Sugi Variant

Sugi Variant/NPHP1

NPHP1 — 1003 ClinVar variants

All ClinVar germline NPHP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 333 flagged for review →

58 Pathogenic · 17 Pathogenic/Likely pathogenic · 58 Likely pathogenic · 58 Conflicting · 40 Benign · 13 Benign/Likely benign · 375 Likely benign · 384 Uncertain significance

Full NPHP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 333

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 18

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

Predictors lean, ClinVar uncertain 274

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 274

Predictors split 41

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

All NPHP1 variants

Pathogenic 58

Pathogenic/Likely pathogenic 17

  • c.1270-2A>G Multiple submitters nephronophthisis
  • c.144-1G>A Multiple submitters Joubert syndrome and related disorders
  • c.1716+1G>T Multiple submitters NPHP1-related disorder
  • c.329+1G>A Multiple submitters nephronophthisis
  • c.771+124C>T Multiple submitters nephronophthisis
  • c.771+58C>T Multiple submitters NPHP1-related disorder
  • p.Asn61fs Multiple submitters nephronophthisis 1
  • p.Asp162fs Multiple submitters NPHP1-related disorder
  • p.Gln43Ter Multiple submitters Joubert syndrome with renal defect
  • p.Glu139Ter Multiple submitters nephronophthisis 1
  • p.Glu215Ter Multiple submitters Senior-Loken syndrome 1
  • p.Leu340fs Multiple submitters nephronophthisis
  • p.Ser129fs Multiple submitters nephronophthisis
  • p.Thr461fs Multiple submitters NPHP1-related disorder
  • p.Thr633fs Multiple submitters NPHP1-related disorder
  • p.Trp629Ter Multiple submitters nephronophthisis
  • p.Tyr294Ter Multiple submitters NPHP1-related disorder

Likely pathogenic 58

Conflicting classifications of pathogenicity 58

Benign 40

Benign/Likely benign 13

Likely benign 375

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

Uncertain significance 384

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