AGPAT2 — 284 ClinVar variants

All ClinVar germline AGPAT2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 104 flagged for review →

19 Pathogenic · 7 Pathogenic/Likely pathogenic · 11 Likely pathogenic · 23 Conflicting · 16 Benign · 11 Benign/Likely benign · 58 Likely benign · 139 Uncertain significance

Full AGPAT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 104

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 8

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

Predictors lean, ClinVar uncertain 68

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

Predictors split 27

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

All AGPAT2 variants

Pathogenic 19

  • c.589-2A>G Multiple submitters AGPAT2-related disorder
  • p.Arg68Ter Multiple submitters congenital generalized lipodystrophy type 1
  • p.Leu124fs Multiple submitters congenital generalized lipodystrophy type 1
  • p.Asn59fs Single submitter congenital generalized lipodystrophy
  • p.Asp180fs Single submitter congenital generalized lipodystrophy type 1
  • p.Gly136Arg Single submitter congenital generalized lipodystrophy type 1
  • p.Ile94fs Single submitter
  • p.Leu13Ter Single submitter congenital generalized lipodystrophy type 1
  • p.Ser100Asn Single submitter congenital generalized lipodystrophy type 1
  • c.316+1G>T No assertion criteria congenital generalized lipodystrophy type 1
  • c.366_588+534del No assertion criteria congenital generalized lipodystrophy type 1
  • p.Glu172fs No assertion criteria congenital generalized lipodystrophy type 1
  • p.Leu107AlafsTer279 No assertion criteria congenital generalized lipodystrophy type 1
  • p.Leu228Pro No assertion criteria congenital generalized lipodystrophy type 1
  • p.Lys215Ter No assertion criteria congenital generalized lipodystrophy type 1
  • p.Met105Val No assertion criteria congenital generalized lipodystrophy ⚠
  • p.Ser208fs No assertion criteria congenital generalized lipodystrophy type 1
  • p.Trp168Ter No assertion criteria congenital generalized lipodystrophy type 1
  • p.Tyr190Ter No assertion criteria congenital generalized lipodystrophy type 1

Pathogenic/Likely pathogenic 7

  • c.492+1G>A Multiple submitters congenital generalized lipodystrophy type 1
  • c.493-1G>C Multiple submitters congenital generalized lipodystrophy type 1
  • c.662-2A>C Multiple submitters congenital generalized lipodystrophy type 1
  • p.Glu172Lys Multiple submitters congenital generalized lipodystrophy type 1
  • p.Lys216Ter Multiple submitters congenital generalized lipodystrophy type 1
  • p.Pro112fs Multiple submitters congenital generalized lipodystrophy type 1
  • p.Pro128fs Multiple submitters congenital generalized lipodystrophy type 1

Likely pathogenic 11

  • c.493-2A>G Multiple submitters congenital generalized lipodystrophy type 1
  • p.Gln264Ter Multiple submitters congenital generalized lipodystrophy type 1
  • p.Thr219fs Multiple submitters AGPAT2-related disorder
  • p.Arg81fs Single submitter congenital generalized lipodystrophy type 1
  • p.Gln87fs Single submitter congenital generalized lipodystrophy type 1
  • p.Glu229Ter Single submitter congenital generalized lipodystrophy type 1
  • p.Gly53fs Single submitter congenital generalized lipodystrophy type 1
  • p.Leu11fs Single submitter AGPAT2-related disorder
  • p.Leu12fs Single submitter congenital generalized lipodystrophy type 1
  • p.Leu257fs Single submitter congenital generalized lipodystrophy type 1
  • p.Pro112Leu Single submitter congenital generalized lipodystrophy type 1

Conflicting classifications of pathogenicity 23

  • c.316+15G>A Single submitter congenital generalized lipodystrophy type 1
  • c.492+4_492+7del Single submitter congenital generalized lipodystrophy type 1
  • p.Ala268Val Single submitter Inborn genetic diseases ⚠
  • p.Arg114Cys Single submitter monogenic diabetes ⚠
  • p.Arg250Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg77His Single submitter monogenic diabetes ⚠
  • p.Arg90His Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Asp240= Single submitter congenital generalized lipodystrophy type 1
  • p.Glu79Lys Single submitter Inborn genetic diseases ⚠
  • p.Gly64Ser Single submitter Inborn genetic diseases ⚠
  • p.Ile94= Single submitter congenital generalized lipodystrophy type 1
  • p.Leu244= Single submitter congenital generalized lipodystrophy type 1
  • p.Leu244Pro Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Lys120Arg Single submitter monogenic diabetes ⚠
  • p.Lys214Glu Single submitter monogenic diabetes ⚠
  • p.Lys216Met Single submitter Inborn genetic diseases
  • p.Lys261= Single submitter congenital generalized lipodystrophy type 1
  • p.Met105Ile Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Phe78= Single submitter congenital generalized lipodystrophy type 1
  • p.Thr254= Single submitter congenital generalized lipodystrophy type 1
  • p.Val161= Single submitter congenital generalized lipodystrophy type 1
  • p.Val18= Single submitter congenital generalized lipodystrophy type 1
  • p.Val67Met Single submitter monogenic diabetes

