter hyper-IgM syndrome type 1
  • p.Ser128= Single submitter hyper-IgM syndrome type 1
  • p.Ser184= Single submitter hyper-IgM syndrome type 1
  • p.Ser255= Single submitter hyper-IgM syndrome type 1
  • p.Thr147= Single submitter hyper-IgM syndrome type 1
  • p.Thr211= Single submitter hyper-IgM syndrome type 1
  • p.Thr251= Single submitter hyper-IgM syndrome type 1
  • p.Thr74= Single submitter hyper-IgM syndrome type 1
  • p.Tyr172= Single submitter hyper-IgM syndrome type 1
  • p.Val175= Single submitter hyper-IgM syndrome type 1
  • c.289-37_289-36del No assertion criteria CD40LG-related disorder
  • c.-6C>T No assertion criteria CD40LG-related disorder

Uncertain significance 79