PNPLA2 — 620 ClinVar variants

All ClinVar germline PNPLA2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 238 flagged for review →

27 Pathogenic · 3 Pathogenic/Likely pathogenic · 10 Likely pathogenic · 36 Conflicting · 11 Benign · 16 Benign/Likely benign · 233 Likely benign · 284 Uncertain significance

Full PNPLA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 238

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 17

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

Predictors lean, ClinVar uncertain 190

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 190

Predictors split 31

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

All PNPLA2 variants

Pathogenic 27

Pathogenic/Likely pathogenic 3

  • c.187+1G>C Multiple submitters neutral lipid storage myopathy
  • p.Arg351fs Multiple submitters neutral lipid storage myopathy
  • p.Leu264fs Multiple submitters neutral lipid storage myopathy

Likely pathogenic 10

  • c.421-1G>A Single submitter neutral lipid storage myopathy
  • c.421-2A>T Single submitter neutral lipid storage myopathy
  • c.758-1G>C Single submitter neutral lipid storage myopathy
  • p.Arg303fs Single submitter neutral lipid storage myopathy
  • p.Asp473fs Single submitter PNPLA2-related disorder
  • p.Cys449fs Single submitter Abnormality of the musculature
  • p.Glu31Ter Single submitter neutral lipid storage myopathy
  • p.Glu75Ter Single submitter PNPLA2-related disorder
  • p.Gly253fs Single submitter PNPLA2-related disorder
  • p.Ser281fs Single submitter PNPLA2-related disorder

Conflicting classifications of pathogenicity 36

  • c.487-15T>G Single submitter neutral lipid storage myopathy
  • c.487-7G>A Single submitter neutral lipid storage myopathy
  • c.487-7G>C Single submitter neutral lipid storage myopathy
  • c.487-8C>T Single submitter neutral lipid storage myopathy
  • c.920-13C>T Single submitter neutral lipid storage myopathy
  • p.Ala413Thr Single submitter neutral lipid storage myopathy ⚠
  • p.Ala414Thr Single submitter neutral lipid storage myopathy ⚠
  • p.Ala470Thr Single submitter neutral lipid storage myopathy ⚠
  • p.Ala482= Single submitter neutral lipid storage myopathy
  • p.Arg364Trp Single submitter neutral lipid storage myopathy ⚠
  • p.Arg79Gln Single submitter neutral lipid storage myopathy ⚠
  • p.Asn133= Single submitter neutral lipid storage myopathy
  • p.Asn426Ser Single submitter neutral lipid storage myopathy ⚠
  • p.Asp123= Single submitter neutral lipid storage myopathy
  • p.Asp166Gly Single submitter neutral lipid storage myopathy ⚠
  • p.Asp197= Single submitter neutral lipid storage myopathy
  • p.Gly292Glu Single submitter Inborn genetic diseases ⚠
  • p.Gly483Arg Single submitter neutral lipid storage myopathy ⚠
  • p.His109Arg Single submitter neutral lipid storage myopathy ⚠
  • p.Leu249= Single submitter neutral lipid storage myopathy
  • p.Leu322Phe Single submitter neutral lipid storage myopathy ⚠
  • p.Leu443Val Single submitter Inborn genetic diseases ⚠
  • p.Phe12= Single submitter neutral lipid storage myopathy
  • p.Pro229= Single submitter neutral lipid storage myopathy
  • p.Pro269Leu Single submitter neutral lipid storage myopathy ⚠
  • p.Pro301= Single submitter neutral lipid storage myopathy
  • p.Pro315Ser Single submitter neutral lipid storage myopathy ⚠
  • p.Pro455Gln Single submitter neutral lipid storage myopathy ⚠
  • p.Pro469Leu Single submitter neutral lipid storage myopathy ⚠
  • p.Pro477Leu Single submitter neutral lipid storage myopathy ⚠
  • p.Pro497= Single submitter neutral lipid storage myopathy
  • p.Ser199= Single submitter neutral lipid storage myopathy
  • p.Ser407Phe Single submitter neutral lipid storage myopathy ⚠
  • p.Trp422Ter Single submitter neutral lipid storage myopathy
  • p.Tyr164= Single submitter neutral lipid storage myopathy
  • p.Tyr242= Single submitter neutral lipid storage myopathy