Benign 16

  • c.182+99C>G Multiple submitters
  • c.183-60G>C Multiple submitters congenital generalized lipodystrophy type 1
  • c.317-7C>T Multiple submitters congenital generalized lipodystrophy type 1
  • c.661+121T>C Multiple submitters congenital generalized lipodystrophy type 1
  • c.-67G>C Multiple submitters congenital generalized lipodystrophy type 1
  • c.*157C>T Multiple submitters congenital generalized lipodystrophy type 1
  • c.*239G>A Multiple submitters congenital generalized lipodystrophy type 1
  • c.*442C>G Multiple submitters congenital generalized lipodystrophy type 1
  • c.*517C>T Multiple submitters congenital generalized lipodystrophy type 1
  • c.*535C>T Multiple submitters congenital generalized lipodystrophy type 1
  • p.Ala270Val Multiple submitters monogenic diabetes
  • p.Leu17dup Multiple submitters
  • p.Ser234= Multiple submitters congenital generalized lipodystrophy type 1
  • c.588+21C>G Single submitter
  • c.662-308G>A Single submitter
  • c.*212_*217dup Single submitter

Benign/Likely benign 11

  • c.182+6G>A Multiple submitters congenital generalized lipodystrophy type 1
  • c.182+8C>T Multiple submitters congenital generalized lipodystrophy type 1
  • c.493-17C>A Multiple submitters congenital generalized lipodystrophy type 1
  • c.662-5C>G Multiple submitters congenital generalized lipodystrophy type 1
  • c.*79C>G Multiple submitters congenital generalized lipodystrophy type 1
  • p.Ala239Val Multiple submitters congenital generalized lipodystrophy type 1
  • p.Arg159Cys Multiple submitters monogenic diabetes
  • p.Cys115= Multiple submitters congenital generalized lipodystrophy type 1
  • p.Ile63= Multiple submitters congenital generalized lipodystrophy type 1
  • p.Pro91= Multiple submitters congenital generalized lipodystrophy type 1
  • p.Thr247= Multiple submitters congenital generalized lipodystrophy type 1

