Sugi Variant

Sugi Variant/NPHP3

NPHP3 — 1180 ClinVar variants

All ClinVar germline NPHP3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 456 flagged for review →

70 Pathogenic · 24 Pathogenic/Likely pathogenic · 48 Likely pathogenic · 93 Conflicting · 50 Benign · 20 Benign/Likely benign · 352 Likely benign · 523 Uncertain significance

Full NPHP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 456

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 vs ClinVar 1

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 29

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 311

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 311

Predictors split 115

The independent predictors disagree with each other — read with care.

All NPHP3 variants

Pathogenic 70

Pathogenic/Likely pathogenic 24

Likely pathogenic 48

Conflicting classifications of pathogenicity 93

Benign 50

Benign/Likely benign 20

Likely benign 352

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 523

Showing the top 300 by review status; the full set is in the sitemap.