Sugi Variant

Sugi Variant/NYX

NYX — 522 ClinVar variants

All ClinVar germline NYX variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 177 flagged for review →

32 Pathogenic · 5 Pathogenic/Likely pathogenic · 27 Likely pathogenic · 24 Conflicting · 6 Benign · 11 Benign/Likely benign · 110 Likely benign · 307 Uncertain significance

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

⚑ Evidence disagreements 177

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 9

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

Predicted LoF vs a conflicting call 2

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 146

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 20

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

All NYX variants

Pathogenic 32

Pathogenic/Likely pathogenic 5

Likely pathogenic 27

  • p.Ala267fs Single submitter NYX-related disorder
  • p.Arg89Pro Single submitter NYX-related disorder
  • p.Asp271fs Single submitter NYX-related disorder
  • p.Cys140Ter Single submitter congenital stationary night blindness 1A
  • p.Cys26fs Single submitter NYX-related disorder
  • p.Cys357Ter Single submitter
  • p.Glu74fs Single submitter NYX-related disorder
  • p.His122fs Single submitter NYX-related disorder
  • p.Leu156fs Single submitter NYX-related disorder
  • p.Leu272fs Single submitter NYX-related disorder
  • p.Leu280Arg Single submitter NYX-related disorder
  • p.Leu302fs Single submitter inherited retinal disease
  • p.Pro170Leu Single submitter NYX-related disorder
  • p.Pro170Ser Single submitter NYX-related disorder
  • p.Pro56fs Single submitter NYX-related disorder
  • p.Ser377fs Single submitter NYX-related disorder
  • p.326LF[1] No assertion criteria congenital stationary night blindness
  • p.Ala161Pro No assertion criteria congenital stationary night blindness
  • p.Asn307Lys No assertion criteria Abnormality of the eye
  • p.Asn331Thr No assertion criteria inherited retinal dystrophy
  • p.Cys335Gly No assertion criteria congenital stationary night blindness
  • p.Cys337Arg No assertion criteria inherited retinal dystrophy
  • p.Cys43Ter No assertion criteria NYX-related disorder
  • p.Glu289Lys No assertion criteria inherited retinal dystrophy
  • p.Leu159Arg No assertion criteria inherited retinal dystrophy
  • p.Leu432fs No assertion criteria congenital stationary night blindness 1A
  • p.Phe327fs No assertion criteria congenital stationary night blindness 1A

Conflicting classifications of pathogenicity 24

Benign 6

  • c.22+16G>A Multiple submitters
  • c.-57+60A>G Multiple submitters congenital stationary night blindness 1A
  • c.-57+95T>C Multiple submitters congenital stationary night blindness 1A
  • c.*509G>C Multiple submitters congenital stationary night blindness 1A
  • p.Gly379= Single submitter
  • p.Pro418= Single submitter

Benign/Likely benign 11

  • p.Ala401Gly Multiple submitters congenital stationary night blindness 1A
  • p.Glu276= Multiple submitters congenital stationary night blindness 1A
  • p.Glu340= Multiple submitters congenital stationary night blindness 1A
  • p.Gly395Ser Multiple submitters congenital stationary night blindness 1A
  • p.Leu389Phe Multiple submitters
  • p.Leu412= Multiple submitters
  • p.Leu69= Multiple submitters congenital stationary night blindness 1A
  • p.Ser410Asn Multiple submitters
  • p.Ser413Cys Multiple submitters congenital stationary night blindness 1A
  • p.Thr253Met Multiple submitters
  • p.Thr404= Multiple submitters congenital stationary night blindness 1A

Likely benign 110

Uncertain significance 307

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