Sugi Variant

Sugi Variant/PCK1

PCK1 — 314 ClinVar variants

All ClinVar germline PCK1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 139 flagged for review →

3 Pathogenic · 4 Likely pathogenic · 26 Conflicting · 26 Benign · 10 Benign/Likely benign · 79 Likely benign · 166 Uncertain significance

Full PCK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 139

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 99

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

Predictors split 32

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

All PCK1 variants

Pathogenic 3

  • c.962-1G>C Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Gln412Ter Single submitter Inborn genetic diseases
  • p.Cys192Arg No assertion criteria phosphoenolpyruvate carboxykinase deficiency, cytosolic

Likely pathogenic 4

  • c.961+1G>A Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Glu611fs Single submitter
  • p.Gly434fs Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Tyr235Ter Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic

Conflicting classifications of pathogenicity 26

  • p.Ala548= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ala548Thr Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic ⚠
  • p.Arg249= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Arg483Gln Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Arg55Gln Single submitter Inborn genetic diseases ⚠
  • p.Asn34= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Asp186Asn Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic ⚠
  • p.Asp318= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Asp47= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Cys399Ter Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Gly242Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly275fs Single submitter PCK1-related disorder
  • p.Gly309Arg Single submitter PCK1-related disorder ⚠
  • p.Gly440= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.His452Pro Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic ⚠
  • p.Ile158= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ile65Val Single submitter Inborn genetic diseases ⚠
  • p.Leu300Phe Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic ⚠
  • p.Pro301= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Pro3Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro423Leu Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic ⚠
  • p.Pro427Ser Single submitter Inborn genetic diseases ⚠
  • p.Ser286= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Thr138= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Thr138Ile Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic ⚠
  • p.Thr384= Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic

Benign 26

  • c.1318+202C>T Multiple submitters
  • c.1319-129C>T Multiple submitters
  • c.225-117C>G Multiple submitters
  • c.225-134T>C Multiple submitters
  • c.225-173G>C Multiple submitters
  • c.225-66C>T Multiple submitters
  • c.407-65A>C Multiple submitters
  • c.611-44G>C Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • c.*120T>G Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • c.*431T>C Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Gln4= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ile267Val Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic ⚠
  • p.Leu23= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ser151= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ser154= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ser163= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Thr291= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Tyr235= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Val368Ile Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • c.1319-11del Single submitter
  • c.1319-11dup Single submitter
  • c.1319-12_1319-11dup Single submitter
  • c.*359G>A Single submitter phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Asn403= Single submitter
  • p.Ile219= Single submitter
  • p.Val15Phe Single submitter ⚠

Benign/Likely benign 10

  • c.611-16G>A Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ala281= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Cys288= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Glu276Lys Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Gly380= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ile558= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ile612= Multiple submitters
  • p.Ile94= Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic
  • p.Ser579Arg Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic ⚠
  • p.Val184Leu Multiple submitters phosphoenolpyruvate carboxykinase deficiency, cytosolic

Likely benign 79

Uncertain significance 166