Sugi Variant

Sugi Variant/PHKG2

PHKG2 — 413 ClinVar variants

All ClinVar germline PHKG2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 105 flagged for review →

35 Pathogenic · 9 Pathogenic/Likely pathogenic · 11 Likely pathogenic · 24 Conflicting · 14 Benign · 4 Benign/Likely benign · 201 Likely benign · 115 Uncertain significance

Full PHKG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 105

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 7

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

Predictors lean, ClinVar uncertain 74

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

Predictors split 23

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

All PHKG2 variants

Pathogenic 35

  • p.Arg185Ter Multiple submitters Glycogen storage disease type IXc
  • p.Arg44Ter Multiple submitters PHKG2-related disorder
  • p.Glu157Lys Multiple submitters glycogen storage disease IXc
  • p.Glu8Ter Multiple submitters glycogen storage disease IXc
  • p.Phe224Ter Multiple submitters Inborn genetic diseases
  • c.326+1G>C Single submitter glycogen storage disease IXc
  • c.393-1G>C Single submitter
  • c.557-1_557delinsAG Single submitter glycogen storage disease IXc
  • c.648-2_648del Single submitter glycogen storage disease IXc
  • c.802-2A>C Single submitter glycogen storage disease IXc
  • c.927+1G>A Single submitter glycogen storage disease IXc
  • p.Arg152Gln Single submitter glycogen storage disease IXc
  • p.Arg168Ter Single submitter glycogen storage disease IXc
  • p.Cys176Ter Single submitter Inborn genetic diseases
  • p.Cys219fs Single submitter glycogen storage disease IXc
  • p.Gln249Ter Single submitter glycogen storage disease IXc
  • p.Gln284Ter Single submitter glycogen storage disease IXc
  • p.Gln287Ter Single submitter glycogen storage disease IXc
  • p.Glu129Ter Single submitter glycogen storage disease IXc
  • p.Glu256fs Single submitter glycogen storage disease IXc
  • p.His89fs Single submitter glycogen storage disease IXc
  • p.Leu227fs Single submitter glycogen storage disease IXc
  • p.Leu302fs Single submitter glycogen storage disease IXc
  • p.Lys18fs Single submitter glycogen storage disease IXc
  • p.Pro180fs Single submitter glycogen storage disease IXc
  • p.Pro276fs Single submitter glycogen storage disease IXc
  • p.Trp300Ter Single submitter glycogen storage disease IXc
  • p.Tyr24Ter Single submitter glycogen storage disease IXc
  • p.Val106_Phe107insTer Single submitter glycogen storage disease IXc
  • p.Val84fs Single submitter glycogen storage disease IXc
  • p.Gly189Glu No assertion criteria glycogen storage disease IXc
  • p.His145Tyr No assertion criteria glycogen storage disease IXc
  • p.Leu226Arg No assertion criteria glycogen storage disease IXc
  • p.Leu93fs No assertion criteria glycogen storage disease IXc
  • p.Ser262fs No assertion criteria glycogen storage disease IXc

Pathogenic/Likely pathogenic 9

  • c.800_801+34del Multiple submitters glycogen storage disease IXc
  • c.96-11G>A Multiple submitters glycogen storage disease IXc
  • p.Arg152Ter Multiple submitters glycogen storage disease IXc
  • p.Arg279Cys Multiple submitters glycogen storage disease IXc
  • p.Arg76Ter Multiple submitters PHKG2-related disorder
  • p.Asp215Asn Multiple submitters glycogen storage disease IX
  • p.Leu144Pro Multiple submitters glycogen storage disease IXc
  • p.Lys112fs Multiple submitters glycogen storage disease IXc
  • p.Val106Glu Multiple submitters glycogen storage disease IXc

