Sugi Variant

Sugi Variant/PGM1

PGM1 — 456 ClinVar variants

All ClinVar germline PGM1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 131 flagged for review →

23 Pathogenic · 7 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 19 Conflicting · 48 Benign · 14 Benign/Likely benign · 171 Likely benign · 165 Uncertain significance

Full PGM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 131

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 8

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

Predictors lean, ClinVar uncertain 103

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

Predictors split 20

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

All PGM1 variants

Pathogenic 23

  • p.Ala461fs Multiple submitters Inborn genetic diseases
  • p.Arg217Ter Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Arg503Ter Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Asn364fs Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Gly363fs Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Phe29fs Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ala142fs Single submitter PGM1-congenital disorder of glycosylation
  • p.Arg221fs Single submitter PGM1-congenital disorder of glycosylation
  • p.Arg333fs Single submitter PGM1-congenital disorder of glycosylation
  • p.Glu432Ter Single submitter PGM1-congenital disorder of glycosylation
  • p.Glu475Ter Single submitter PGM1-congenital disorder of glycosylation
  • p.Gly171Ter Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile500fs Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu492fs Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu516Pro Single submitter PGM1-congenital disorder of glycosylation
  • p.Lys105Ter Single submitter PGM1-congenital disorder of glycosylation
  • p.Pro231_Tyr232insTer Single submitter PGM1-congenital disorder of glycosylation
  • p.Pro231fs Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr507fs Single submitter PGM1-congenital disorder of glycosylation
  • p.Val310fs Single submitter PGM1-congenital disorder of glycosylation
  • c.1145-1G>C No assertion criteria PGM1-congenital disorder of glycosylation
  • p.Gly121Arg No assertion criteria PGM1-congenital disorder of glycosylation
  • p.Thr115Ala No assertion criteria PGM1-congenital disorder of glycosylation

Pathogenic/Likely pathogenic 7

  • c.1144+3A>T Multiple submitters
  • p.Arg293Ter Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Arg499Ter Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Arg515Gln Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Asp263Tyr Multiple submitters PGM1-related disorder
  • p.Gly291Arg Multiple submitters PGM1-related disorder
  • p.Gly330Arg Multiple submitters PGM1-related disorder

Likely pathogenic 9

  • c.1280+1G>C Single submitter PGM1-congenital disorder of glycosylation
  • c.1281-2A>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1464+1G>A Single submitter PGM1-congenital disorder of glycosylation
  • p.Arg503Gln Single submitter PGM1-congenital disorder of glycosylation
  • p.Gln324Ter Single submitter PGM1-related disorder
  • p.Gln530Ter Single submitter Inborn genetic diseases
  • p.Gly230Glu Single submitter PGM1-congenital disorder of glycosylation
  • p.Tyr268Ter Single submitter
  • p.Tyr517Ter Single submitter

Conflicting classifications of pathogenicity 19

  • c.1028+11C>A Single submitter PGM1-congenital disorder of glycosylation
  • c.1029-8C>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1599+5C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1600-3C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1600-523G>A Single submitter PGM1-congenital disorder of glycosylation
  • c.247-5696A>T Single submitter PGM1-congenital disorder of glycosylation
  • p.Ala368Val Single submitter PGM1-congenital disorder of glycosylation ⚠
  • p.Arg293Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg422Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg515Trp Single submitter PGM1-congenital disorder of glycosylation ⚠
  • p.Gly437= Single submitter PGM1-congenital disorder of glycosylation
  • p.His300= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile109= Single submitter PGM1-congenital disorder of glycosylation
  • p.Lys68Met Single submitter PGM1-congenital disorder of glycosylation ⚠
  • p.Phe148Val Single submitter PGM1-congenital disorder of glycosylation ⚠
  • p.Ser338Arg Single submitter PGM1-congenital disorder of glycosylation ⚠
  • p.Ser369Arg Single submitter PGM1-congenital disorder of glycosylation ⚠
  • p.Thr467Asn Single submitter PGM1-congenital disorder of glycosylation ⚠
  • p.Tyr232= Single submitter PGM1-congenital disorder of glycosylation