Benign 11

Benign/Likely benign 16

  • c.1052+17dup Multiple submitters neutral lipid storage myopathy
  • c.1053-21C>T Multiple submitters
  • c.696+15G>A Multiple submitters neutral lipid storage myopathy
  • c.696+16A>G Multiple submitters neutral lipid storage myopathy
  • c.757+16C>T Multiple submitters neutral lipid storage myopathy
  • c.919+4C>T Multiple submitters neutral lipid storage myopathy
  • p.Arg383= Multiple submitters neutral lipid storage myopathy
  • p.Asn252Lys Multiple submitters neutral lipid storage myopathy ⚠
  • p.Leu226= Multiple submitters neutral lipid storage myopathy
  • p.Leu389= Multiple submitters neutral lipid storage myopathy
  • p.Pro265Ser Multiple submitters neutral lipid storage myopathy
  • p.Pro291= Multiple submitters neutral lipid storage myopathy
  • p.Pro477Arg Multiple submitters neutral lipid storage myopathy
  • p.Pro486= Multiple submitters neutral lipid storage myopathy
  • p.Ser288Trp Multiple submitters neutral lipid storage myopathy
  • p.Ser489Ile Multiple submitters neutral lipid storage myopathy

Likely benign 233

  • c.1052+20G>A Multiple submitters neutral lipid storage myopathy
  • c.421-17C>T Multiple submitters neutral lipid storage myopathy
  • c.487-18_487-15del Multiple submitters neutral lipid storage myopathy
  • c.696+14C>T Multiple submitters neutral lipid storage myopathy
  • c.758-11C>T Multiple submitters neutral lipid storage myopathy
  • c.919+18G>A Multiple submitters neutral lipid storage myopathy
  • c.919+18G>C Multiple submitters neutral lipid storage myopathy
  • c.919+42G>A Multiple submitters
  • c.*288C>T Multiple submitters neutral lipid storage myopathy
  • p.Ala434= Multiple submitters neutral lipid storage myopathy
  • p.Arg120= Multiple submitters neutral lipid storage myopathy
  • p.Asp136= Multiple submitters neutral lipid storage myopathy
  • p.Cys374= Multiple submitters neutral lipid storage myopathy
  • p.Glu306= Multiple submitters neutral lipid storage myopathy
  • p.Gly271= Multiple submitters neutral lipid storage myopathy
  • p.Ile94= Multiple submitters neutral lipid storage myopathy
  • p.Leu234= Multiple submitters neutral lipid storage myopathy
  • p.Leu444= Multiple submitters neutral lipid storage myopathy
  • p.Leu445= Multiple submitters neutral lipid storage myopathy
  • p.Pro149= Multiple submitters neutral lipid storage myopathy
  • p.Pro394= Multiple submitters neutral lipid storage myopathy
  • p.Pro420= Multiple submitters neutral lipid storage myopathy
  • p.Pro486_Leu487= Multiple submitters neutral lipid storage myopathy
  • p.Pro493= Multiple submitters neutral lipid storage myopathy
  • p.Val397= Multiple submitters neutral lipid storage myopathy
  • c.1052+10C>T Single submitter neutral lipid storage myopathy
  • c.1052+13G>A Single submitter neutral lipid storage myopathy
  • c.1052+15G>C Single submitter neutral lipid storage myopathy
  • c.1052+17del Single submitter
  • c.1052+17G>A Single submitter neutral lipid storage myopathy
  • c.1052+19dup Single submitter neutral lipid storage myopathy
  • c.1053-10C>A Single submitter neutral lipid storage myopathy
  • c.1053-10C>T Single submitter neutral lipid storage myopathy
  • c.1053-12C>T Single submitter neutral lipid storage myopathy
  • c.1053-13G>C Single submitter neutral lipid storage myopathy
  • c.1053-14C>T Single submitter neutral lipid storage myopathy