Likely pathogenic 11

  • p.Arg309Trp Multiple submitters glycogen storage disease IX ⚠
  • c.271+124_327-492del Single submitter glycogen storage disease IXc
  • c.392+2T>G Single submitter glycogen storage disease IXc
  • c.393-2A>G Single submitter glycogen storage disease IXc
  • p.Asn334fs Single submitter PHKG2-related disorder
  • p.Glu56fs Single submitter glycogen storage disease IXc
  • p.Gly220Glu Single submitter glycogen storage disease IXc
  • p.His326fs Single submitter glycogen storage disease IXc
  • p.Leu357Pro Single submitter glycogen storage disease IXc ⚠
  • p.Phe116fs Single submitter glycogen storage disease IXc
  • p.Ser36Phe Single submitter glycogen storage disease IXc

Conflicting classifications of pathogenicity 24

  • c.271+14C>T Single submitter glycogen storage disease IXc
  • c.556+11C>G Single submitter glycogen storage disease IXc
  • c.927+13G>A Single submitter glycogen storage disease IXc
  • c.95+11G>A Single submitter glycogen storage disease IXc
  • c.96-7C>G Single submitter glycogen storage disease IXc
  • c.-28G>T Single submitter glycogen storage disease IXc
  • p.Ala195= Single submitter glycogen storage disease IXc
  • p.Ala395Val Single submitter Inborn genetic diseases ⚠
  • p.Arg131= Single submitter glycogen storage disease IXc
  • p.Arg307= Single submitter glycogen storage disease IXc
  • p.Arg309Gln Single submitter Mauriac syndrome ⚠
  • p.Arg320Ter Single submitter glycogen storage disease IXc
  • p.Arg344Gln Single submitter Inborn genetic diseases ⚠
  • p.Asp108= Single submitter glycogen storage disease IXc
  • p.Asp153Val Single submitter ⚠
  • p.Asp351Asn Single submitter glycogen storage disease IXc ⚠
  • p.Glu77Lys Single submitter glycogen storage disease IXc ⚠
  • p.Gly359= Single submitter glycogen storage disease IXc
  • p.Gly86Ser Single submitter glycogen storage disease IXc ⚠
  • p.Phe233Ser Single submitter glycogen storage disease IXc ⚠
  • p.Pro379= Single submitter glycogen storage disease IXc
  • p.Ser96= Single submitter glycogen storage disease IXc
  • p.Thr120= Single submitter glycogen storage disease IXc
  • p.Val106= Single submitter glycogen storage disease IXc

Benign 14

Benign/Likely benign 4

  • c.802-17C>T Multiple submitters glycogen storage disease IXc
  • c.927+17C>G Multiple submitters glycogen storage disease IXc
  • c.96-10G>T Multiple submitters glycogen storage disease IXc
  • p.Thr58= Multiple submitters glycogen storage disease IXc

