Sugi Variant

Sugi Variant/PYCR2

PYCR2 — 180 ClinVar variants

All ClinVar germline PYCR2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 68 flagged for review →

10 Pathogenic · 5 Pathogenic/Likely pathogenic · 21 Likely pathogenic · 11 Conflicting · 6 Benign · 5 Benign/Likely benign · 52 Likely benign · 70 Uncertain significance

Full PYCR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 68

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 8

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

Predictors lean, ClinVar uncertain 49

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

Predictors split 10

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

All PYCR2 variants

Pathogenic 10

Pathogenic/Likely pathogenic 5

  • p.Arg119Cys Multiple submitters leukodystrophy, hypomyelinating, 10
  • p.Asp85fs Multiple submitters leukodystrophy, hypomyelinating, 10
  • p.Gln226Ter Multiple submitters leukodystrophy, hypomyelinating, 10
  • p.Leu254fs Multiple submitters leukodystrophy, hypomyelinating, 10
  • p.Val104fs Multiple submitters PYCR2-related disorder

Likely pathogenic 21

  • p.Arg119His Multiple submitters leukodystrophy, hypomyelinating, 10
  • c.138+1G>T Single submitter leukodystrophy, hypomyelinating, 10
  • c.318+1G>A Single submitter leukodystrophy, hypomyelinating, 10
  • c.633+1G>A Single submitter leukodystrophy, hypomyelinating, 10
  • p.Ala181Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg119Leu Single submitter
  • p.Arg264Ter Single submitter
  • p.Asp229Gly Single submitter leukodystrophy, hypomyelinating, 10
  • p.Gln10Ter Single submitter leukodystrophy
  • p.Gly177Arg Single submitter leukodystrophy, hypomyelinating, 10
  • p.Gly192fs Single submitter PYCR2-related disorder
  • p.Ile239fs Single submitter PYCR2-related disorder
  • p.Met1Leu Single submitter PYCR2-related disorder
  • p.Pro125His Single submitter
  • p.Thr124fs Single submitter metachromatic leukodystrophy
  • p.Thr133fs Single submitter leukodystrophy, hypomyelinating, 10
  • p.Tyr135fs Single submitter leukodystrophy, hypomyelinating, 10
  • p.Val134Met Single submitter leukodystrophy, hypomyelinating, 10
  • p.Val193Met Single submitter leukodystrophy, hypomyelinating, 10
  • p.Val258Ala Single submitter leukodystrophy, hypomyelinating, 10
  • p.Val86Gly Single submitter leukodystrophy, hypomyelinating, 10

Conflicting classifications of pathogenicity 11

Benign 6

Benign/Likely benign 5

Likely benign 52

Uncertain significance 70