TLR9 — 141 ClinVar variants

All ClinVar germline TLR9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 108 flagged for review →

1 Likely pathogenic · 9 Benign · 16 Likely benign · 115 Uncertain significance

Full TLR9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 108

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.

TLR9 p.Pro183Arg Likely pathogenic No assertion criteria
esophageal atresia/tracheoesophageal fistula

Predictors lean, ClinVar uncertain 90

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

Predictors split 17

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

All TLR9 variants

Likely pathogenic 1

p.Pro183Arg No assertion criteria esophageal atresia/tracheoesophageal fistula ⚠

Benign 9

p.Arg5Cys Multiple submitters
p.Arg863Gln Multiple submitters
p.Gly563= Multiple submitters
p.Ser147= Multiple submitters
p.Ser509= Multiple submitters
p.Thr383= Multiple submitters
p.Ala1031= Single submitter
p.Gln804= Single submitter
p.Ile232= Single submitter

Likely benign 16

p.Ala717= Single submitter
p.Arg1023Gln Single submitter
p.Arg639His Single submitter
p.Asn64= Single submitter
p.Asp421Val Single submitter ⚠
p.Glu548= Single submitter
p.Gly409Ser Single submitter
p.Gly522Ser Single submitter
p.His91Arg Single submitter
p.Ile18Met Single submitter
p.Leu600= Single submitter
p.Leu643= Single submitter
p.Ser599= Single submitter
p.Ser628Arg Single submitter
p.Ser750Gly Single submitter
p.Val571Met Single submitter

Uncertain significance 115

p.828LG[1] Single submitter
p.Ala140Val Single submitter ⚠
p.Ala191Thr Single submitter ⚠
p.Ala236Val Single submitter ⚠
p.Ala241Thr Single submitter ⚠
p.Ala572Thr Single submitter ⚠
p.Ala685Thr Single submitter ⚠
p.Ala734Ser Single submitter ⚠
p.Ala734Thr Single submitter ⚠
p.Ala736Thr Single submitter ⚠
p.Ala765Thr Single submitter ⚠
p.Ala780Val Single submitter ⚠
p.Ala813Asp Single submitter ⚠
p.Arg1015Gly Single submitter ⚠
p.Arg1023Trp Single submitter ⚠
p.Arg185Ser Single submitter Meniere disease ⚠
p.Arg247Cys Single submitter ⚠
p.Arg256Cys Single submitter
p.Arg256His Single submitter ⚠
p.Arg389Cys Single submitter ⚠
p.Arg418His Single submitter ⚠
p.Arg426Cys Single submitter ⚠
p.Arg467Gly Single submitter ⚠
p.Arg481Gly Single submitter ⚠
p.Arg481Trp Single submitter ⚠
p.Arg5His Single submitter ⚠
p.Arg5Leu Single submitter ⚠
p.Arg601Gln Single submitter ⚠
p.Arg639Cys Single submitter ⚠
p.Arg649Cys Single submitter ⚠
p.Arg659Cys Single submitter ⚠
p.Arg659His Single submitter ⚠
p.Arg74Cys Single submitter ⚠
p.Arg74His Single submitter ⚠
p.Arg787Gln Single submitter ⚠
p.Arg787Pro Single submitter ⚠
p.Arg787Trp Single submitter ⚠
p.Arg807Cys Single submitter ⚠
p.Arg807His Single submitter ⚠
p.Arg857Trp Single submitter ⚠
p.Arg859Gln Single submitter ⚠
p.Arg901Cys Single submitter ⚠
p.Arg901His Single submitter ⚠
p.Arg905His Single submitter ⚠
p.Arg931Cys Single submitter ⚠
p.Arg948Cys Single submitter ⚠
p.Arg948Pro Single submitter ⚠
p.Arg957Cys Single submitter
p.Arg977Cys Single submitter ⚠
p.Arg979His Single submitter ⚠
p.Arg982Trp Single submitter ⚠
p.Asn177Tyr Single submitter ⚠
p.Asn217Asp Single submitter ⚠
p.Asn506Ser Single submitter
p.Asn513Ser Single submitter ⚠
p.Asn567Ser Single submitter ⚠
p.Asn585Lys Single submitter ⚠
p.Asn93Ser Single submitter ⚠
p.Asp250Asn Single submitter ⚠
p.Asp452Glu Single submitter ⚠
p.Asp527His Single submitter ⚠
p.Asp683Asn Single submitter
p.Asp877Asn Single submitter ⚠
p.Glu543Ala Single submitter
p.Glu616Lys Single submitter ⚠
p.Glu890Lys Single submitter ⚠
p.Gly197Ala Single submitter ⚠
p.Gly361Arg Single submitter ⚠
p.Gly783Ser Single submitter ⚠
p.Gly794Ser Single submitter ⚠
p.Gly975Ser Single submitter ⚠
p.His1018Asn Single submitter ⚠
p.His271Tyr Single submitter ⚠
p.His530Tyr Single submitter ⚠
p.His55Asn Single submitter ⚠
p.His85Tyr Single submitter ⚠
p.His9Tyr Single submitter ⚠
p.Leu163Ile Single submitter ⚠
p.Leu206Phe Single submitter
p.Leu243Gln Single submitter
p.Leu341Pro Single submitter ⚠
p.Leu453Phe Single submitter ⚠
p.Leu673Val Single submitter Meniere disease ⚠
p.Leu775Val Single submitter ⚠
p.Lys678Ile Single submitter ⚠
p.Lys917Arg Single submitter ⚠
p.Met1011Val Single submitter ⚠
p.Met136Val Single submitter ⚠
p.Met437Ile Single submitter ⚠
p.Met834Ile Single submitter ⚠
p.Phe272Leu Single submitter ⚠
p.Phe675Ile Single submitter ⚠
p.Pro142Ser Single submitter ⚠
p.Pro455Arg Single submitter ⚠
p.Pro457Leu Single submitter ⚠
p.Pro489Leu Single submitter ⚠
p.Pro793Arg Single submitter ⚠
p.Pro793Leu Single submitter
p.Pro869Arg Single submitter ⚠
p.Pro973Ser Single submitter ⚠
p.Ser302Ile Single submitter ⚠
p.Ser362Ile Single submitter ⚠
p.Ser714Arg Single submitter ⚠
p.Ser750Asn Single submitter ⚠
p.Ser881Asn Single submitter ⚠
p.Thr879Lys Single submitter ⚠
p.Thr933Met Single submitter ⚠
p.Thr940Met Single submitter ⚠
p.Val349Met Single submitter ⚠
p.Val420Met Single submitter ⚠
p.Val446Ile Single submitter ⚠
p.Val446Phe Single submitter ⚠
p.Val485Leu Single submitter ⚠
p.Val564Leu Single submitter ⚠
p.Val716Met Single submitter ⚠