NPRL3 — 95 ClinVar variants
All ClinVar germline NPRL3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 42 flagged for review →
3 Pathogenic · 3 Likely pathogenic · 5 Benign · 1 Benign/Likely benign · 26 Likely benign · 57 Uncertain significance
Full NPRL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 42
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 27
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
NPRL3 p.His525Leu
Uncertain significance
Multiple submitters
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Arg521His
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
- NPRL3 p.Arg523His Uncertain significance Single submitter
-
NPRL3 p.Arg523Ser
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Arg536Gln
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Arg537Cys
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Arg537His
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Arg548Leu
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Asn532Ser
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Glu528Gly
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Glu533Gln
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Glu533Lys
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
- NPRL3 p.His518Arg Uncertain significance Single submitter
-
NPRL3 p.His524Tyr
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.His525Tyr
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.His556Pro
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Ile529Ser
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Ile561Thr
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Leu543Arg
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Leu543Pro
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Leu567Val
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Met530Thr
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Ser549Gly
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
- NPRL3 p.Ser549Ile Uncertain significance Single submitter
-
NPRL3 p.Thr535Met
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Val560Phe
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Val563Ile
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
Predictors split 15
The independent predictors disagree with each other — read with care.
-
NPRL3 p.Arg548Cys
Uncertain significance
Multiple submitters
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Arg548His
Uncertain significance
Multiple submitters
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Glu557Lys
Uncertain significance
Multiple submitters
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Val550Met
Uncertain significance
Multiple submitters
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Arg521Cys
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Arg523Cys
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
- NPRL3 p.Arg523Leu Uncertain significance Single submitter
- NPRL3 p.Asn532Asp Uncertain significance Single submitter
-
NPRL3 p.Asn534Ser
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Asp558Gly
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Gly522Ser
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Met530Ile
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Phe520Leu
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Ser549Arg
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
-
NPRL3 p.Val550Leu
Uncertain significance
Single submitter
epilepsy, familial focal, with variable foci 3
All NPRL3 variants
Pathogenic 3
- c.(118+1_119-1 Single submitter epilepsy, familial focal, with variable foci 3
- c.931= Single submitter epilepsy, familial focal, with variable foci 3
- p.Ser279fs No assertion criteria epilepsy, familial focal, with variable foci 3
Likely pathogenic 3
- c.547+1G>C Single submitter epilepsy, familial focal, with variable foci 3
- c.(629+1_630-1 Single submitter epilepsy, familial focal, with variable foci 1
- c.(767+1_768-1 Single submitter epilepsy, familial focal, with variable foci 3
Benign 5
- c.1545-19A>G Multiple submitters epilepsy, familial focal, with variable foci 3
- c.*68T>G Multiple submitters
- c.630-332C>A Single submitter
- c.-67-2_-38del Single submitter
- c.*38G>C Single submitter
Benign/Likely benign 1
- p.Met542Thr Multiple submitters epilepsy, familial focal, with variable foci 3
Likely benign 26
- p.Arg521= Multiple submitters epilepsy, familial focal, with variable foci 3
- p.Ser549= Multiple submitters epilepsy, familial focal, with variable foci 3
- p.Tyr531= Multiple submitters epilepsy, familial focal, with variable foci 3
- c.1545-15A>T Single submitter epilepsy, familial focal, with variable foci 3
- c.1545-20_1545-19inv Single submitter epilepsy, familial focal, with variable foci 3
- c.1545-20C>T Single submitter epilepsy, familial focal, with variable foci 3
- c.1545-8C>T Single submitter epilepsy, familial focal, with variable foci 3
- c.*185G>A Single submitter
- c.*20G>A Single submitter
- c.*43C>T Single submitter
- c.*75G>A Single submitter
- c.*8C>T Single submitter
- p.Ala562= Single submitter epilepsy, familial focal, with variable foci 3
- p.Asn532= Single submitter epilepsy, familial focal, with variable foci 3
- p.Gln565Glu Single submitter
- p.Glu527= Single submitter epilepsy, familial focal, with variable foci 3
- p.His556= Single submitter epilepsy, familial focal, with variable foci 3
- p.Leu516= Single submitter epilepsy, familial focal, with variable foci 3
- p.Leu526= Single submitter epilepsy, familial focal, with variable foci 3
- p.Leu541= Single submitter epilepsy, familial focal, with variable foci 3
- p.Leu567= Single submitter epilepsy, familial focal, with variable foci 3
- p.Phe520= Single submitter epilepsy, familial focal, with variable foci 3
- p.Pro559= Single submitter epilepsy, familial focal, with variable foci 3
- p.Thr535= Single submitter epilepsy, familial focal, with variable foci 3
- p.Thr554= Single submitter epilepsy, familial focal, with variable foci 3
- p.Val552= Single submitter epilepsy, familial focal, with variable foci 3
Uncertain significance 57
- p.Arg515= Multiple submitters epilepsy, familial focal, with variable foci 3
- p.Arg521fs Multiple submitters epilepsy, familial focal, with variable foci 3
- p.Arg548Cys Multiple submitters epilepsy, familial focal, with variable foci 3 ⚠
- p.Arg548His Multiple submitters epilepsy, familial focal, with variable foci 3 ⚠
- p.Glu528del Multiple submitters epilepsy, familial focal, with variable foci 3
- p.Glu557Lys Multiple submitters epilepsy, familial focal, with variable foci 3 ⚠
- p.His525Leu Multiple submitters epilepsy, familial focal, with variable foci 3 ⚠
- p.Ter570SerextTer? Multiple submitters epilepsy, familial focal, with variable foci 3
- p.Tyr519Ter Multiple submitters epilepsy, familial focal, with variable foci 3
- p.Val550Met Multiple submitters epilepsy, familial focal, with variable foci 3 ⚠
- c.*1096C>T Single submitter
- p.Arg521Cys Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Arg521His Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Arg523Cys Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Arg523fs Single submitter epilepsy, familial focal, with variable foci 3
- p.Arg523His Single submitter ⚠
- p.Arg523Leu Single submitter ⚠
- p.Arg523Ser Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Arg536Gln Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Arg537Cys Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Arg537His Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Arg537Ser Single submitter epilepsy, familial focal, with variable foci 3
- p.Arg548Leu Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Asn532Asp Single submitter ⚠
- p.Asn532Ser Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Asn534Ser Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Asp558Gly Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Gln539Ter Single submitter epilepsy, familial focal, with variable foci 3
- p.Glu528Gly Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Glu533Gln Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Glu533Lys Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Gly522fs Single submitter epilepsy, familial focal, with variable foci 3
- p.Gly522Ser Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.His518Arg Single submitter ⚠
- p.His524Tyr Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.His525Tyr Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.His556fs Single submitter epilepsy, familial focal, with variable foci 3
- p.His556Pro Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Ile529Ser Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Ile561Thr Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Leu540_Leu543del Single submitter epilepsy, familial focal, with variable foci 3
- p.Leu543Arg Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Leu543Pro Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Leu567Val Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Met530Ile Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Met530Thr Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Phe520Leu Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Pro559fs Single submitter
- p.Ser549Arg Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Ser549Gly Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Ser549Ile Single submitter ⚠
- p.Ter570Arg Single submitter epilepsy, familial focal, with variable foci 3
- p.Thr535Met Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Val550Leu Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Val552fs Single submitter epilepsy, familial focal, with variable foci 3
- p.Val560Phe Single submitter epilepsy, familial focal, with variable foci 3 ⚠
- p.Val563Ile Single submitter epilepsy, familial focal, with variable foci 3 ⚠