Sugi Variant

Sugi Variant/PHKA1

PHKA1 — 760 ClinVar variants

All ClinVar germline PHKA1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 347 flagged for review →

29 Pathogenic · 3 Pathogenic/Likely pathogenic · 21 Likely pathogenic · 34 Conflicting · 44 Benign · 17 Benign/Likely benign · 234 Likely benign · 378 Uncertain significance

Full PHKA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 347

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 20

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

Predictors lean, ClinVar uncertain 218

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 218

Predictors split 109

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

All PHKA1 variants

Pathogenic 29

  • p.Arg298Ter Multiple submitters glycogen storage disease IX
  • p.Arg863Ter Multiple submitters Inborn genetic diseases
  • p.Glu1112Ter Multiple submitters glycogen storage disease IXd
  • p.Ser868fs Multiple submitters glycogen storage disease IXd
  • p.Arg497Ter Single submitter glycogen storage disease IXd
  • p.Arg587Ter Single submitter glycogen storage disease IXd
  • p.Arg821fs Single submitter glycogen storage disease IXd
  • p.Arg827Ter Single submitter
  • p.Arg906Ter Single submitter glycogen storage disease IXd
  • p.Arg919Ter Single submitter glycogen storage disease IXd
  • p.Arg971Ter Single submitter glycogen storage disease IX
  • p.Asp272fs Single submitter glycogen storage disease IXd
  • p.Cys238fs Single submitter glycogen storage disease IXd
  • p.Cys697Ter Single submitter glycogen storage disease IX
  • p.Gln347Ter Single submitter
  • p.Gln777Ter Single submitter Inborn genetic diseases
  • p.Gln779Ter Single submitter glycogen storage disease IXd
  • p.Gln895Ter Single submitter glycogen storage disease IXd
  • p.Gly684Ter Single submitter
  • p.Ile525fs Single submitter glycogen storage disease IX
  • p.Leu212Ter Single submitter glycogen storage disease IXd
  • p.Pro951fs Single submitter glycogen storage disease IXd
  • p.Tyr511fs Single submitter glycogen storage disease IXd
  • p.Val375fs Single submitter glycogen storage disease IXd
  • p.Val899fs Single submitter
  • c.3498+1G>C No assertion criteria glycogen storage disease IXd
  • p.Ala232fs No assertion criteria glycogen storage disease IXd
  • p.Asp299Val No assertion criteria glycogen storage disease IXd
  • p.Gly223Arg No assertion criteria glycogen storage disease IXd

Pathogenic/Likely pathogenic 3

  • c.2606+1G>A Multiple submitters glycogen storage disease IX
  • p.Arg392Ter Multiple submitters glycogen storage disease IXd
  • p.Trp130Ter Multiple submitters glycogen storage disease IXd

Likely pathogenic 21

  • c.2137+1G>A Multiple submitters glycogen storage disease IXd
  • c.2527-1G>T Multiple submitters glycogen storage disease IXd
  • c.537+1G>A Multiple submitters glycogen storage disease IXd
  • p.Arg739Ter Multiple submitters glycogen storage disease IXd
  • p.Glu449fs Multiple submitters glycogen storage disease IXd
  • c.1042-2A>G Single submitter glycogen storage disease IXd
  • c.1715-2A>T Single submitter
  • c.1960+1G>T Single submitter glycogen storage disease IXd
  • c.238-2A>T Single submitter glycogen storage disease IXd
  • c.2815+1G>A Single submitter glycogen storage disease IXd
  • c.3072+1G>T Single submitter glycogen storage disease IXd
  • c.3072+2T>G Single submitter glycogen storage disease IXd
  • c.3244-155_3618del Single submitter glycogen storage disease IX
  • c.3297+2T>A Single submitter disorder of glycogen metabolism
  • c.3298-2A>T Single submitter glycogen storage disease IXd
  • c.919-2A>G Single submitter glycogen storage disease IXd
  • p.Arg936Ter Single submitter glycogen storage disease IXd
  • p.Leu578Ter Single submitter ornithine carbamoyltransferase deficiency
  • p.Leu833Ter Single submitter glycogen storage disease IXd
  • p.Ser1045Ter Single submitter glycogen storage disease IXd
  • p.Val227fs Single submitter glycogen storage disease IXd

Conflicting classifications of pathogenicity 34

Benign 44

Benign/Likely benign 17

  • c.2229+15G>T Multiple submitters glycogen storage disease IXd
  • c.238-4G>A Multiple submitters glycogen storage disease IXd
  • c.2918-4A>G Multiple submitters glycogen storage disease IXd
  • c.3499-30del Multiple submitters
  • c.538-25T>C Multiple submitters
  • c.864+11A>G Multiple submitters glycogen storage disease IXd
  • c.-261C>A Multiple submitters glycogen storage disease IXd
  • p.Arg821His Multiple submitters glycogen storage disease IXd
  • p.Asp160Asn Multiple submitters glycogen storage disease IXd ⚠
  • p.Asp381Asn Multiple submitters glycogen storage disease IXd
  • p.Met1175Val Multiple submitters glycogen storage disease IXd
  • p.Met789Val Multiple submitters glycogen storage disease IXd
  • p.Phe164= Multiple submitters glycogen storage disease IXd
  • p.Ser580= Multiple submitters glycogen storage disease IXd
  • p.Ser952= Multiple submitters glycogen storage disease IXd
  • p.Thr720= Multiple submitters glycogen storage disease IXd
  • p.Thr811= Multiple submitters glycogen storage disease IXd

Likely benign 234

Uncertain significance 378

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