WNT3 — 138 ClinVar variants
All ClinVar germline WNT3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 46 flagged for review →
1 Pathogenic · 1 Likely pathogenic · 8 Benign · 3 Benign/Likely benign · 72 Likely benign · 53 Uncertain significance
Full WNT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 46
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 36
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- WNT3 p.Arg87Cys Uncertain significance Multiple submitters
- WNT3 p.Gly46Ser Uncertain significance Multiple submitters
- WNT3 p.Lys54Arg Uncertain significance Multiple submitters
- WNT3 p.Val351Met Uncertain significance Multiple submitters
- WNT3 p.Ala119Thr Uncertain significance Single submitter
- WNT3 p.Ala126Pro Uncertain significance Single submitter
- WNT3 p.Ala162Ser Uncertain significance Single submitter
- WNT3 p.Ala229Val Uncertain significance Single submitter
- WNT3 p.Arg326Gln Uncertain significance Single submitter
- WNT3 p.Arg85Gln Uncertain significance Single submitter
- WNT3 p.Asp311Asn Uncertain significance Single submitter
- WNT3 p.Asp96His Uncertain significance Single submitter
- WNT3 p.Glu151Asp Uncertain significance Single submitter
- WNT3 p.Glu177Asp Uncertain significance Single submitter
- WNT3 p.Glu177Val Uncertain significance Single submitter
- WNT3 p.Gly32Ser Uncertain significance Single submitter
- WNT3 p.Gly39Asp Uncertain significance Single submitter
- WNT3 p.Ile138Phe Uncertain significance Single submitter
- WNT3 p.Ile230Val Uncertain significance Single submitter
- WNT3 p.Ile25Val Uncertain significance Single submitter
- WNT3 p.Ile333Val Uncertain significance Single submitter
- WNT3 p.Ile348Val Uncertain significance Single submitter
- WNT3 p.Ile77Val Uncertain significance Single submitter
- WNT3 p.Leu6Phe Uncertain significance Single submitter
- WNT3 p.Lys146Glu Uncertain significance Single submitter
- WNT3 p.Lys237Arg Uncertain significance Single submitter
- WNT3 p.Pro281Ser Uncertain significance Single submitter
- WNT3 p.Pro288Leu Uncertain significance Single submitter
- WNT3 p.Pro3Ser Uncertain significance Single submitter
- WNT3 p.Ser242Trp Uncertain significance Single submitter
- WNT3 p.Thr17Ser Uncertain significance Single submitter
- WNT3 p.Trp155Ser Uncertain significance Single submitter
- WNT3 p.Tyr276Asn Uncertain significance Single submitter
- WNT3 p.Val104Ile Uncertain significance Single submitter
- WNT3 p.Val340Ile Uncertain significance Single submitter
-
WNT3 p.Gly213Asp
Uncertain significance
No assertion criteria
bladder exstrophy-epispadias-cloacal exstrophy complex
Predictors split 10
The independent predictors disagree with each other — read with care.
- WNT3 p.Arg87His Uncertain significance Multiple submitters
- WNT3 p.Asp106Tyr Uncertain significance Multiple submitters
- WNT3 p.Leu5Met Uncertain significance Multiple submitters
- WNT3 p.Leu8Gln Uncertain significance Multiple submitters
- WNT3 p.Arg170Ser Uncertain significance Single submitter
- WNT3 p.Arg85Trp Uncertain significance Single submitter
- WNT3 p.Glu171Gln Uncertain significance Single submitter
- WNT3 p.Gly291Asp Uncertain significance Single submitter
- WNT3 p.Ile138Thr Uncertain significance Single submitter
- WNT3 p.Ser136Tyr Uncertain significance Single submitter
All WNT3 variants
Pathogenic 1
- p.Gln83Ter No assertion criteria tetraamelia syndrome 1
Likely pathogenic 1
- p.Cys91Arg No assertion criteria bladder exstrophy-epispadias-cloacal exstrophy complex
Benign 8
- c.322+18A>G Multiple submitters
- c.322+28A>G Multiple submitters
- c.322+38T>G Multiple submitters
- c.323-293G>C Multiple submitters
- c.*8+232T>C Multiple submitters
- c.322+19dup Single submitter
- c.323-252C>G Single submitter
- p.Leu6= Single submitter
Benign/Likely benign 3
- c.322+18del Multiple submitters
- p.Cys45= Multiple submitters
- p.Ser143= Multiple submitters
Likely benign 72
- c.80+53G>T Multiple submitters
- c.80+72G>C Multiple submitters
