Sugi Variant

Sugi Variant/PYCR1

PYCR1 — 373 ClinVar variants

All ClinVar germline PYCR1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 110 flagged for review →

17 Pathogenic · 12 Pathogenic/Likely pathogenic · 16 Likely pathogenic · 27 Conflicting · 13 Benign · 7 Benign/Likely benign · 151 Likely benign · 130 Uncertain significance

Full PYCR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 110

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 11

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

Predictors lean, ClinVar uncertain 67

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

Predictors split 31

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

All PYCR1 variants

Pathogenic 17

Pathogenic/Likely pathogenic 12

  • c.138+1G>A Multiple submitters cutis laxa
  • c.633+1G>C Multiple submitters autosomal recessive cutis laxa type 2B
  • c.797+2_797+5del Multiple submitters PYCR1-related de Barsy syndrome
  • p.Ala179Thr Multiple submitters PYCR1-related disorder
  • p.Arg119Cys Multiple submitters PYCR1-related disorder
  • p.Arg119Gly Multiple submitters PYCR1-related disorder
  • p.Arg119His Multiple submitters PYCR1-related disorder
  • p.Arg251His Multiple submitters Inborn genetic diseases
  • p.Gly192fs Multiple submitters cutis laxa
  • p.Gly206Arg Multiple submitters autosomal recessive cutis laxa type 2B
  • p.Lys51Ter Multiple submitters cutis laxa
  • p.Val117Phe Multiple submitters PYCR1-related disorder

Likely pathogenic 16

  • p.Glu130fs Multiple submitters autosomal recessive cutis laxa type 2B
  • c.318+1G>A Single submitter PYCR1-related de Barsy syndrome
  • c.540+1G>T Single submitter autosomal recessive cutis laxa type 2B
  • c.798-1G>A Single submitter
  • p.Ala132fs Single submitter PYCR1-related de Barsy syndrome
  • p.Ala213Thr Single submitter ⚠
  • p.Asp186Gly Single submitter autosomal recessive cutis laxa type 2B
  • p.Asp186Tyr Single submitter autosomal recessive cutis laxa type 2B
  • p.Gln142Ter Single submitter
  • p.Glu267Ter Single submitter Fetal anomalies with a likely genetic cause
  • p.Ile74fs Single submitter autosomal recessive cutis laxa type 2B
  • p.Ile78fs Single submitter PYCR1-related de Barsy syndrome
  • p.Val99fs Single submitter autosomal recessive cutis laxa type 2B
  • p.Gln61Ter No assertion criteria autosomal recessive cutis laxa type 2B
  • p.Lys71fs No assertion criteria PYCR1-related disorder
  • p.Val258Leu No assertion criteria Wiedemann-Rautenstrauch-like progeroid syndrome

Conflicting classifications of pathogenicity 27

Benign 13

Benign/Likely benign 7

Likely benign 151

Uncertain significance 130