Likely benign 58

Uncertain significance 139

  • c.-18C>A Multiple submitters congenital generalized lipodystrophy type 1
  • c.*354C>T Multiple submitters congenital generalized lipodystrophy type 1
  • p.Ala154Asp Multiple submitters monogenic diabetes ⚠
  • p.Ala35Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Arg114His Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Arg121Gly Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Arg121Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg159Leu Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Arg250Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg51Cys Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Arg77Cys Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Arg90Pro Multiple submitters Inborn genetic diseases ⚠
  • p.Gly75Arg Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Leu11Arg Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Lys216del Multiple submitters congenital generalized lipodystrophy type 1
  • p.Lys216Leu Multiple submitters congenital generalized lipodystrophy type 1
  • p.Met108Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Met133Val Multiple submitters Inborn genetic diseases ⚠
  • p.Phe139Val Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Phe140del Multiple submitters congenital generalized lipodystrophy type 1
  • p.Phe70Val Multiple submitters congenital generalized lipodystrophy type 1
  • p.Pro263Leu Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Pro276Leu Multiple submitters ⚠
  • p.Ser208Phe Multiple submitters Inborn genetic diseases
  • p.Thr247Ile Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Thr254Asn Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Val152Ala Multiple submitters monogenic diabetes ⚠
  • p.Val202Met Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Val241Leu Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • p.Val274Met Multiple submitters congenital generalized lipodystrophy type 1 ⚠
  • c.493-3C>T Single submitter congenital generalized lipodystrophy type 1
  • c.493-7C>T Single submitter congenital generalized lipodystrophy type 1
  • c.661+5C>T Single submitter
  • c.-19T>C Single submitter congenital generalized lipodystrophy type 1
  • c.-4G>C Single submitter congenital generalized lipodystrophy type 1
  • c.-51GGAGCG[2] Single submitter
  • c.-61G>C Single submitter congenital generalized lipodystrophy type 1
  • c.-62G>A Single submitter congenital generalized lipodystrophy type 1
  • c.-68C>G Single submitter congenital generalized lipodystrophy type 1
  • c.*164C>A Single submitter congenital generalized lipodystrophy type 1
  • c.*201G>C Single submitter congenital generalized lipodystrophy type 1
  • c.*211G>A Single submitter congenital generalized lipodystrophy type 1
  • c.*217G>A Single submitter congenital generalized lipodystrophy type 1
  • c.*232C>T Single submitter congenital generalized lipodystrophy type 1
  • c.*277C>T Single submitter congenital generalized lipodystrophy type 1
  • c.*34C>G Single submitter congenital generalized lipodystrophy type 1
  • c.*382C>T Single submitter congenital generalized lipodystrophy type 1
  • c.*411C>T Single submitter congenital generalized lipodystrophy type 1
  • c.*418G>A Single submitter congenital generalized lipodystrophy type 1
  • c.*45C>A Single submitter congenital generalized lipodystrophy type 1
  • c.*488C>T Single submitter congenital generalized lipodystrophy type 1
  • c.*512G>A Single submitter congenital generalized lipodystrophy type 1
  • c.*514A>C Single submitter congenital generalized lipodystrophy type 1
  • c.*572C>T Single submitter congenital generalized lipodystrophy type 1
  • p.205SSF[1] Single submitter congenital generalized lipodystrophy type 1
  • p.Ala10Gly Single submitter monogenic diabetes ⚠
  • p.Ala188Asp Single submitter ⚠
  • p.Ala238Val Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Ala23Val Single submitter ⚠
  • p.Ala251Thr Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Ala35Val Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Ala89Ser Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Ala8Thr Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Arg121Gln Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Arg143Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg143Trp Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Arg145Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg145His Single submitter Inborn genetic diseases ⚠
  • p.Arg145Ser Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Arg162Gly Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Arg162Lys Single submitter Inborn genetic diseases ⚠
  • p.Arg55Pro Single submitter Inborn genetic diseases ⚠
  • p.Arg81Trp Single submitter ⚠
  • p.Arg84Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg85Gly Single submitter Inborn genetic diseases ⚠
  • p.Arg85Lys Single submitter Lipodystrophy - childhood onset ⚠
  • p.Arg90Leu Single submitter Inborn genetic diseases ⚠
  • p.Asn142Thr Single submitter Inborn genetic diseases ⚠
  • p.Asn176Asp Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Asn178Asp Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Asn266Asp Single submitter Inborn genetic diseases ⚠
  • p.Asn59His Single submitter Inborn genetic diseases ⚠
  • p.Asp155Asn Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Cys115Tyr Single submitter Inborn genetic diseases ⚠
  • p.Cys6Arg Single submitter ⚠
  • p.Cys92Arg Single submitter monogenic diabetes ⚠
  • p.Glu122Ala Single submitter ⚠
  • p.Glu2Lys Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Glu2Val Single submitter Inborn genetic diseases ⚠
  • p.Gly127Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly136Glu Single submitter Inborn genetic diseases ⚠
  • p.Gly235Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly271= Single submitter congenital generalized lipodystrophy type 1
  • p.Ile132Leu Single submitter ⚠
  • p.Ile62Ser Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Ile63Thr Single submitter Inborn genetic diseases
  • p.Leu11Val Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Leu17= Single submitter congenital generalized lipodystrophy type 1
  • p.Leu17Arg Single submitter ⚠
  • p.Leu236Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu46Pro Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Leu76= Single submitter congenital generalized lipodystrophy type 1
  • p.Lys216= Single submitter monogenic diabetes
  • p.Lys29Arg Single submitter Inborn genetic diseases ⚠
  • p.Lys71Arg Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Met160Ile Single submitter Inborn genetic diseases ⚠
  • p.Met160Thr Single submitter Inborn genetic diseases ⚠
  • p.Met252Thr Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Met60Arg Single submitter Inborn genetic diseases ⚠
  • p.Phe210Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro263Arg Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Pro83Leu Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Ser206Phe Single submitter Inborn genetic diseases ⚠
  • p.Ser209_Phe210del Single submitter congenital generalized lipodystrophy type 1
  • p.Ser209del Single submitter congenital generalized lipodystrophy type 1
  • p.Ser260Cys Single submitter Inborn genetic diseases
  • p.Ser45Leu Single submitter Inborn genetic diseases ⚠
  • p.Ter279Gln Single submitter
  • p.Thr151= Single submitter congenital generalized lipodystrophy type 1
  • p.Thr151Arg Single submitter ⚠
  • p.Thr174Ile Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Thr233Ile Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Thr254Ile Single submitter ⚠
  • p.Thr262Ile Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Thr269Asn Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Thr39= Single submitter congenital generalized lipodystrophy type 1
  • p.Tyr170Cys Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Tyr33Cys Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Tyr74His Single submitter
  • p.Val116Met Single submitter Inborn genetic diseases
  • p.Val138Ile Single submitter Inborn genetic diseases ⚠
  • p.Val161Phe Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Val200Ile Single submitter congenital generalized lipodystrophy type 1 ⚠
  • p.Val203Leu Single submitter Inborn genetic diseases ⚠
  • p.Val40Ala Single submitter ⚠
  • p.Leu16_Leu17dup No assertion criteria
  • p.Lys186Thr No assertion criteria ⚠
  • p.Pro83fs No assertion criteria prostate cancer
  • p.Thr233Asn No assertion criteria congenital generalized lipodystrophy type 1 ⚠