Sugi Variant

Sugi Variant/HPGD

HPGD — 198 ClinVar variants

All ClinVar germline HPGD variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 60 flagged for review →

22 Pathogenic · 6 Likely pathogenic · 4 Conflicting · 28 Benign · 4 Benign/Likely benign · 42 Likely benign · 92 Uncertain significance

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

⚑ Evidence disagreements 60

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 1

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

Predictors lean, ClinVar uncertain 45

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

Predictors split 14

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

All HPGD variants

Pathogenic 22

  • c.218-1G>A Multiple submitters
  • c.324+5G>A Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.421+1G>T Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Ala140Pro Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Ala41fs Multiple submitters HPGD-related disorder
  • p.Gln68Ter Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Leu104fs Multiple submitters HPGD-related disorder
  • p.Leu59fs Multiple submitters Autosomal recessive primary hypertrophic osteoarthropathy
  • c.218-1G>T Single submitter
  • c.325-1G>C Single submitter
  • c.325-2A>C Single submitter
  • c.421+1G>A Single submitter
  • c.662+2T>A Single submitter hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Gln105Ter Single submitter hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Gln125fs Single submitter
  • p.Gly175fs Single submitter
  • p.Met1Leu Single submitter hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Met1Thr Single submitter
  • p.Tyr121fs Single submitter
  • c.498+1G>A No assertion criteria hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Cys63Ter No assertion criteria hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Gly12Ser No assertion criteria hypertrophic osteoarthropathy, primary, autosomal recessive, 1

Likely pathogenic 6

  • p.Thr103fs Multiple submitters isolated congenital digital clubbing
  • p.Leu229Ter Single submitter isolated congenital digital clubbing
  • p.Ser193Pro Single submitter isolated congenital digital clubbing ⚠
  • p.Tyr151Ter Single submitter isolated congenital digital clubbing
  • p.Val78fs Single submitter hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Pro149Arg No assertion criteria hypertrophic osteoarthropathy, primary, autosomal recessive, 1

Conflicting classifications of pathogenicity 4

  • c.*41A>G Single submitter isolated congenital digital clubbing
  • p.Ala13Glu Single submitter hypertrophic osteoarthropathy, primary, autosomal recessive, 1 ⚠
  • p.Gln202= Single submitter isolated congenital digital clubbing
  • p.Leu26= Single submitter hypertrophic osteoarthropathy, primary, autosomal recessive, 1

Benign 28

  • c.324+66A>G Multiple submitters
  • c.421+39C>T Multiple submitters
  • c.422-191C>T Multiple submitters
  • c.499-191T>C Multiple submitters
  • c.499-213A>T Multiple submitters
  • c.662+24C>G Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.662+56T>C Multiple submitters
  • c.662+68A>G Multiple submitters
  • c.663-16T>C Multiple submitters
  • c.94-104T>C Multiple submitters
  • c.94-16C>T Multiple submitters
  • c.94-43C>A Multiple submitters
  • c.-502G>C Multiple submitters
  • c.*1154T>C Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.*132G>A Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.*1725G>A Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.*1726C>T Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.*418G>T Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.*630G>A Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Arg163= Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Asn227Ser Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • p.Gln52= Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.217+273A>G Single submitter
  • c.325-247A>T Single submitter
  • c.662+100G>A Single submitter
  • c.93+85dup Single submitter
  • p.Ser123= Single submitter
  • p.Ser174= Single submitter

Benign/Likely benign 4

  • c.422-20G>A Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1
  • c.93+1_93+3dup Multiple submitters
  • p.Asp212Asn Multiple submitters isolated congenital digital clubbing
  • p.Pro144= Multiple submitters hypertrophic osteoarthropathy, primary, autosomal recessive, 1

Likely benign 42

Uncertain significance 92