WNT3A — 180 ClinVar variants
All ClinVar germline WNT3A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 102 flagged for review →
7 Benign · 60 Likely benign · 113 Uncertain significance
Full WNT3A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 102
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 lean, ClinVar uncertain 79
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- WNT3A p.Ala318Pro Uncertain significance Multiple submitters
- WNT3A p.Arg141His Uncertain significance Multiple submitters
- WNT3A p.Arg322Gln Uncertain significance Multiple submitters
- WNT3A p.Arg324Trp Uncertain significance Multiple submitters
- WNT3A p.Glu160Lys Uncertain significance Multiple submitters
- WNT3A p.Glu68Lys Uncertain significance Multiple submitters
- WNT3A p.Gly147Asp Uncertain significance Multiple submitters
- WNT3A p.Ile115Met Uncertain significance Multiple submitters
- WNT3A p.Ile62Met Uncertain significance Multiple submitters
- WNT3A p.Ile72Ser Uncertain significance Multiple submitters
- WNT3A p.Ile97Val Uncertain significance Multiple submitters
- WNT3A p.Leu95Gln Uncertain significance Multiple submitters
- WNT3A p.Met164Ile Uncertain significance Multiple submitters
- WNT3A p.Pro222Ala Uncertain significance Multiple submitters
- WNT3A p.Pro266Leu Uncertain significance Multiple submitters
- WNT3A p.Pro30Ser Uncertain significance Multiple submitters
- WNT3A p.Ser166Cys Uncertain significance Multiple submitters
- WNT3A p.Ser19Asn Uncertain significance Multiple submitters
- WNT3A p.Trp219Arg Uncertain significance Multiple submitters
- WNT3A p.Tyr262Ser Uncertain significance Multiple submitters
- WNT3A p.Val299Ile Uncertain significance Multiple submitters
- WNT3A p.Val60Met Uncertain significance Multiple submitters
- WNT3A p.Val91Ile Uncertain significance Multiple submitters
- WNT3A p.Ala114Thr Uncertain significance Single submitter
- WNT3A p.Ala16Thr Uncertain significance Single submitter
- WNT3A p.Ala16Val Uncertain significance Single submitter
- WNT3A p.Ala276Pro Uncertain significance Single submitter
- WNT3A p.Ala96Ser Uncertain significance Single submitter
- WNT3A p.Arg167Gln Uncertain significance Single submitter
- WNT3A p.Arg173Trp Uncertain significance Single submitter
- WNT3A p.Arg176Gln Uncertain significance Single submitter
- WNT3A p.Arg295His Uncertain significance Single submitter
- WNT3A p.Arg322Trp Uncertain significance Single submitter
- WNT3A p.Arg324Gln Uncertain significance Single submitter
- WNT3A p.Arg328Gly Uncertain significance Single submitter
- WNT3A p.Arg328His Uncertain significance Single submitter
- WNT3A p.Arg82Cys Uncertain significance Single submitter
- WNT3A p.Arg84Cys Uncertain significance Single submitter
- WNT3A p.Arg85Gln Uncertain significance Single submitter
- WNT3A p.Asn184Ser Uncertain significance Single submitter
- WNT3A p.Asn298Ile Uncertain significance Single submitter
- WNT3A p.Asn317Lys Uncertain significance Single submitter
- WNT3A p.Asp158Asn Uncertain significance Single submitter
- WNT3A p.Asp158Gly Uncertain significance Single submitter