Benign 48

Benign/Likely benign 14

  • c.1145-7C>G Multiple submitters PGM1-congenital disorder of glycosylation
  • c.1280+7C>T Multiple submitters PGM1-congenital disorder of glycosylation
  • c.1600-518C>T Multiple submitters
  • c.247-5664G>A Multiple submitters PGM1-congenital disorder of glycosylation
  • c.*198C>T Multiple submitters
  • c.*22C>T Multiple submitters PGM1-congenital disorder of glycosylation
  • c.*37G>A Multiple submitters
  • c.*93A>C Multiple submitters
  • p.Arg221Cys Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Arg329= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ile500= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ile88Val Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ser191= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Val501Ile Multiple submitters PGM1-congenital disorder of glycosylation

Likely benign 171

  • c.1029-101A>G Multiple submitters
  • c.1144+10A>G Multiple submitters PGM1-congenital disorder of glycosylation
  • c.1464+14G>A Multiple submitters PGM1-congenital disorder of glycosylation
  • c.1464+15G>A Multiple submitters PGM1-congenital disorder of glycosylation
  • c.1600-524C>T Multiple submitters
  • c.246+320G>C Multiple submitters
  • c.247-6400T>A Multiple submitters
  • c.682+168A>G Multiple submitters
  • c.*406T>C Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ala243= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ala245= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ala368= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ala98= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Asp367= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ile83= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ile88= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Phe379= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Pro138= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Pro140= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Pro253= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Pro321= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Pro538= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Ser505= Multiple submitters PGM1-congenital disorder of glycosylation
  • p.Tyr430= Multiple submitters PGM1-congenital disorder of glycosylation
  • c.1028+10T>C Single submitter
  • c.1028+13A>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1028+18C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1028+211C>T Single submitter
  • c.1029-19T>C Single submitter PGM1-congenital disorder of glycosylation
  • c.1029-261T>C Single submitter
  • c.1144+16G>A Single submitter PGM1-congenital disorder of glycosylation
  • c.1144+9C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1145-10C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1145-11C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1145-214A>G Single submitter
  • c.1145-241GA[4] Single submitter
  • c.1145-6C>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1145-7C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1145-8C>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1145-9C>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1280+12C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1281-14G>A Single submitter PGM1-congenital disorder of glycosylation
  • c.1281-15C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1281-17T>A Single submitter PGM1-congenital disorder of glycosylation
  • c.1281-5T>C Single submitter PGM1-congenital disorder of glycosylation
  • c.1464+9A>T Single submitter PGM1-congenital disorder of glycosylation
  • c.1465-16_1465-15del Single submitter PGM1-congenital disorder of glycosylation
  • c.1465-4C>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1599+322A>G Single submitter
  • c.1599+568T>C Single submitter
  • c.1600-13_1600-12del Single submitter
  • c.1600-13A>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1600-15C>G Single submitter PGM1-congenital disorder of glycosylation
  • c.1600-527C>T Single submitter
  • c.246+19C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.246+312C>T Single submitter
  • c.247-5752G>A Single submitter
  • c.247-5872C>T Single submitter
  • c.247-5929T>C Single submitter
  • c.247-7C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.409+12G>C Single submitter PGM1-congenital disorder of glycosylation
  • c.409+19T>G Single submitter
  • c.410-11T>C Single submitter PGM1-congenital disorder of glycosylation
  • c.410-13G>C Single submitter PGM1-congenital disorder of glycosylation
  • c.410-17T>G Single submitter PGM1-congenital disorder of glycosylation
  • c.410-18T>C Single submitter PGM1-congenital disorder of glycosylation
  • c.556+12T>C Single submitter
  • c.556+177G>A Single submitter
  • c.556+20C>G Single submitter PGM1-congenital disorder of glycosylation
  • c.556+216C>T Single submitter
  • c.556+288A>G Single submitter
  • c.556+47G>C Single submitter
  • c.557-10G>A Single submitter PGM1-congenital disorder of glycosylation
  • c.557-11del Single submitter PGM1-congenital disorder of glycosylation
  • c.557-14G>T Single submitter PGM1-congenital disorder of glycosylation
  • c.557-15del Single submitter PGM1-congenital disorder of glycosylation
  • c.557-5C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.557-5del Single submitter PGM1-congenital disorder of glycosylation
  • c.682+197G>A Single submitter
  • c.682+20C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.682+297C>G Single submitter
  • c.683-235C>G Single submitter
  • c.683-291A>G Single submitter
  • c.683-6A>G Single submitter PGM1-congenital disorder of glycosylation
