CNPY3 — 84 ClinVar variants
All ClinVar germline CNPY3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 51 flagged for review →
3 Pathogenic · 4 Likely pathogenic · 2 Conflicting · 1 Benign · 15 Likely benign · 59 Uncertain significance
Full CNPY3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 51
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 39
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CNPY3 p.Glu154Lys Uncertain significance Multiple submitters
- CNPY3 p.Glu98Lys Uncertain significance Multiple submitters
-
CNPY3 p.Gly67Ser
Uncertain significance
Multiple submitters
developmental and epileptic encephalopathy, 60
- CNPY3 p.Tyr149Cys Uncertain significance Multiple submitters
- CNPY3 p.Ala157Thr Uncertain significance Single submitter
- CNPY3 p.Ala195Val Uncertain significance Single submitter
- CNPY3 p.Ala267Pro Uncertain significance Single submitter
- CNPY3 p.Ala27Thr Uncertain significance Single submitter
- CNPY3 p.Ala37Val Uncertain significance Single submitter
- CNPY3 p.Ala8Pro Uncertain significance Single submitter
- CNPY3 p.Arg116Thr Uncertain significance Single submitter
- CNPY3 p.Arg239Ser Uncertain significance Single submitter
- CNPY3 p.Arg44Leu Uncertain significance Single submitter
- CNPY3 p.Asp217Gly Uncertain significance Single submitter
- CNPY3 p.Asp81Glu Uncertain significance Single submitter
- CNPY3 p.Glu178Lys Uncertain significance Single submitter
- CNPY3 p.Glu259Lys Uncertain significance Single submitter
- CNPY3 p.Glu29Gly Uncertain significance Single submitter
- CNPY3 p.Glu39Lys Uncertain significance Single submitter
- CNPY3 p.Glu6Asp Uncertain significance Single submitter
-
CNPY3 p.Gly213Ser
Uncertain significance
Single submitter
developmental and epileptic encephalopathy, 60
-
CNPY3 p.Gly216Arg
Uncertain significance
Single submitter
developmental and epileptic encephalopathy, 60
- CNPY3 p.Gly251Asp Uncertain significance Single submitter
- CNPY3 p.Gly251Ser Uncertain significance Single submitter
- CNPY3 p.Ile177Leu Uncertain significance Single submitter
- CNPY3 p.Lys142Arg Uncertain significance Single submitter
- CNPY3 p.Lys215Glu Uncertain significance Single submitter
-
CNPY3 p.Lys225Arg
Uncertain significance
Single submitter
developmental and epileptic encephalopathy, 60
- CNPY3 p.Lys68Arg Uncertain significance Single submitter
- CNPY3 p.Pro256His Uncertain significance Single submitter
- CNPY3 p.Pro269Leu Uncertain significance Single submitter
- CNPY3 p.Pro275Ala Uncertain significance Single submitter
- CNPY3 p.Pro28Arg Uncertain significance Single submitter
- CNPY3 p.Ser226Ala Uncertain significance Single submitter
- CNPY3 p.Trp211Cys Uncertain significance Single submitter
- CNPY3 p.Tyr110His Uncertain significance Single submitter
- CNPY3 p.Val170Leu Uncertain significance Single submitter
-
CNPY3 p.Arg106Met
Uncertain significance
No assertion criteria
CNPY3-related disorder
-
CNPY3 p.Ser92Leu
Uncertain significance
No assertion criteria
CNPY3-related disorder
Predictors split 12
The independent predictors disagree with each other — read with care.
