Sugi Variant

Sugi Variant/PFKM

PFKM — 1071 ClinVar variants

All ClinVar germline PFKM variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 235 flagged for review →

29 Pathogenic · 17 Pathogenic/Likely pathogenic · 85 Likely pathogenic · 17 Conflicting · 54 Benign · 12 Benign/Likely benign · 577 Likely benign · 280 Uncertain significance

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

⚑ Evidence disagreements 235

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 4

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

Predictors lean, ClinVar uncertain 192

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 192

Predictors split 38

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

All PFKM variants

Pathogenic 29

  • p.Arg98Ter Multiple submitters glycogen storage disease VII
  • p.Pro668fs Multiple submitters glycogen storage disease VII
  • c.237+1G>C Single submitter glycogen storage disease VII
  • p.Ala216fs Single submitter glycogen storage disease VII
  • p.Ala588fs Single submitter glycogen storage disease VII
  • p.Ala8fs Single submitter glycogen storage disease VII
  • p.Arg35fs Single submitter glycogen storage disease VII
  • p.Cys244Ter Single submitter glycogen storage disease VII
  • p.Cys351fs Single submitter glycogen storage disease VII
  • p.Cys553fs Single submitter glycogen storage disease VII
  • p.Gln197Ter Single submitter glycogen storage disease VII
  • p.Gln491Ter Single submitter glycogen storage disease VII
  • p.Glu364fs Single submitter glycogen storage disease VII
  • p.Glu449fs Single submitter glycogen storage disease VII
  • p.Glu610fs Single submitter glycogen storage disease VII
  • p.Gly25fs Single submitter glycogen storage disease VII
  • p.Gly97fs Single submitter glycogen storage disease VII
  • p.Ile260fs Single submitter glycogen storage disease VII
  • p.Leu387fs Single submitter glycogen storage disease VII
  • p.Leu643_Tyr644insTer Single submitter glycogen storage disease VII
  • p.Lys476Ter Single submitter glycogen storage disease VII
  • p.Lys692fs Single submitter glycogen storage disease VII
  • p.Phe568fs Single submitter glycogen storage disease VII
  • p.Tyr55Ter Single submitter glycogen storage disease VII
  • c.1341+1G>T No assertion criteria glycogen storage disease VII
  • c.237+1G>T No assertion criteria Peroxisomal biogenesis disorder 3b
  • c.428-2A>C No assertion criteria glycogen storage disease VII
  • p.Arg39Leu No assertion criteria glycogen storage disease VII
  • p.Trp686Cys No assertion criteria glycogen storage disease VII

Pathogenic/Likely pathogenic 17

  • c.1413-2A>G Multiple submitters glycogen storage disease VII
  • c.1413-64A>G Multiple submitters glycogen storage disease VII
  • c.237+1G>A Multiple submitters glycogen storage disease VII
  • p.Arg129fs Multiple submitters glycogen storage disease VII
  • p.Arg246Ter Multiple submitters glycogen storage disease VII
  • p.Arg292fs Multiple submitters glycogen storage disease VII
  • p.Arg376Gln Multiple submitters glycogen storage disease VII ⚠
  • p.Arg39Pro Multiple submitters glycogen storage disease VII
  • p.Arg39Ter Multiple submitters glycogen storage disease VII
  • p.Arg432Ter Multiple submitters glycogen storage disease VII
  • p.Arg603Ter Multiple submitters glycogen storage disease VII
  • p.Arg95Ter Multiple submitters glycogen storage disease VII
  • p.Gln353Ter Multiple submitters glycogen storage disease VII
  • p.Gln447fs Multiple submitters glycogen storage disease VII
  • p.Glu441Ter Multiple submitters glycogen storage disease VII
  • p.Gly535_Ser536insTer Multiple submitters glycogen storage disease VII
  • p.Ser694fs Multiple submitters glycogen storage disease VII