  • c.873+10A>G Single submitter PGM1-congenital disorder of glycosylation
  • c.873+7A>T Single submitter PGM1-congenital disorder of glycosylation
  • c.874-14C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.874-5C>T Single submitter PGM1-congenital disorder of glycosylation
  • c.874-6C>A Single submitter PGM1-congenital disorder of glycosylation
  • c.874-7C>T Single submitter PGM1-congenital disorder of glycosylation
  • p.Ala116= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ala397= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ala403= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ala447= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ala471= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ala510= Single submitter PGM1-congenital disorder of glycosylation
  • p.Arg499Gln Single submitter PGM1-congenital disorder of glycosylation
  • p.Arg52= Single submitter PGM1-congenital disorder of glycosylation
  • p.Arg85= Single submitter PGM1-congenital disorder of glycosylation
  • p.Asn119= Single submitter PGM1-congenital disorder of glycosylation
  • p.Asn216= Single submitter PGM1-congenital disorder of glycosylation
  • p.Asn81= Single submitter PGM1-congenital disorder of glycosylation
  • p.Asp223= Single submitter PGM1-congenital disorder of glycosylation
  • p.Asp390= Single submitter PGM1-congenital disorder of glycosylation
  • p.Asp411= Single submitter PGM1-congenital disorder of glycosylation
  • p.Asp444= Single submitter PGM1-congenital disorder of glycosylation
  • p.Asp478= Single submitter PGM1-congenital disorder of glycosylation
  • p.Cys251= Single submitter PGM1-congenital disorder of glycosylation
  • p.Gln41= Single submitter PGM1-congenital disorder of glycosylation
  • p.Gln418= Single submitter PGM1-congenital disorder of glycosylation
  • p.Gln72= Single submitter
  • p.Glu187= Single submitter PGM1-congenital disorder of glycosylation
  • p.Glu376= Single submitter PGM1-congenital disorder of glycosylation
  • p.Glu431= Single submitter PGM1-congenital disorder of glycosylation
  • p.Gly122= Single submitter
  • p.Gly301= Single submitter PGM1-congenital disorder of glycosylation
  • p.Gly327= Single submitter PGM1-congenital disorder of glycosylation
  • p.Gly508= Single submitter PGM1-congenital disorder of glycosylation
  • p.His416= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile102= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile112= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile133= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile188= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile222= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile317= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile4= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ile518= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu211= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu212= Single submitter
  • p.Leu241= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu272= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu341= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu352= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu396= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu402= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu413= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu492= Single submitter PGM1-congenital disorder of glycosylation
  • p.Leu94= Single submitter PGM1-congenital disorder of glycosylation
  • p.Lys180= Single submitter PGM1-congenital disorder of glycosylation
  • p.Lys419= Single submitter PGM1-congenital disorder of glycosylation
  • p.Lys440= Single submitter PGM1-congenital disorder of glycosylation
  • p.Lys457= Single submitter PGM1-congenital disorder of glycosylation
  • p.Phe474= Single submitter PGM1-congenital disorder of glycosylation
  • p.Pro120= Single submitter PGM1-congenital disorder of glycosylation
  • p.Pro17= Single submitter PGM1-congenital disorder of glycosylation
  • p.Pro264= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ser100= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ser20= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ser206= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ser247= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ser372= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ser477= Single submitter PGM1-congenital disorder of glycosylation
  • p.Ser485= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr267= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr348= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr355= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr426= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr46= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr467= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr495= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr556= Single submitter PGM1-congenital disorder of glycosylation
  • p.Thr56= Single submitter PGM1-congenital disorder of glycosylation
  • p.Tyr35= Single submitter PGM1-congenital disorder of glycosylation
  • p.Tyr66= Single submitter PGM1-congenital disorder of glycosylation
  • p.Val433= Single submitter PGM1-congenital disorder of glycosylation
  • p.Val87= Single submitter PGM1-congenital disorder of glycosylation
  • c.1145-212A>G No assertion criteria PGM1-related disorder
  • c.1600-505T>C No assertion criteria PGM1-related disorder
  • c.682+5A>G No assertion criteria PGM1-related disorder
  • c.*9G>A No assertion criteria PGM1-related disorder
  • p.Asp463= No assertion criteria PGM1-related disorder

Uncertain significance 165