Sugi Variant

Sugi Variant/CNNM2

CNNM2 — 478 ClinVar variants

All ClinVar germline CNNM2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 229 flagged for review →

21 Pathogenic · 1 Pathogenic/Likely pathogenic · 17 Likely pathogenic · 12 Conflicting · 38 Benign · 12 Benign/Likely benign · 118 Likely benign · 259 Uncertain significance

Full CNNM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 229

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 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 6

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

Predictors lean, ClinVar uncertain 146

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

Predictors split 75

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

All CNNM2 variants

Pathogenic 21

  • p.Ala92fs Single submitter
  • p.Ala92Pro Single submitter hypomagnesemia, seizures, and intellectual disability 1 ⚠
  • p.Cys4Ter Single submitter
  • p.Glu122Lys Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Glu357Lys Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Glu431Lys Single submitter renal hypomagnesemia 6
  • p.Glu646fs Single submitter CNNM2-Related Disorders
  • p.Gly437Glu Single submitter renal hypomagnesemia 6
  • p.Met534fs Single submitter
  • p.Ser795Ter Single submitter renal hypomagnesemia 6
  • p.Tyr106Ter Single submitter
  • p.Val324Leu Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Ile40fs No assertion criteria renal hypomagnesemia 6
  • p.Leu321del No assertion criteria hypomagnesemia, seizures, and intellectual disability 1
  • p.Leu418Pro No assertion criteria hypomagnesemia, seizures, and intellectual disability 1
  • p.Leu48Pro No assertion criteria hypomagnesemia, seizures, and intellectual disability 1 ⚠
  • p.Met383Val No assertion criteria familial primary hypomagnesemia
  • p.Ser614_Glu615delinsArg No assertion criteria hypomagnesemia, seizures, and intellectual disability 1
  • p.Thr568Ile No assertion criteria renal hypomagnesemia 6
  • p.Tyr314Ter No assertion criteria hypomagnesemia, seizures, and intellectual disability 1
  • p.Val324Met No assertion criteria hypomagnesemia, seizures, and intellectual disability 1

Pathogenic/Likely pathogenic 1

  • p.Ser269Trp Multiple submitters hypomagnesemia, seizures, and intellectual disability 1

Likely pathogenic 17

  • p.Arg602Ter Multiple submitters renal hypomagnesemia 6
  • p.Ala19fs Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Arg797Ter Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Asn327Ser Single submitter
  • p.Asp335Asn Single submitter renal hypomagnesemia 6
  • p.Gln403Ter Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Gly356Glu Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Gly46fs Single submitter
  • p.Gly59delinsArgCysSerCysTer Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Ile175fs Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Ile435del Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Ser621Ter Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Thr331Ile Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Tyr106fs Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Tyr588Ter Single submitter hypomagnesemia, seizures, and intellectual disability 1
  • p.Cys859Tyr No assertion criteria renal hypomagnesemia 6 ⚠
  • p.Gly351Arg No assertion criteria Moyamoya angiopathy

Conflicting classifications of pathogenicity 12

Benign 38

Benign/Likely benign 12

  • c.2073+14T>C Multiple submitters renal hypomagnesemia 6
  • c.2233+17C>T Multiple submitters hypomagnesemia, seizures, and intellectual disability 1
  • c.*52C>T Multiple submitters renal hypomagnesemia 6
  • p.Ala202Thr Multiple submitters renal hypomagnesemia 6
  • p.Asn855= Multiple submitters renal hypomagnesemia 6
  • p.Leu632= Multiple submitters
  • p.Leu837= Multiple submitters
  • p.Phe120= Multiple submitters hypomagnesemia, seizures, and intellectual disability 1
  • p.Pro505= Multiple submitters renal hypomagnesemia 6
  • p.Ser188= Multiple submitters renal hypomagnesemia 6
  • p.Thr114= Multiple submitters renal hypomagnesemia 6
  • p.Tyr301= Multiple submitters renal hypomagnesemia 6

Likely benign 118

Uncertain significance 259