Likely benign 201

  • c.648-13G>A Multiple submitters glycogen storage disease IXc
  • c.927+18A>G Multiple submitters glycogen storage disease IXc
  • c.95+143G>C Multiple submitters
  • c.95+149G>C Multiple submitters
  • p.Ala342= Multiple submitters glycogen storage disease IXc
  • p.Ala51= Multiple submitters glycogen storage disease IXc
  • p.Asn301= Multiple submitters glycogen storage disease IXc
  • p.Asp163= Multiple submitters glycogen storage disease IXc
  • p.Pro12= Multiple submitters glycogen storage disease IXc
  • p.Thr263= Multiple submitters glycogen storage disease IXc
  • c.271+12T>C Single submitter glycogen storage disease IXc
  • c.271+19C>T Single submitter glycogen storage disease IXc
  • c.272-12C>G Single submitter glycogen storage disease IXc
  • c.272-12C>T Single submitter glycogen storage disease IXc
  • c.272-15T>C Single submitter glycogen storage disease IXc
  • c.272-18C>T Single submitter glycogen storage disease IXc
  • c.272-20C>T Single submitter glycogen storage disease IXc
  • c.272-9T>C Single submitter glycogen storage disease IXc
  • c.326+15G>C Single submitter glycogen storage disease IXc
  • c.327-15C>T Single submitter glycogen storage disease IXc
  • c.327-16C>T Single submitter glycogen storage disease IXc
  • c.327-17G>A Single submitter glycogen storage disease IXc
  • c.327-7C>T Single submitter glycogen storage disease IXc
  • c.392+10G>A Single submitter glycogen storage disease IXc
  • c.392+13C>T Single submitter glycogen storage disease IXc
  • c.392+18A>C Single submitter glycogen storage disease IXc
  • c.392+19G>T Single submitter glycogen storage disease IXc
  • c.392+7G>T Single submitter glycogen storage disease IXc
  • c.393-12C>G Single submitter glycogen storage disease IXc
  • c.393-12C>T Single submitter glycogen storage disease IXc
  • c.393-17G>A Single submitter glycogen storage disease IXc
  • c.393-18C>T Single submitter glycogen storage disease IXc
  • c.393-4C>T Single submitter glycogen storage disease IXc
  • c.393-6C>T Single submitter glycogen storage disease IXc
  • c.393-7C>T Single submitter glycogen storage disease IXc
  • c.556+141G>A Single submitter
  • c.556+14G>A Single submitter glycogen storage disease IXc
  • c.556+18C>T Single submitter glycogen storage disease IXc
  • c.556+8G>T Single submitter glycogen storage disease IXc
  • c.557-13C>T Single submitter glycogen storage disease IXc
  • c.557-20T>C Single submitter glycogen storage disease IXc
  • c.647+12G>A Single submitter glycogen storage disease IXc
  • c.647+14C>T Single submitter glycogen storage disease IXc
  • c.647+16C>T Single submitter glycogen storage disease IXc
  • c.647+17C>G Single submitter glycogen storage disease IXc
  • c.647+20C>G Single submitter glycogen storage disease IXc
  • c.648-11C>T Single submitter glycogen storage disease IXc
  • c.648-15C>T Single submitter glycogen storage disease IXc
  • c.648-4C>G Single submitter glycogen storage disease IXc
  • c.648-7T>C Single submitter glycogen storage disease IXc
  • c.801+10G>T Single submitter glycogen storage disease IXc
  • c.801+11G>A Single submitter glycogen storage disease IXc
  • c.801+13T>C Single submitter glycogen storage disease IXc
  • c.801+14G>C Single submitter glycogen storage disease IXc
  • c.801+15A>G Single submitter glycogen storage disease IXc
  • c.801+17A>G Single submitter glycogen storage disease IXc
  • c.801+18G>A Single submitter glycogen storage disease IXc
  • c.801+20del Single submitter glycogen storage disease IXc
  • c.801+7G>A Single submitter glycogen storage disease IXc
  • c.802-10T>G Single submitter glycogen storage disease IXc
  • c.802-11G>C Single submitter glycogen storage disease IXc
  • c.802-13G>T Single submitter glycogen storage disease IXc
  • c.802-16T>C Single submitter glycogen storage disease IXc
  • c.927+12T>C Single submitter glycogen storage disease IXc
  • c.927+15A>G Single submitter glycogen storage disease IXc
  • c.927+15A>T Single submitter glycogen storage disease IXc