  • c.1053-16C>G Single submitter neutral lipid storage myopathy
  • c.1053-16C>T Single submitter neutral lipid storage myopathy
  • c.1053-17G>A Single submitter neutral lipid storage myopathy
  • c.1053-18C>T Single submitter neutral lipid storage myopathy
  • c.1053-20G>A Single submitter neutral lipid storage myopathy
  • c.1053-29C>T Single submitter
  • c.1053-5C>G Single submitter neutral lipid storage myopathy
  • c.1175+10C>T Single submitter neutral lipid storage myopathy
  • c.1175+18C>A Single submitter neutral lipid storage myopathy
  • c.1175+18C>G Single submitter neutral lipid storage myopathy
  • c.1175+7C>T Single submitter neutral lipid storage myopathy
  • c.1175+8G>A Single submitter neutral lipid storage myopathy
  • c.1176-11C>T Single submitter neutral lipid storage myopathy
  • c.1176-18C>T Single submitter neutral lipid storage myopathy
  • c.1176-4G>T Single submitter neutral lipid storage myopathy
  • c.1176-6_1176-5del Single submitter neutral lipid storage myopathy
  • c.1176-9G>A Single submitter neutral lipid storage myopathy
  • c.187+18_187+30dup Single submitter neutral lipid storage myopathy
  • c.187+20G>A Single submitter neutral lipid storage myopathy
  • c.187+9G>A Single submitter neutral lipid storage myopathy
  • c.188-19C>G Single submitter neutral lipid storage myopathy
  • c.188-4C>T Single submitter neutral lipid storage myopathy
  • c.420+14G>A Single submitter neutral lipid storage myopathy
  • c.420+8C>G Single submitter neutral lipid storage myopathy
  • c.421-12C>T Single submitter neutral lipid storage myopathy
  • c.421-5T>C Single submitter neutral lipid storage myopathy
  • c.421-6C>T Single submitter neutral lipid storage myopathy
  • c.421-7C>G Single submitter neutral lipid storage myopathy
  • c.421-9G>T Single submitter neutral lipid storage myopathy
  • c.486+15C>T Single submitter neutral lipid storage myopathy
  • c.486+9T>G Single submitter neutral lipid storage myopathy
  • c.487-15T>C Single submitter neutral lipid storage myopathy
  • c.487-17TG[2] Single submitter neutral lipid storage myopathy
  • c.696+14C>G Single submitter neutral lipid storage myopathy
  • c.696+15_696+16delinsAG Single submitter neutral lipid storage myopathy
  • c.696+18G>A Single submitter neutral lipid storage myopathy
  • c.696+18G>C Single submitter neutral lipid storage myopathy
  • c.696+19A>G Single submitter neutral lipid storage myopathy
  • c.697-10_697-8del Single submitter neutral lipid storage myopathy
  • c.697-15C>A Single submitter neutral lipid storage myopathy
  • c.697-15C>T Single submitter neutral lipid storage myopathy
  • c.757+10C>T Single submitter
  • c.757+11C>A Single submitter neutral lipid storage myopathy
  • c.757+13G>A Single submitter neutral lipid storage myopathy
  • c.757+14G>A Single submitter neutral lipid storage myopathy
  • c.757+15del Single submitter neutral lipid storage myopathy
  • c.757+15dup Single submitter neutral lipid storage myopathy
  • c.757+15G>A Single submitter neutral lipid storage myopathy
  • c.757+19G>A Single submitter neutral lipid storage myopathy
  • c.757+20_757+33dup Single submitter neutral lipid storage myopathy
  • c.757+7G>A Single submitter neutral lipid storage myopathy
  • c.757+7G>C Single submitter
  • c.757+9A>C Single submitter neutral lipid storage myopathy
  • c.758-10C>G Single submitter neutral lipid storage myopathy
  • c.758-10C>T Single submitter neutral lipid storage myopathy