Likely pathogenic 85

  • c.1062+1G>A Multiple submitters glycogen storage disease VII
  • c.1128-2A>G Multiple submitters glycogen storage disease VII
  • c.1191+1G>A Multiple submitters glycogen storage disease VII
  • c.1412+1G>T Multiple submitters glycogen storage disease VII
  • c.1412+2T>C Multiple submitters glycogen storage disease VII
  • c.1500+1G>A Multiple submitters glycogen storage disease VII
  • c.1501-2del Multiple submitters glycogen storage disease VII
  • c.159+1G>T Multiple submitters glycogen storage disease VII
  • c.160-1G>C Multiple submitters glycogen storage disease VII
  • c.1876_1880+2del Multiple submitters glycogen storage disease VII
  • c.238-3A>G Multiple submitters glycogen storage disease VII
  • c.936+2T>G Multiple submitters glycogen storage disease VII
  • p.Arg39Gln Multiple submitters glycogen storage disease VII
  • p.Gly209Asp Multiple submitters glycogen storage disease VII
  • p.Tyr635Ter Multiple submitters glycogen storage disease VII
  • c.1062+2T>C Single submitter glycogen storage disease VII
  • c.1127+1G>T Single submitter glycogen storage disease VII
  • c.1191+1del Single submitter glycogen storage disease VII
  • c.1192-2A>G Single submitter glycogen storage disease VII
  • c.1341+1G>A Single submitter glycogen storage disease VII
  • c.1341+1G>C Single submitter glycogen storage disease VII
  • c.1342-1G>C Single submitter glycogen storage disease VII
  • c.1412+1G>A Single submitter glycogen storage disease VII
  • c.1500+2T>A Single submitter glycogen storage disease VII
  • c.1653+2T>G Single submitter glycogen storage disease VII
  • c.1881-1G>A Single submitter glycogen storage disease VII
  • c.1992+1G>T Single submitter glycogen storage disease VII
  • c.2047_2092+14del Single submitter glycogen storage disease VII
  • c.2092+1G>C Single submitter glycogen storage disease VII
  • c.2092+2T>C Single submitter glycogen storage disease VII
  • c.594-1G>A Single submitter glycogen storage disease VII
  • c.594-2_594del Single submitter glycogen storage disease VII
  • c.638+1G>T Single submitter glycogen storage disease VII
  • c.85+1G>A Single submitter glycogen storage disease VII
  • c.86-1G>C Single submitter glycogen storage disease VII
  • c.936+1G>A Single submitter glycogen storage disease VII
  • c.-8-2A>G Single submitter glycogen storage disease VII
  • p.Ala142fs Single submitter glycogen storage disease VII
  • p.Ala410fs Single submitter glycogen storage disease VII
  • p.Ala542fs Single submitter glycogen storage disease VII
  • p.Asn532fs Single submitter
  • p.Asp309Gly Single submitter
  • p.Asp591Ala Single submitter glycogen storage disease VII
  • p.Gln462fs Single submitter glycogen storage disease VII
  • p.Gln56Ter Single submitter glycogen storage disease VII
  • p.Glu725fs Single submitter glycogen storage disease VII
  • p.Gly118_Asp119insTer Single submitter PFKM-related disorders
  • p.Gly118fs Single submitter glycogen storage disease VII
  • p.Gly271Ter Single submitter glycogen storage disease VII
  • p.Gly498fs Single submitter glycogen storage disease VII
  • p.Gly505fs Single submitter glycogen storage disease VII
  • p.Gly574fs Single submitter glycogen storage disease VII
  • p.Gly62Ter Single submitter glycogen storage disease VII
  • p.His211fs Single submitter glycogen storage disease VII
  • p.Ile428fs Single submitter glycogen storage disease VII
  • p.Leu156fs Single submitter glycogen storage disease VII
  • p.Leu348fs Single submitter glycogen storage disease VII
  • p.Leu427fs Single submitter glycogen storage disease VII
  • p.Leu626fs Single submitter glycogen storage disease VII
  • p.Lys487Ter Single submitter glycogen storage disease VII
  • p.Met573fs Single submitter glycogen storage disease VII
  • p.Phe522fs Single submitter glycogen storage disease VII
  • p.Pro235fs Single submitter glycogen storage disease VII
  • p.Pro670fs Single submitter glycogen storage disease VII
  • p.Ser133fs Single submitter glycogen storage disease VII
  • p.Ser164fs Single submitter glycogen storage disease VII
  • p.Ser180Cys Single submitter glycogen storage disease VII
  • p.Ser400Ter Single submitter glycogen storage disease VII
  • p.Ser536Ter Single submitter glycogen storage disease VII
  • p.Ser539fs Single submitter glycogen storage disease VII
  • p.Thr11fs Single submitter glycogen storage disease VII
  • p.Thr195fs Single submitter glycogen storage disease VII
  • p.Thr486_Lys487insTer Single submitter glycogen storage disease VII
  • p.Thr636fs Single submitter glycogen storage disease VII
  • p.Thr69fs Single submitter glycogen storage disease VII
  • p.Trp132Ter Single submitter glycogen storage disease VII
  • p.Trp382Ter Single submitter glycogen storage disease VII
  • p.Trp453Ter Single submitter glycogen storage disease VII
  • p.Tyr289Ter Single submitter glycogen storage disease VII
  • p.Tyr579fs Single submitter glycogen storage disease VII
  • p.Tyr644Ter Single submitter glycogen storage disease VII
  • p.Val21fs Single submitter glycogen storage disease VII
  • p.Val284fs Single submitter glycogen storage disease VII
  • p.Val293fs Single submitter glycogen storage disease VII
  • p.Val620fs Single submitter glycogen storage disease VII