  • c.927+19G>T Single submitter glycogen storage disease IXc
  • c.927+7C>T Single submitter glycogen storage disease IXc
  • c.927+8T>C Single submitter glycogen storage disease IXc
  • c.928-12C>T Single submitter glycogen storage disease IXc
  • c.928-13C>A Single submitter glycogen storage disease IXc
  • c.928-13C>T Single submitter glycogen storage disease IXc
  • c.928-16C>T Single submitter glycogen storage disease IXc
  • c.928-20C>T Single submitter glycogen storage disease IXc
  • c.928-5C>G Single submitter glycogen storage disease IXc
  • c.928-8C>G Single submitter glycogen storage disease IXc
  • c.928-9C>A Single submitter glycogen storage disease IXc
  • c.95+122_95+178del Single submitter
  • c.95+12G>A Single submitter glycogen storage disease IXc
  • c.95+12G>T Single submitter glycogen storage disease IXc
  • c.95+15A>G Single submitter glycogen storage disease IXc
  • c.95+85GGT[13] Single submitter
  • c.96-12C>T Single submitter glycogen storage disease IXc
  • c.96-14T>C Single submitter glycogen storage disease IXc
  • c.96-18A>G Single submitter glycogen storage disease IXc
  • c.-21C>G Single submitter
  • c.-28G>A Single submitter
  • p.Ala140= Single submitter glycogen storage disease IXc
  • p.Ala16= Single submitter glycogen storage disease IXc
  • p.Ala17= Single submitter glycogen storage disease IXc
  • p.Ala285= Single submitter glycogen storage disease IXc
  • p.Ala322= Single submitter glycogen storage disease IXc
  • p.Ala371= Single submitter glycogen storage disease IXc
  • p.Ala401= Single submitter glycogen storage disease IXc
  • p.Ala59= Single submitter glycogen storage disease IXc
  • p.Ala73= Single submitter glycogen storage disease IXc
  • p.Ala85= Single submitter glycogen storage disease IXc
  • p.Arg135= Single submitter glycogen storage disease IXc
  • p.Arg152= Single submitter glycogen storage disease IXc
  • p.Arg236= Single submitter glycogen storage disease IXc
  • p.Arg243= Single submitter glycogen storage disease IXc
  • p.Arg279= Single submitter glycogen storage disease IXc
  • p.Arg293= Single submitter glycogen storage disease IXc
  • p.Arg327= Single submitter glycogen storage disease IXc
  • p.Arg338= Single submitter glycogen storage disease IXc
  • p.Arg344= Single submitter glycogen storage disease IXc
  • p.Asn164= Single submitter glycogen storage disease IXc
  • p.Asn334= Single submitter glycogen storage disease IXc
  • p.Asp153= Single submitter glycogen storage disease IXc
  • p.Asp204= Single submitter glycogen storage disease IXc
  • p.Asp215= Single submitter glycogen storage disease IXc
  • p.Asp339= Single submitter glycogen storage disease IXc
  • p.Asp351= Single submitter glycogen storage disease IXc
  • p.Asp95= Single submitter glycogen storage disease IXc
  • p.Gln273= Single submitter glycogen storage disease IXc
  • p.Gln284= Single submitter glycogen storage disease IXc
  • p.Gln306= Single submitter glycogen storage disease IXc
  • p.Glu197= Single submitter glycogen storage disease IXc
  • p.Glu277= Single submitter glycogen storage disease IXc
  • p.Glu390= Single submitter glycogen storage disease IXc
  • p.Glu60= Single submitter glycogen storage disease IXc
  • p.Glu8= Single submitter glycogen storage disease IXc
  • p.Gly173= Single submitter glycogen storage disease IXc
  • p.Gly181= Single submitter glycogen storage disease IXc
  • p.Gly192= Single submitter glycogen storage disease IXc
  • p.Gly209= Single submitter glycogen storage disease IXc
  • p.Gly319= Single submitter glycogen storage disease IXc
  • p.Gly365= Single submitter glycogen storage disease IXc
  • p.Gly6= Single submitter glycogen storage disease IXc
  • p.His177= Single submitter glycogen storage disease IXc
  • p.His235= Single submitter glycogen storage disease IXc
  • p.His288= Single submitter glycogen storage disease IXc
  • p.His348= Single submitter glycogen storage disease IXc
  • p.His360= Single submitter glycogen storage disease IXc