- WNT3A p.Asp171Glu Uncertain significance Single submitter
- WNT3A p.Asp229Tyr Uncertain significance Single submitter
- WNT3A p.Gln31Arg Uncertain significance Single submitter
- WNT3A p.Gln340Arg Uncertain significance Single submitter
- WNT3A p.Gln38Pro Uncertain significance Single submitter
- WNT3A p.Gly119Ser Uncertain significance Single submitter
- WNT3A p.Gly154Asp Uncertain significance Single submitter
- WNT3A p.Gly162Asp Uncertain significance Single submitter
- WNT3A p.Gly207Glu Uncertain significance Single submitter
- WNT3A p.Gly306Arg Uncertain significance Single submitter
- WNT3A p.Gly83Ser Uncertain significance Single submitter
- WNT3A p.Gly99Arg Uncertain significance Single submitter
- WNT3A p.Ile159Thr Uncertain significance Single submitter
- WNT3A p.Ile159Val Uncertain significance Single submitter
- WNT3A p.Leu10Phe Uncertain significance Single submitter
- WNT3A p.Leu309Arg Uncertain significance Single submitter
- WNT3A p.Leu4Pro Uncertain significance Single submitter
- WNT3A p.Leu9Phe Uncertain significance Single submitter
- WNT3A p.Lys51Arg Uncertain significance Single submitter
- WNT3A p.Phe81Leu Uncertain significance Single submitter
- WNT3A p.Pro146Ala Uncertain significance Single submitter
- WNT3A p.Pro146Leu Uncertain significance Single submitter
- WNT3A p.Ser140Arg Uncertain significance Single submitter
- WNT3A p.Ser301Ala Uncertain significance Single submitter
- WNT3A p.Ser37Leu Uncertain significance Single submitter
- WNT3A p.Thr261Pro Uncertain significance Single submitter
- WNT3A p.Thr267Lys Uncertain significance Single submitter
- WNT3A p.Thr296Ile Uncertain significance Single submitter
- WNT3A p.Trp152Leu Uncertain significance Single submitter
- WNT3A p.Trp218Arg Uncertain significance Single submitter
- WNT3A p.Trp219Cys Uncertain significance Single submitter
- WNT3A p.Tyr336Ser Uncertain significance Single submitter
- WNT3A p.Val214Met Uncertain significance Single submitter
- WNT3A p.Val345Phe Uncertain significance Single submitter
- WNT3A p.Val348Leu Uncertain significance Single submitter
Predictors split 23
The independent predictors disagree with each other — read with care.
- WNT3A p.Arg141Pro Uncertain significance Multiple submitters
- WNT3A p.Arg82His Uncertain significance Multiple submitters
- WNT3A p.Gly313Ser Uncertain significance Multiple submitters
- WNT3A p.His332Arg Uncertain significance Multiple submitters
- WNT3A p.Arg126His Uncertain significance Single submitter
- WNT3A p.Arg185His Uncertain significance Single submitter
- WNT3A p.Arg247Leu Uncertain significance Single submitter
- WNT3A p.Arg247Pro Uncertain significance Single submitter
- WNT3A p.Asp294Tyr Uncertain significance Single submitter
- WNT3A p.Glu157Lys Uncertain significance Single submitter
- WNT3A p.Glu189Lys Uncertain significance Single submitter
- WNT3A p.Glu213Lys Uncertain significance Single submitter
- WNT3A p.Glu248Val Uncertain significance Single submitter
- WNT3A p.Glu254Asp Uncertain significance Single submitter
- WNT3A p.His349Gln Uncertain significance Single submitter
- WNT3A p.Leu17Pro Uncertain significance Single submitter
