UPK3A — 96 ClinVar variants
All ClinVar germline UPK3A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 54 flagged for review →
1 Likely pathogenic · 4 Conflicting · 8 Benign · 7 Benign/Likely benign · 14 Likely benign · 62 Uncertain significance
Full UPK3A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 54
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 4
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
- UPK3A p.Arg271Gln Conflicting Single submitter
-
UPK3A p.Gly140Arg
Conflicting
Single submitter
renal hypodysplasia/aplasia 1
-
UPK3A p.Pro273Leu
Conflicting
Single submitter
renal hypodysplasia/aplasia 1
-
UPK3A p.Thr244Met
Conflicting
Single submitter
UPK3A-related disorder
Predictors lean, ClinVar uncertain 42
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
UPK3A p.Arg187His
Uncertain significance
Multiple submitters
renal hypodysplasia/aplasia 1
-
UPK3A p.Asp68Asn
Uncertain significance
Multiple submitters
renal hypodysplasia/aplasia 1
-
UPK3A p.Ile119Ser
Uncertain significance
Multiple submitters
UPK3A-related disorder
-
UPK3A p.Ser111Asn
Uncertain significance
Multiple submitters
renal hypodysplasia/aplasia 1
-
UPK3A p.Ser157Leu
Uncertain significance
Multiple submitters
renal hypodysplasia/aplasia 1
-
UPK3A p.Ser258Leu
Uncertain significance
Multiple submitters
UPK3A-related disorder
- UPK3A p.Ala158Glu Uncertain significance Single submitter
- UPK3A p.Ala231Thr Uncertain significance Single submitter
- UPK3A p.Ala254Pro Uncertain significance Single submitter
- UPK3A p.Ala278Val Uncertain significance Single submitter
-
UPK3A p.Arg135Lys
Uncertain significance
Single submitter
renal hypodysplasia/aplasia 1
- UPK3A p.Arg187Cys Uncertain significance Single submitter
- UPK3A p.Arg203Gln Uncertain significance Single submitter
- UPK3A p.Arg73Gly Uncertain significance Single submitter
- UPK3A p.Asn147Ser Uncertain significance Single submitter
- UPK3A p.Asp112Ala Uncertain significance Single submitter
- UPK3A p.Asp184Val Uncertain significance Single submitter
-
UPK3A p.Asp50His
Uncertain significance
Single submitter
UPK3A-related disorder
- UPK3A p.Gln24Glu Uncertain significance Single submitter
- UPK3A p.Glu161Val Uncertain significance Single submitter
- UPK3A p.Glu177Lys Uncertain significance Single submitter
-
UPK3A p.Gly120Glu
Uncertain significance
Single submitter
renal hypodysplasia/aplasia 1
- UPK3A p.Gly242Arg Uncertain significance Single submitter
- UPK3A p.His59Gln Uncertain significance Single submitter
- UPK3A p.Ile211Leu Uncertain significance Single submitter
- UPK3A p.Leu223Arg Uncertain significance Single submitter
- UPK3A p.Leu37Val Uncertain significance Single submitter
- UPK3A p.Met237Lys Uncertain significance Single submitter
- UPK3A p.Pro109Leu Uncertain significance Single submitter
- UPK3A p.Pro155Ser Uncertain significance Single submitter
- UPK3A p.Pro45Ser Uncertain significance Single submitter
- UPK3A p.Ser157Trp Uncertain significance Single submitter
- UPK3A p.Ser195Leu Uncertain significance Single submitter
-
UPK3A p.Ser268Pro
Uncertain significance
Single submitter
renal hypodysplasia/aplasia 1
- UPK3A p.Ser76Leu Uncertain significance Single submitter
- UPK3A p.Thr251Ile Uncertain significance Single submitter
- UPK3A p.Thr267Met Uncertain significance Single submitter
- UPK3A p.Thr32Asn Uncertain significance Single submitter
- UPK3A p.Thr83Ile Uncertain significance Single submitter
- UPK3A p.Trp144Leu Uncertain significance Single submitter
- UPK3A p.Tyr281His Uncertain significance Single submitter
- UPK3A p.Thr39Ala Uncertain significance No assertion criteria
Predictors split 8
The independent predictors disagree with each other — read with care.