  • c.758-14C>G Single submitter neutral lipid storage myopathy
  • c.758-14C>T Single submitter neutral lipid storage myopathy
  • c.758-20C>T Single submitter neutral lipid storage myopathy
  • c.758-4C>T Single submitter
  • c.919+18_919+25del Single submitter neutral lipid storage myopathy
  • c.919+18G>T Single submitter neutral lipid storage myopathy
  • c.919+20del Single submitter neutral lipid storage myopathy
  • c.919+21_919+24del Single submitter neutral lipid storage myopathy
  • c.919+8C>T Single submitter neutral lipid storage myopathy
  • c.919+9C>A Single submitter neutral lipid storage myopathy
  • c.919+9C>G Single submitter neutral lipid storage myopathy
  • c.920-17C>T Single submitter neutral lipid storage myopathy
  • c.920-18C>A Single submitter neutral lipid storage myopathy
  • c.920-20G>A Single submitter neutral lipid storage myopathy
  • c.920-4G>T Single submitter neutral lipid storage myopathy
  • c.920-5C>T Single submitter neutral lipid storage myopathy
  • c.920-6C>T Single submitter neutral lipid storage myopathy
  • c.920-7C>T Single submitter neutral lipid storage myopathy
  • c.920-9C>T Single submitter neutral lipid storage myopathy
  • c.-19C>A Single submitter neutral lipid storage myopathy
  • c.*24C>T Single submitter
  • c.*479C>T Single submitter neutral lipid storage myopathy
  • p.Ala225= Single submitter neutral lipid storage myopathy
  • p.Ala263= Single submitter neutral lipid storage myopathy
  • p.Ala278= Single submitter
  • p.Ala282= Single submitter neutral lipid storage myopathy
  • p.Ala284= Single submitter neutral lipid storage myopathy
  • p.Ala302= Single submitter neutral lipid storage myopathy
  • p.Ala307= Single submitter neutral lipid storage myopathy
  • p.Ala311= Single submitter neutral lipid storage myopathy
  • p.Ala453= Single submitter neutral lipid storage myopathy
  • p.Ala458= Single submitter neutral lipid storage myopathy
  • p.Ala46= Single submitter neutral lipid storage myopathy
  • p.Ala465= Single submitter neutral lipid storage myopathy
  • p.Ala468= Single submitter neutral lipid storage myopathy
  • p.Ala485= Single submitter neutral lipid storage myopathy
  • p.Ala492= Single submitter neutral lipid storage myopathy
  • p.Ala495Thr Single submitter neutral lipid storage myopathy
  • p.Ala67= Single submitter neutral lipid storage myopathy
  • p.Arg251= Single submitter neutral lipid storage myopathy
  • p.Arg257= Single submitter neutral lipid storage myopathy
  • p.Arg387= Single submitter
  • p.Arg401= Single submitter neutral lipid storage myopathy
  • p.Arg416= Single submitter neutral lipid storage myopathy
  • p.Arg462= Single submitter
  • p.Asn142= Single submitter neutral lipid storage myopathy
  • p.Asn172= Single submitter neutral lipid storage myopathy
  • p.Asn215= Single submitter neutral lipid storage myopathy
  • p.Asn426= Single submitter neutral lipid storage myopathy
  • p.Asn89= Single submitter neutral lipid storage myopathy
  • p.Asp274Glu Single submitter Inborn genetic diseases
  • p.Asp276= Single submitter neutral lipid storage myopathy
  • p.Asp317= Single submitter neutral lipid storage myopathy
  • p.Asp358= Single submitter neutral lipid storage myopathy
  • p.Asp431= Single submitter neutral lipid storage myopathy
  • p.Asp473= Single submitter neutral lipid storage myopathy
  • p.Cys312= Single submitter neutral lipid storage myopathy
