Sugi Variant

Sugi Variant/HPS1

HPS1 — 1232 ClinVar variants

All ClinVar germline HPS1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 332 flagged for review →

64 Pathogenic · 41 Pathogenic/Likely pathogenic · 82 Likely pathogenic · 60 Conflicting · 62 Benign · 24 Benign/Likely benign · 535 Likely benign · 364 Uncertain significance

Full HPS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 332

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 36

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

Predictors lean, ClinVar uncertain 241

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 241

Predictors split 54

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

All HPS1 variants

Pathogenic 64

Pathogenic/Likely pathogenic 41

  • c.1744-2A>C Multiple submitters Hermansky-Pudlak syndrome 1
  • c.1857+2T>C Multiple submitters Hermansky-Pudlak syndrome
  • c.1858-1G>A Multiple submitters Hermansky-Pudlak syndrome
  • c.1940+1G>A Multiple submitters Hermansky-Pudlak syndrome
  • c.1940+2T>C Multiple submitters Hermansky-Pudlak syndrome 1
  • c.398+2T>C Multiple submitters Hermansky-Pudlak syndrome
  • c.398+5G>A Multiple submitters Hermansky-Pudlak syndrome
  • c.399-2A>G Multiple submitters Hermansky-Pudlak syndrome
  • c.938-1G>A Multiple submitters Hermansky-Pudlak syndrome 1
  • c.987+1G>A Multiple submitters Hermansky-Pudlak syndrome 1
  • c.988-1G>T Multiple submitters Hermansky-Pudlak syndrome
  • p.Arg261fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Arg591Ter Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Asn78fs Multiple submitters HPS1-related disorder
  • p.Asp104fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Asp400fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Cys3Ter Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Cys479Ter Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Gln162Ter Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Gln272Ter Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Gln397fs Multiple submitters HPS1-related disorders
  • p.Gln505Ter Multiple submitters Hermansky-Pudlak syndrome
  • p.Gln553Ter Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Gly313Ser Multiple submitters Hermansky-Pudlak syndrome ⚠
  • p.Gly321fs Multiple submitters Hermansky-Pudlak syndrome
  • p.Gly642fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Ile184fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Ile481fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Leu239Pro Multiple submitters Hermansky-Pudlak syndrome
  • p.Leu391fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Leu593fs Multiple submitters Hermansky-Pudlak syndrome
  • p.Leu668Pro Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Leu80fs Multiple submitters Hermansky-Pudlak syndrome
  • p.Met325fs Multiple submitters HPS1-related disorders
  • p.Pro307fs Multiple submitters Hermansky-Pudlak syndrome
  • p.Ser285fs Multiple submitters Hermansky-Pudlak syndrome
  • p.Ser33fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Ser492fs Multiple submitters Hermansky-Pudlak syndrome 1
  • p.Trp17Ter Multiple submitters Hermansky-Pudlak syndrome
  • p.Trp375Ter Multiple submitters Hermansky-Pudlak syndrome
  • p.Tyr645fs Multiple submitters Hermansky-Pudlak syndrome

Likely pathogenic 82

Conflicting classifications of pathogenicity 60

Benign 62

Benign/Likely benign 24

Likely benign 535

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

Uncertain significance 364

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