-
UPK3A p.Ala154Pro
Benign
Multiple submitters
renal hypodysplasia/aplasia 1
- UPK3A p.Arg204Trp Uncertain significance Single submitter
-
UPK3A p.Asp121Tyr
Uncertain significance
Single submitter
renal hypodysplasia/aplasia 1
- UPK3A p.Asp68His Uncertain significance Single submitter
- UPK3A p.Gly206Arg Uncertain significance Single submitter
- UPK3A p.Thr173Met Uncertain significance Single submitter
- UPK3A p.Thr88Met Uncertain significance Single submitter
-
UPK3A p.Gly202Asp
Uncertain significance
No assertion criteria
congenital anomalies of kidney and urinary tract 1
All UPK3A variants
Likely pathogenic 1
- c.53-1G>A Single submitter
Conflicting classifications of pathogenicity 4
- p.Arg271Gln Single submitter ⚠
- p.Gly140Arg Single submitter renal hypodysplasia/aplasia 1 ⚠
- p.Pro273Leu Single submitter renal hypodysplasia/aplasia 1 ⚠
- p.Thr244Met Single submitter UPK3A-related disorder ⚠
Benign 8
- c.209-78A>G Multiple submitters
- p.Ala154Pro Multiple submitters renal hypodysplasia/aplasia 1 ⚠
- p.Gln286= Multiple submitters renal hypodysplasia/aplasia 1
- p.Gln91Leu Multiple submitters renal hypodysplasia/aplasia 1
- p.Pro155= Multiple submitters renal hypodysplasia/aplasia 1
- p.Ser183= Multiple submitters renal hypodysplasia/aplasia 1
- p.Val134= Multiple submitters renal hypodysplasia/aplasia 1
- c.208+298G>C Single submitter
Benign/Likely benign 7
- c.571+1G>A Multiple submitters renal hypodysplasia/aplasia 1
- p.Ile119Thr Multiple submitters renal hypodysplasia/aplasia 1
- p.Phe30= Multiple submitters renal hypodysplasia/aplasia 1
- p.Ser87Ala Multiple submitters renal hypodysplasia/aplasia 1
- p.Ser87Ter Multiple submitters renal hypodysplasia/aplasia 1
- p.Thr196= Multiple submitters renal hypodysplasia/aplasia 1
- p.Trp182Ter Multiple submitters renal hypodysplasia/aplasia 1
Likely benign 14
- c.704+8C>G Multiple submitters renal hypodysplasia/aplasia 1
- p.Val210Ile Multiple submitters renal hypodysplasia/aplasia 1
- c.572-19G>C Single submitter
- c.*26C>T Single submitter renal hypodysplasia/aplasia 1
- c.*73C>T Single submitter renal hypodysplasia/aplasia 1
- p.Ala254= Single submitter
- p.Asn139= Single submitter renal hypodysplasia/aplasia 1
- p.Asn170= Single submitter
- p.Gln249= Single submitter
- p.Leu191Pro Single submitter
- p.Ser195= Single submitter
- p.Thr58= Single submitter
- p.Gln149His No assertion criteria UPK3A-related disorder
- p.Ser262= No assertion criteria UPK3A-related disorder
Uncertain significance 62
- p.Arg187His Multiple submitters renal hypodysplasia/aplasia 1 ⚠
- p.Asp68Asn Multiple submitters renal hypodysplasia/aplasia 1 ⚠
- p.Ile119Ser Multiple submitters UPK3A-related disorder ⚠
- p.Ser111Asn Multiple submitters renal hypodysplasia/aplasia 1 ⚠
- p.Ser157Leu Multiple submitters renal hypodysplasia/aplasia 1 ⚠
- p.Ser258Leu Multiple submitters UPK3A-related disorder ⚠
- c.209-11C>T Single submitter renal hypodysplasia/aplasia 1
- c.488+2T>C Single submitter
- c.704+8C>A Single submitter renal hypodysplasia/aplasia 1
- c.-26C>G Single submitter renal hypodysplasia/aplasia 1
- c.*107T>C Single submitter renal hypodysplasia/aplasia 1
- c.*42C>T Single submitter renal hypodysplasia/aplasia 1
- p.Ala158Glu Single submitter ⚠
- p.Ala231Thr Single submitter ⚠
- p.Ala254Pro Single submitter ⚠
- p.Ala278Val Single submitter ⚠
- p.Arg135Lys Single submitter renal hypodysplasia/aplasia 1 ⚠
- p.Arg187Cys Single submitter ⚠
- p.Arg203Gln Single submitter ⚠
- p.Arg204Gln Single submitter
- p.Arg204Trp Single submitter ⚠
- p.Arg73Gly Single submitter ⚠
- p.Asn147Ser Single submitter ⚠
- p.Asn33Ile Single submitter
- p.Asp112Ala Single submitter ⚠
- p.Asp121Tyr Single submitter renal hypodysplasia/aplasia 1 ⚠
- p.Asp184Val Single submitter ⚠
- p.Asp50His Single submitter UPK3A-related disorder ⚠
- p.Asp68His Single submitter ⚠
- p.Gln24Glu Single submitter ⚠
- p.Glu161Val Single submitter ⚠
- p.Glu177Lys Single submitter ⚠
- p.Gly120Glu Single submitter renal hypodysplasia/aplasia 1 ⚠
- p.Gly150= Single submitter renal hypodysplasia/aplasia 1
- p.Gly206Arg Single submitter ⚠
- p.Gly242Arg Single submitter ⚠
- p.His59Gln Single submitter ⚠
- p.Ile209Met Single submitter
- p.Ile211Leu Single submitter ⚠
- p.Leu223Arg Single submitter ⚠
- p.Leu37Val Single submitter ⚠
- p.Met237Lys Single submitter ⚠
- p.Pro109Leu Single submitter ⚠
- p.Pro155Ser Single submitter ⚠
- p.Pro45Ser Single submitter ⚠
- p.Ser157Trp Single submitter ⚠
- p.Ser195Leu Single submitter ⚠
- p.Ser268Pro Single submitter renal hypodysplasia/aplasia 1 ⚠
- p.Ser76Leu Single submitter ⚠
- p.Thr160= Single submitter renal hypodysplasia/aplasia 1
- p.Thr173Met Single submitter ⚠
- p.Thr244= Single submitter renal hypodysplasia/aplasia 1
- p.Thr251Ile Single submitter ⚠
- p.Thr267Met Single submitter ⚠
- p.Thr32Asn Single submitter ⚠
- p.Thr83Ile Single submitter ⚠
- p.Thr88Met Single submitter ⚠
- p.Trp144Leu Single submitter ⚠
- p.Tyr281His Single submitter ⚠
- p.Gly202Asp No assertion criteria congenital anomalies of kidney and urinary tract 1 ⚠
- p.Ser183Leu No assertion criteria
- p.Thr39Ala No assertion criteria ⚠