IGLL1 — 256 ClinVar variants

All ClinVar germline IGLL1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 122 flagged for review →

6 Conflicting · 14 Benign · 16 Benign/Likely benign · 71 Likely benign · 149 Uncertain significance

Full IGLL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 122

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 2

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

Predictors lean, ClinVar uncertain 83

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

Predictors split 37

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

All IGLL1 variants

Conflicting classifications of pathogenicity 6

  • p.Arg23Cys Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gln88fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Pro142Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr117Ile Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr146Met Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr206Ser Single submitter agammaglobulinemia 2, autosomal recessive ⚠

Benign 14

Benign/Likely benign 16

  • c.207-9T>A Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ala131= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ala174Met Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ala174Thr Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ala174Val Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Arg189His Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Arg85Leu Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Asn171Ser Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Gln103= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Gly159Ser Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Met162Lys Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Pro155Leu Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Thr148Ile Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Thr95Lys Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Tyr141= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Val33Met Multiple submitters agammaglobulinemia 2, autosomal recessive

Likely benign 71

  • p.Ala112= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ala12= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Arg74= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Gln109= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.His198= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ile156= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Leu133= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Phe140= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Pro120= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Pro121= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ser115= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ser45= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Thr146= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Thr206= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Thr78= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Tyr173= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Val196= Multiple submitters agammaglobulinemia 2, autosomal recessive
  • c.207-20G>A Single submitter
  • c.207-8C>T Single submitter agammaglobulinemia 2, autosomal recessive
  • c.322+15C>T Single submitter agammaglobulinemia 2, autosomal recessive
  • c.322+8G>A Single submitter agammaglobulinemia 2, autosomal recessive
  • c.322+9C>T Single submitter agammaglobulinemia 2, autosomal recessive
  • c.323-18C>G Single submitter agammaglobulinemia 2, autosomal recessive
  • c.323-20C>T Single submitter agammaglobulinemia 2, autosomal recessive
  • c.323-6A>C Single submitter agammaglobulinemia 2, autosomal recessive
  • c.323-7C>T Single submitter agammaglobulinemia 2, autosomal recessive
  • c.*12C>T Single submitter
  • p.Ala174= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Ala175= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Ala32= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Arg187= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Arg60= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Arg66= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Arg85Trp Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Asn138Ser Single submitter
  • p.Gln7= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gln73= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Glu15= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Glu211= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gly159= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gly37= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gly75Ser Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gly86= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.His36= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Leu118= Single submitter
  • p.Leu28= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Leu39= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Leu71= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Leu72= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Lys130= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Phe70= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Phe98= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Pro114= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Pro120Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro165= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Pro18= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Pro183= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Pro41= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Pro84= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Ser213= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Ser89= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Thr102= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Thr105= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Thr148= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Thr163= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Thr182= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Thr202= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Thr95= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Val106= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Val203= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Val34= Single submitter agammaglobulinemia 2, autosomal recessive

Uncertain significance 149

  • p.Ala112Thr Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Ala12Val Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ala174Ser Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg23His Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg2Lys Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg40Cys Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg48Gly Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg60Gln Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg60Gly Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg60Trp Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg66Gln Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg66Trp Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg85Gln Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Asn129Asp Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Asp139Asn Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Asp152Asn Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gln7His Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gln88Pro Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Glu199Lys Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gly153Val Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gly53Ter Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.His198Gln Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.His91Tyr Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Leu126Pro Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Leu179Arg Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Met197Thr Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro114Leu Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro18Leu Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro25His Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro80Ala Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser108Asn Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser123Cys Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser89Phe Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr164Met Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr202Ser Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr206Met Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Trp149Leu Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Tyr141fs Multiple submitters agammaglobulinemia 2, autosomal recessive
  • p.Val106Ile Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • p.Val160Met Multiple submitters agammaglobulinemia 2, autosomal recessive ⚠
  • c.206+3A>G Single submitter agammaglobulinemia 2, autosomal recessive
  • c.207-3C>G Single submitter agammaglobulinemia 2, autosomal recessive
  • c.207-4G>T Single submitter agammaglobulinemia 2, autosomal recessive
  • c.322+3_322+6del Single submitter agammaglobulinemia 2, autosomal recessive
  • c.322+4A>G Single submitter agammaglobulinemia 2, autosomal recessive
  • c.322+4A>T Single submitter agammaglobulinemia 2, autosomal recessive
  • c.323-3C>A Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Ala112Asp Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ala12Asp Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ala131Val Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ala174fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Ala54_Gly56dup Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Ala54Asp Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ala54fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Arg187Lys Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg2Thr Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg40His Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg40Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg66Gly Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg66Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg69Thr Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg74Cys Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg74His Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg81Gly Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Arg85fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Asn129His Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Asn170Asp Single submitter ⚠
  • p.Asn171del Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Asn171Lys Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Asn19Asp Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Asp139fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gln103Arg Single submitter ⚠
  • p.Gln127fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gln168His Single submitter ⚠
  • p.Gln185fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gln185Ter Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gln195Arg Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gln195His Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gln22Ter Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gln88Leu Single submitter ⚠
  • p.Glu124Ter Single submitter
  • p.Glu125Gly Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Glu184Lys Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Glu204Gly Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gly101Arg Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gly30Cys Single submitter ⚠
  • p.Gly30Val Single submitter ⚠
  • p.Gly56fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Gly57Arg Single submitter ⚠
  • p.Gly68Asp Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gly6Val Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gly79Asp Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Gly86Glu Single submitter ⚠
  • p.Gly99Ser Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.His198Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.His91Arg Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.His96fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.His96Gln Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.His96Tyr Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ile156fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Leu107= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Leu10fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Leu118Val Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Leu181Pro Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Leu50Pro Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Lys130Asn Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Lys172Arg Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Lys205Met Single submitter ⚠
  • p.Met137Val Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Met162Val Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Met197Arg Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Met197Ile Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Phe119Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Phe119Tyr Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro120Gln Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro121Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro142= Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Pro165Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro16Ser Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro18Ser Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Pro55Ser Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser115fs Single submitter
  • p.Ser115Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser123Pro Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser166Cys Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser176Asn Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser180Asn Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser188Cys Single submitter ⚠
  • p.Ser213Leu Single submitter ⚠
  • p.Ser45fs Single submitter
  • p.Ser45Leu Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser59del Single submitter
  • p.Ser65Gly Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Ser76Phe Single submitter ⚠
  • p.Ser89Tyr Single submitter ⚠
  • p.Thr113Asn Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr154Ser Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr182Met Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr5Arg Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr5fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Thr78Pro Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Thr95Met Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Trp24Cys Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Trp67Ter Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Trp77Arg Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Val203Ala Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Val203fs Single submitter agammaglobulinemia 2, autosomal recessive
  • p.Val203Met Single submitter agammaglobulinemia 2, autosomal recessive ⚠
  • p.Val207Met Single submitter agammaglobulinemia 2, autosomal recessive ⚠