- CNPY3 p.Lys105Met Uncertain significance Multiple submitters
- CNPY3 p.Ser231Cys Uncertain significance Multiple submitters
- CNPY3 p.Arg182Ser Uncertain significance Single submitter
- CNPY3 p.Glu178Gln Uncertain significance Single submitter
- CNPY3 p.His197Tyr Uncertain significance Single submitter
- CNPY3 p.Leu19Pro Uncertain significance Single submitter
- CNPY3 p.Leu23Pro Uncertain significance Single submitter
- CNPY3 p.Leu25Pro Uncertain significance Single submitter
- CNPY3 p.Met126Ile Uncertain significance Single submitter
- CNPY3 p.Phe173Ile Uncertain significance Single submitter
- CNPY3 p.Ser226Cys Uncertain significance Single submitter
-
CNPY3 p.Val198Met
Uncertain significance
Single submitter
developmental and epileptic encephalopathy, 60
All CNPY3 variants
Pathogenic 3
- p.Asn183fs Single submitter developmental and epileptic encephalopathy, 60
- c.495+1G>A No assertion criteria developmental and epileptic encephalopathy, 60
- p.Gly125Arg No assertion criteria developmental and epileptic encephalopathy, 60
Likely pathogenic 4
- c.152-1G>A Single submitter
- c.496-3_496-2del Single submitter developmental and epileptic encephalopathy, 60
- p.Gln210Ter Single submitter developmental and epileptic encephalopathy, 60
- p.Gln245fs Single submitter developmental and epileptic encephalopathy, 60
Conflicting classifications of pathogenicity 2
- p.Arg121Ter Single submitter developmental and epileptic encephalopathy, 60
- p.Leu22_Leu25del Single submitter developmental and epileptic encephalopathy, 60
Benign 1
- p.Leu25del No assertion criteria CNPY3-related disorder
Likely benign 15
- p.Cys194= Multiple submitters
- p.Gly237= Multiple submitters
- p.Leu21= Multiple submitters
- c.614-8C>T Single submitter
- p.Gly36Arg Single submitter
- p.Leu108= Single submitter
- p.Leu23_Leu25del Single submitter
- p.Ser212= Single submitter
- p.Ser241Gly Single submitter
- p.Ser33= Single submitter
- p.Thr66= Single submitter
- p.Thr75= Single submitter
- p.Ala220Thr No assertion criteria CNPY3-related disorder
- p.Leu25_Pro26insLeu No assertion criteria CNPY3-related disorder
- p.Pro258= No assertion criteria CNPY3-related disorder
Uncertain significance 59
- p.Glu154Lys Multiple submitters ⚠
- p.Glu98Lys Multiple submitters ⚠
- p.Gly67Ser Multiple submitters developmental and epileptic encephalopathy, 60 ⚠
- p.Lys105Met Multiple submitters ⚠
- p.Ser231Cys Multiple submitters ⚠
- p.Tyr149Cys Multiple submitters ⚠
- c.275+1G>A Single submitter developmental and epileptic encephalopathy, 60
- c.276-32G>A Single submitter developmental and epileptic encephalopathy, 60
- c.613+6T>A Single submitter
- c.614-1G>A Single submitter
- p.Ala157Thr Single submitter ⚠
- p.Ala195Val Single submitter ⚠
- p.Ala267Pro Single submitter ⚠
- p.Ala27Thr Single submitter ⚠
- p.Ala37Val Single submitter ⚠
- p.Ala8Pro Single submitter ⚠
- p.Arg116Thr Single submitter ⚠
- p.Arg182Ser Single submitter ⚠
- p.Arg239Ser Single submitter ⚠
- p.Arg44Leu Single submitter ⚠
- p.Asp217Gly Single submitter ⚠
- p.Asp81Glu Single submitter ⚠
- p.Asp81Tyr Single submitter developmental and epileptic encephalopathy, 60
- p.Glu178Gln Single submitter ⚠
- p.Glu178Lys Single submitter ⚠
- p.Glu259Lys Single submitter ⚠
- p.Glu29Gly Single submitter ⚠
- p.Glu39Lys Single submitter ⚠
- p.Glu6Asp Single submitter ⚠
- p.Gly118Ser Single submitter
- p.Gly213Ser Single submitter developmental and epileptic encephalopathy, 60 ⚠
- p.Gly216Arg Single submitter developmental and epileptic encephalopathy, 60 ⚠
- p.Gly251Asp Single submitter ⚠
- p.Gly251Ser Single submitter ⚠
- p.His197Tyr Single submitter ⚠
- p.Ile177Leu Single submitter ⚠
- p.Leu19Pro Single submitter ⚠
- p.Leu23Pro Single submitter ⚠
- p.Leu25_Pro26insLeuLeu Single submitter
- p.Leu25_Pro26insLeuLeuLeuLeuLeu Single submitter developmental and epileptic encephalopathy, 60
- p.Leu25Pro Single submitter ⚠
- p.Lys142Arg Single submitter ⚠
- p.Lys215Glu Single submitter ⚠
- p.Lys225Arg Single submitter developmental and epileptic encephalopathy, 60 ⚠
- p.Lys68Arg Single submitter ⚠
- p.Met126Ile Single submitter ⚠
- p.Phe173Ile Single submitter ⚠
- p.Pro256His Single submitter ⚠
- p.Pro269Leu Single submitter ⚠
- p.Pro275Ala Single submitter ⚠
- p.Pro28Arg Single submitter ⚠
- p.Ser226Ala Single submitter ⚠
- p.Ser226Cys Single submitter ⚠
- p.Trp211Cys Single submitter ⚠
- p.Tyr110His Single submitter ⚠
- p.Val170Leu Single submitter ⚠
- p.Val198Met Single submitter developmental and epileptic encephalopathy, 60 ⚠
- p.Arg106Met No assertion criteria CNPY3-related disorder ⚠
- p.Ser92Leu No assertion criteria CNPY3-related disorder ⚠