- c.*8+140G>A Multiple submitters
- p.Gly86= Multiple submitters
- p.Arg176= Single submitter
- c.322+14G>A Single submitter
- c.322+15C>G Single submitter
- c.322+16T>G Single submitter
- c.322+20G>C Single submitter
- c.322+20G>T Single submitter
- c.322+33_322+34del Single submitter
- c.322+33C>G Single submitter
- c.322+34T>G Single submitter
- c.322+9T>G Single submitter
- c.323-11C>T Single submitter
- c.323-13G>T Single submitter
- c.323-17C>G Single submitter
- c.323-20T>G Single submitter
- c.323-7C>T Single submitter
- c.588+13A>G Single submitter
- c.588+18C>T Single submitter
- c.588+20C>T Single submitter
- c.588+8del Single submitter
- c.588+9G>A Single submitter
- c.589-20C>T Single submitter
- c.589-210G>A Single submitter
- c.589-7C>G Single submitter
- c.80+10G>A Single submitter
- c.81-10C>T Single submitter
- c.81-16C>A Single submitter
- c.81-17C>A Single submitter
- p.Ala126= Single submitter
- p.Ala132= Single submitter
- p.Ala173= Single submitter
- p.Ala193= Single submitter
- p.Arg176= Single submitter
- p.Arg272= Single submitter
- p.Asn301= Single submitter
- p.Asp106= Single submitter
- p.Asp239= Single submitter
- p.Cys59= Single submitter
- p.Gln33= Single submitter
- p.Glu192= Single submitter
- p.Gly157= Single submitter
- p.Gly194= Single submitter
- p.Gly72= Single submitter
- p.His305= Single submitter
- p.His4= Single submitter
- p.Ile230= Single submitter
- p.Ile307= Single submitter
- p.Ile63= Single submitter
- p.Leu167= Single submitter
- p.Leu9= Single submitter
- p.Lys237= Single submitter
- p.Pro103= Single submitter
- p.Pro148= Single submitter
- p.Pro180= Single submitter
- p.Pro281= Single submitter
- p.Ser112= Single submitter
- p.Ser120= Single submitter
- p.Ser169= Single submitter
- p.Ser184= Single submitter
- p.Ser212= Single submitter
- p.Ser214= Single submitter
- p.Ser264= Single submitter
- p.Thr258= Single submitter
- p.Thr270= Single submitter
- p.Thr323= Single submitter
- p.Tyr276= Single submitter
- p.Tyr277= Single submitter
- p.Tyr339= Single submitter
- p.Val217= Single submitter
Uncertain significance 53
- p.Ala173Val Multiple submitters
- p.Arg87Cys Multiple submitters ⚠
- p.Arg87His Multiple submitters ⚠
- p.Asp106Tyr Multiple submitters ⚠
- p.Gly46Ser Multiple submitters ⚠
- p.Leu5Met Multiple submitters ⚠
- p.Leu8Gln Multiple submitters ⚠
- p.Lys325Asn Multiple submitters
- p.Lys54Arg Multiple submitters ⚠
- p.Val351Met Multiple submitters ⚠
- c.80+3A>C Single submitter
- p.Ala119Thr Single submitter ⚠
- p.Ala126Pro Single submitter ⚠
- p.Ala162Ser Single submitter ⚠
- p.Ala229Val Single submitter ⚠
- p.Arg170Ser Single submitter ⚠
- p.Arg183_Ser184insGluAsnArgProAspAlaArg Single submitter
- p.Arg253Gln Single submitter
- p.Arg326Gln Single submitter ⚠
- p.Arg85Gln Single submitter ⚠
- p.Arg85Trp Single submitter ⚠
- p.Asp311Asn Single submitter ⚠
- p.Asp96His Single submitter ⚠
- p.Glu151Asp Single submitter ⚠
- p.Glu171Gln Single submitter ⚠
- p.Glu177Asp Single submitter ⚠
- p.Glu177Val Single submitter ⚠
- p.Gly291Asp Single submitter ⚠
- p.Gly32Ser Single submitter ⚠
- p.Gly39Asp Single submitter ⚠
- p.Ile138Phe Single submitter ⚠
- p.Ile138Thr Single submitter ⚠
- p.Ile230Val Single submitter ⚠
- p.Ile25Val Single submitter ⚠
- p.Ile333Val Single submitter ⚠
- p.Ile348Val Single submitter ⚠
- p.Ile77Val Single submitter ⚠
- p.Leu6Phe Single submitter ⚠
- p.Lys146Glu Single submitter ⚠
- p.Lys237Arg Single submitter ⚠
- p.Phe293Val Single submitter
- p.Pro281Ser Single submitter ⚠
- p.Pro288Leu Single submitter ⚠
- p.Pro3Ser Single submitter ⚠
- p.Ser130= Single submitter
- p.Ser136Tyr Single submitter ⚠
- p.Ser242Trp Single submitter ⚠
- p.Thr17Ser Single submitter ⚠
- p.Trp155Ser Single submitter ⚠
- p.Tyr276Asn Single submitter ⚠
- p.Val104Ile Single submitter ⚠
- p.Val340Ile Single submitter ⚠
- p.Gly213Asp No assertion criteria bladder exstrophy-epispadias-cloacal exstrophy complex ⚠