- WNT3A p.Met63Thr Uncertain significance Single submitter
- WNT3A p.Pro21Leu Uncertain significance Single submitter
- WNT3A p.Ser127Leu Uncertain significance Single submitter
- WNT3A p.Tyr260Asp Uncertain significance Single submitter
- WNT3A p.Val101Met Uncertain significance Single submitter
- WNT3A p.Val49Leu Uncertain significance Single submitter
- WNT3A p.Val66Leu Uncertain significance Single submitter
All WNT3A variants
Benign 7
- p.Ala134Thr Multiple submitters
- p.Asp171= Multiple submitters
- c.579+16G>A Single submitter
- c.72-19C>T Single submitter
- p.Asp93Asn Single submitter
- p.Cys312= Single submitter
- p.Val124= Single submitter
Likely benign 60
- p.Asn188= Multiple submitters
- p.Phe169= Multiple submitters
- c.313+17G>A Single submitter
- c.313+18G>T Single submitter
- c.313+19G>A Single submitter
- c.314-11T>A Single submitter
- c.314-19A>G Single submitter
- c.579+11C>T Single submitter
- c.579+18A>G Single submitter
- c.579+8C>T Single submitter
- c.579+9G>A Single submitter
- c.580-11G>A Single submitter
- c.580-11G>T Single submitter
- c.580-14C>T Single submitter
- c.580-19T>C Single submitter
- c.580-7C>T Single submitter
- c.71+15T>A Single submitter
- c.71+16C>G Single submitter
- c.72-18G>A Single submitter
- p.Ala118= Single submitter
- p.Ala133= Single submitter
- p.Ala170= Single submitter
- p.Ala196= Single submitter
- p.Ala238= Single submitter
- p.Ala318= Single submitter
- p.Arg250= Single submitter
- p.Arg323= Single submitter
- p.Arg82= Single submitter
- p.Arg84= Single submitter
- p.Arg85= Single submitter
- p.Asn284= Single submitter
- p.Asn317= Single submitter
- p.Cys128= Single submitter
- p.Gln340= Single submitter
- p.Glu325= Single submitter
- p.Glu76= Single submitter
- p.Gly191= Single submitter
- p.His113= Single submitter
- p.His302= Single submitter
- p.His92= Single submitter
- p.Ile159= Single submitter
- p.Ile304= Single submitter
- p.Leu4= Single submitter
- p.Leu9= Single submitter
- p.Lys234= Single submitter
- p.Phe81= Single submitter
- p.Pro100= Single submitter
- p.Pro21= Single submitter
- p.Pro258= Single submitter
- p.Pro266= Single submitter
- p.Pro64= Single submitter
- p.Ser109= Single submitter
- p.Ser25= Single submitter
- p.Ser34= Single submitter
- p.Ser37= Single submitter
- p.Thr132= Single submitter
- p.Thr287= Single submitter
- p.Thr90= Single submitter
- p.Tyr59= Single submitter
- p.Val337= Single submitter
Uncertain significance 113
- p.Ala318Pro Multiple submitters ⚠
- p.Arg141His Multiple submitters ⚠
- p.Arg141Pro Multiple submitters ⚠
- p.Arg322Gln Multiple submitters ⚠
- p.Arg324Trp Multiple submitters ⚠
- p.Arg82His Multiple submitters ⚠
- p.Glu160Lys Multiple submitters ⚠
- p.Glu68Lys Multiple submitters ⚠
- p.Gly147Asp Multiple submitters ⚠
- p.Gly313Ser Multiple submitters ⚠
- p.His332Arg Multiple submitters ⚠
- p.Ile115Met Multiple submitters ⚠
- p.Ile62Met Multiple submitters ⚠
- p.Ile72Ser Multiple submitters ⚠
- p.Ile97Val Multiple submitters ⚠
- p.Leu95Gln Multiple submitters ⚠
- p.Met164Ile Multiple submitters ⚠
- p.Phe290Ser Multiple submitters
