Sugi Variant

Sugi Variant/SCAPER

SCAPER — 418 ClinVar variants

All ClinVar germline SCAPER variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 216 flagged for review →

9 Pathogenic · 3 Pathogenic/Likely pathogenic · 25 Likely pathogenic · 6 Conflicting · 15 Benign · 16 Benign/Likely benign · 119 Likely benign · 225 Uncertain significance

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

⚑ Evidence disagreements 216

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 4

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

Predictors lean, ClinVar uncertain 161

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 161

Predictors split 50

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

All SCAPER variants

Pathogenic 9

  • p.Ile746fs Multiple submitters SCAPER-related disorder
  • p.Arg366Ter Single submitter SCAPER-related disorder
  • p.Arg727Ter Single submitter intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Arg814fs Single submitter Inborn genetic diseases
  • p.Gln793Ter Single submitter intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Ile991Metfs Single submitter Rod-cone dystrophy
  • p.Met488fs Single submitter intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Thr935_Leu936insTer Single submitter intellectual disability
  • c.2023-2A>G No assertion criteria intellectual developmental disorder and retinitis pigmentosa; IDDRP

Pathogenic/Likely pathogenic 3

  • p.Lys869Ter Multiple submitters intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Glu620del No assertion criteria intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Ser1219Asn No assertion criteria intellectual developmental disorder and retinitis pigmentosa; IDDRP ⚠

Likely pathogenic 25

  • p.Ala872fs Multiple submitters SCAPER-related disorder
  • p.Arg112Ter Multiple submitters SCAPER-related disorder
  • c.1035+1G>C Single submitter SCAPER-related disorder
  • c.125-1G>A Single submitter intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • c.1613+1G>T Single submitter SCAPER-related disorder
  • c.2955-1G>T Single submitter intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Ala499fs Single submitter SCAPER-related disorder
  • p.Arg277Ter Single submitter SCAPER-related disorder
  • p.Arg361Ter Single submitter intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Cys988fs Single submitter intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Gln551Ter Single submitter SCAPER-related disorder
  • p.Glu290fs Single submitter SCAPER-related disorder
  • p.Glu885Ter Single submitter SCAPER-related disorder
  • p.His816fs Single submitter SCAPER-related disorder
  • p.Lys871fs Single submitter SCAPER-related disorder
  • p.Ser1236fs Single submitter SCAPER-related disorder
  • p.Ser832Ter Single submitter SCAPER-related disorder
  • p.Tyr364Ter Single submitter SCAPER-related disorder
  • p.Tyr788Ter Single submitter intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Val1261fs Single submitter SCAPER-related disorder
  • c.1495+1G>A No assertion criteria intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • c.2166-3C>G No assertion criteria intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Glu885fs No assertion criteria intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Tyr102Ter No assertion criteria SCAPER-related disorder
  • p.Val373fs No assertion criteria intellectual developmental disorder and retinitis pigmentosa; IDDRP

Conflicting classifications of pathogenicity 6

Benign 15

  • c.2645+36T>C Multiple submitters intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • c.3078+39G>T Multiple submitters intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • c.3312-7T>C Multiple submitters
  • c.3705+3A>G Multiple submitters intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • c.612-4A>G Multiple submitters intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • c.772+1881G>T Multiple submitters intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • c.-42T>A Multiple submitters intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Ala1140Thr Multiple submitters
  • p.Ala668= Multiple submitters
  • p.Ile1213= Multiple submitters
  • p.Met1Val Multiple submitters intellectual developmental disorder and retinitis pigmentosa; IDDRP
  • p.Glu1206Lys Single submitter
  • p.Lys1114Thr Single submitter
  • p.Ser832= Single submitter
  • p.Gln635= No assertion criteria SCAPER-related disorder

Benign/Likely benign 16

Likely benign 119

Uncertain significance 225