  • p.His48= Single submitter glycogen storage disease IXc
  • p.Ile198= Single submitter glycogen storage disease IXc
  • p.Ile350= Single submitter glycogen storage disease IXc
  • p.Ile384= Single submitter glycogen storage disease IXc
  • p.Ile91= Single submitter glycogen storage disease IXc
  • p.Ile94= Single submitter glycogen storage disease IXc
  • p.Leu105= Single submitter glycogen storage disease IXc
  • p.Leu11= Single submitter glycogen storage disease IXc
  • p.Leu119= Single submitter glycogen storage disease IXc
  • p.Leu160= Single submitter glycogen storage disease IXc
  • p.Leu187= Single submitter glycogen storage disease IXc
  • p.Leu226= Single submitter glycogen storage disease IXc
  • p.Leu240= Single submitter glycogen storage disease IXc
  • p.Leu271= Single submitter glycogen storage disease IXc
  • p.Leu3= Single submitter glycogen storage disease IXc
  • p.Leu316= Single submitter glycogen storage disease IXc
  • p.Leu331= Single submitter glycogen storage disease IXc
  • p.Leu336= Single submitter glycogen storage disease IXc
  • p.Leu343= Single submitter glycogen storage disease IXc
  • p.Leu357= Single submitter glycogen storage disease IXc
  • p.Leu405= Single submitter glycogen storage disease IXc
  • p.Leu67= Single submitter glycogen storage disease IXc
  • p.Lys112= Single submitter glycogen storage disease IXc
  • p.Lys122= Single submitter glycogen storage disease IXc
  • p.Lys363= Single submitter glycogen storage disease IXc
  • p.Phe104= Single submitter glycogen storage disease IXc
  • p.Phe172= Single submitter glycogen storage disease IXc
  • p.Phe252= Single submitter glycogen storage disease IXc
  • p.Phe290= Single submitter glycogen storage disease IXc
  • p.Pro156= Single submitter glycogen storage disease IXc
  • p.Pro232= Single submitter glycogen storage disease IXc
  • p.Pro255= Single submitter glycogen storage disease IXc
  • p.Pro289= Single submitter glycogen storage disease IXc
  • p.Pro378= Single submitter glycogen storage disease IXc
  • p.Pro381= Single submitter glycogen storage disease IXc
  • p.Pro383= Single submitter glycogen storage disease IXc
  • p.Pro64= Single submitter glycogen storage disease IXc
  • p.Pro7= Single submitter glycogen storage disease IXc
  • p.Pro88= Single submitter glycogen storage disease IXc
  • p.Ser230= Single submitter glycogen storage disease IXc
  • p.Ser262= Single submitter glycogen storage disease IXc
  • p.Ser269= Single submitter glycogen storage disease IXc
  • p.Ser345= Single submitter glycogen storage disease IXc
  • p.Ser393= Single submitter glycogen storage disease IXc
  • p.Ser63= Single submitter glycogen storage disease IXc
  • p.Thr2= Single submitter glycogen storage disease IXc
  • p.Thr206= Single submitter glycogen storage disease IXc
  • p.Thr332= Single submitter glycogen storage disease IXc
  • p.Thr397= Single submitter glycogen storage disease IXc
  • p.Thr46= Single submitter glycogen storage disease IXc
  • p.Thr78= Single submitter glycogen storage disease IXc
  • p.Thr92= Single submitter glycogen storage disease IXc
  • p.Tyr193= Single submitter glycogen storage disease IXc
  • p.Tyr210= Single submitter glycogen storage disease IXc
  • p.Tyr24= Single submitter glycogen storage disease IXc
  • p.Tyr341= Single submitter glycogen storage disease IXc
  • p.Tyr358= Single submitter glycogen storage disease IXc
  • p.Tyr97= Single submitter glycogen storage disease IXc
  • p.Val123= Single submitter glycogen storage disease IXc
  • p.Val214= Single submitter glycogen storage disease IXc
  • p.Val221= Single submitter glycogen storage disease IXc
  • p.Val37= Single submitter glycogen storage disease IXc
  • p.Val38= Single submitter glycogen storage disease IXc
  • p.Val402= Single submitter glycogen storage disease IXc
  • p.Val402Ala Single submitter Inborn genetic diseases
  • p.Val52= Single submitter glycogen storage disease IXc
  • p.Val84= Single submitter glycogen storage disease IXc

Uncertain significance 115