- p.Pro222Ala Multiple submitters ⚠
- p.Pro266Leu Multiple submitters ⚠
- p.Pro30Ser Multiple submitters ⚠
- p.Ser166Cys Multiple submitters ⚠
- p.Ser19Asn Multiple submitters ⚠
- p.Trp219Arg Multiple submitters ⚠
- p.Tyr262Ser Multiple submitters ⚠
- p.Val299Ile Multiple submitters ⚠
- p.Val60Met Multiple submitters ⚠
- p.Val91Ile Multiple submitters ⚠
- p.Ala114Thr Single submitter ⚠
- p.Ala16Thr Single submitter ⚠
- p.Ala16Val Single submitter ⚠
- p.Ala276Pro Single submitter ⚠
- p.Ala96Ser Single submitter ⚠
- p.Arg126His Single submitter ⚠
- p.Arg141Cys Single submitter
- p.Arg167Gln Single submitter ⚠
- p.Arg173Trp Single submitter ⚠
- p.Arg176Gln Single submitter ⚠
- p.Arg185His Single submitter ⚠
- p.Arg247Leu Single submitter ⚠
- p.Arg247Pro Single submitter ⚠
- p.Arg259Leu Single submitter
- p.Arg295His Single submitter ⚠
- p.Arg322Trp Single submitter ⚠
- p.Arg324Gln Single submitter ⚠
- p.Arg324Pro Single submitter
- p.Arg328Cys Single submitter
- p.Arg328Gly Single submitter ⚠
- p.Arg328His Single submitter ⚠
- p.Arg82Cys Single submitter ⚠
- p.Arg84Cys Single submitter ⚠
- p.Arg85Gln Single submitter ⚠
- p.Asn184Ser Single submitter ⚠
- p.Asn298Ile Single submitter ⚠
- p.Asn317Lys Single submitter ⚠
- p.Asp158Asn Single submitter ⚠
- p.Asp158Gly Single submitter ⚠
- p.Asp171Glu Single submitter ⚠
- p.Asp229Tyr Single submitter ⚠
- p.Asp294Tyr Single submitter ⚠
- p.Cys212Ter Single submitter
- p.Gln31Arg Single submitter ⚠
- p.Gln340Arg Single submitter ⚠
- p.Gln38Pro Single submitter ⚠
- p.Glu157Lys Single submitter ⚠
- p.Glu174fs Single submitter
- p.Glu189Lys Single submitter ⚠
- p.Glu213Lys Single submitter ⚠
- p.Glu248Val Single submitter ⚠
- p.Glu254Asp Single submitter ⚠
- p.Glu76Ter Single submitter
- p.Gly119Ser Single submitter ⚠
- p.Gly154Asp Single submitter ⚠
- p.Gly162Asp Single submitter ⚠
- p.Gly207Glu Single submitter ⚠
- p.Gly306Arg Single submitter ⚠
- p.Gly83Ser Single submitter ⚠
- p.Gly99Arg Single submitter ⚠
- p.His349Gln Single submitter ⚠
- p.Ile159Thr Single submitter ⚠
- p.Ile159Val Single submitter ⚠
- p.Leu10Phe Single submitter ⚠
- p.Leu17Pro Single submitter ⚠
- p.Leu309Arg Single submitter ⚠
- p.Leu4Pro Single submitter ⚠
- p.Leu9Phe Single submitter ⚠
- p.Lys215fs Single submitter
- p.Lys51Arg Single submitter ⚠
- p.Met63Thr Single submitter ⚠
- p.Phe81Leu Single submitter ⚠
- p.Pro146Ala Single submitter ⚠
- p.Pro146Leu Single submitter ⚠
- p.Pro21Leu Single submitter ⚠
- p.Ser127Leu Single submitter ⚠
- p.Ser140Arg Single submitter ⚠
- p.Ser181fs Single submitter
- p.Ser301Ala Single submitter ⚠
- p.Ser37Leu Single submitter ⚠
- p.Thr261Pro Single submitter ⚠
- p.Thr267Lys Single submitter ⚠
- p.Thr296Ile Single submitter ⚠
- p.Trp152Leu Single submitter ⚠
- p.Trp218Arg Single submitter ⚠
- p.Trp219Cys Single submitter ⚠
- p.Tyr260Asp Single submitter ⚠
- p.Tyr336Ser Single submitter ⚠
- p.Val101Met Single submitter ⚠
- p.Val214Met Single submitter ⚠
- p.Val243Met Single submitter
- p.Val345Phe Single submitter ⚠
- p.Val348Leu Single submitter ⚠
- p.Val49Leu Single submitter ⚠
- p.Val66Leu Single submitter ⚠