Conflicting classifications of pathogenicity 17

  • c.1063-6C>A Single submitter glycogen storage disease VII
  • c.1063-7C>T Single submitter glycogen storage disease VII
  • c.1191+6G>T Single submitter glycogen storage disease VII
  • c.1412+6T>C Single submitter glycogen storage disease VII
  • c.638+15C>A Single submitter glycogen storage disease VII
  • c.639-10C>G Single submitter glycogen storage disease VII
  • c.843+5G>A Single submitter glycogen storage disease VII
  • c.*3C>T Single submitter glycogen storage disease VII
  • p.Arg100Ter Single submitter glycogen storage disease VII
  • p.Gln447Lys Single submitter glycogen storage disease VII
  • p.Gly288= Single submitter glycogen storage disease VII
  • p.Gly414= Single submitter glycogen storage disease VII
  • p.Ile14Thr Single submitter glycogen storage disease VII ⚠
  • p.Ser400Leu Single submitter glycogen storage disease VII ⚠
  • p.Ser707= Single submitter glycogen storage disease VII
  • p.Thr771Ile Single submitter glycogen storage disease VII ⚠
  • p.Val540Ile Single submitter glycogen storage disease VII ⚠

Benign 54

Benign/Likely benign 12

  • c.1413-19G>A Multiple submitters glycogen storage disease VII
  • c.1413-58C>A Multiple submitters glycogen storage disease VII
  • c.1500+32C>T Multiple submitters glycogen storage disease VII
  • c.206-3523C>A Multiple submitters
  • c.2199-12A>G Multiple submitters glycogen storage disease VII
  • c.594-41A>G Multiple submitters
  • c.844-17T>A Multiple submitters glycogen storage disease VII
  • p.Arg100Gln Multiple submitters glycogen storage disease VII
  • p.Arg696His Multiple submitters glycogen storage disease VII ⚠
  • p.Gly446= Multiple submitters glycogen storage disease VII
  • p.Gly680= Multiple submitters glycogen storage disease VII
  • p.Leu467= Multiple submitters glycogen storage disease VII

Likely benign 577

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

Uncertain significance 280