  • p.Gln403= Single submitter neutral lipid storage myopathy
  • p.Gln440= Single submitter neutral lipid storage myopathy
  • p.Gln478= Single submitter neutral lipid storage myopathy
  • p.Glu230= Single submitter neutral lipid storage myopathy
  • p.Glu398= Single submitter neutral lipid storage myopathy
  • p.Glu417= Single submitter neutral lipid storage myopathy
  • p.Gly161= Single submitter neutral lipid storage myopathy
  • p.Gly245= Single submitter neutral lipid storage myopathy
  • p.Gly446= Single submitter neutral lipid storage myopathy
  • p.His131= Single submitter neutral lipid storage myopathy
  • p.His203= Single submitter neutral lipid storage myopathy
  • p.His299= Single submitter neutral lipid storage myopathy
  • p.His32= Single submitter neutral lipid storage myopathy
  • p.His388= Single submitter neutral lipid storage myopathy
  • p.His479= Single submitter neutral lipid storage myopathy
  • p.Ile128= Single submitter neutral lipid storage myopathy
  • p.Leu138= Single submitter neutral lipid storage myopathy
  • p.Leu154= Single submitter neutral lipid storage myopathy
  • p.Leu246= Single submitter neutral lipid storage myopathy
  • p.Leu255= Single submitter neutral lipid storage myopathy
  • p.Leu261= Single submitter neutral lipid storage myopathy
  • p.Leu264= Single submitter neutral lipid storage myopathy
  • p.Leu290= Single submitter neutral lipid storage myopathy
  • p.Leu297= Single submitter neutral lipid storage myopathy
  • p.Leu300= Single submitter neutral lipid storage myopathy
  • p.Leu304= Single submitter neutral lipid storage myopathy
  • p.Leu309= Single submitter neutral lipid storage myopathy
  • p.Leu322= Single submitter
  • p.Leu346= Single submitter neutral lipid storage myopathy
  • p.Leu352= Single submitter neutral lipid storage myopathy
  • p.Leu356= Single submitter neutral lipid storage myopathy
  • p.Leu393= Single submitter neutral lipid storage myopathy
  • p.Leu419= Single submitter neutral lipid storage myopathy
  • p.Leu427= Single submitter
  • p.Leu429= Single submitter neutral lipid storage myopathy
  • p.Leu443= Single submitter
  • p.Leu447= Single submitter neutral lipid storage myopathy
  • p.Leu459= Single submitter neutral lipid storage myopathy
  • p.Leu481= Single submitter neutral lipid storage myopathy
  • p.Leu487= Single submitter
  • p.Leu488= Single submitter neutral lipid storage myopathy
  • p.Leu81= Single submitter neutral lipid storage myopathy
  • p.Leu84= Single submitter neutral lipid storage myopathy
  • p.Lys367= Single submitter neutral lipid storage myopathy
  • p.Lys68= Single submitter neutral lipid storage myopathy
  • p.Phe132= Single submitter neutral lipid storage myopathy
  • p.Phe147= Single submitter neutral lipid storage myopathy
  • p.Phe97= Single submitter neutral lipid storage myopathy
  • p.Pro157= Single submitter
  • p.Pro195= Single submitter neutral lipid storage myopathy
  • p.Pro228= Single submitter neutral lipid storage myopathy
  • p.Pro231= Single submitter neutral lipid storage myopathy
  • p.Pro265= Single submitter neutral lipid storage myopathy
  • p.Pro406= Single submitter neutral lipid storage myopathy
  • p.Pro409= Single submitter neutral lipid storage myopathy
  • p.Pro455= Single submitter neutral lipid storage myopathy
  • p.Pro456= Single submitter neutral lipid storage myopathy
  • p.Pro464= Single submitter neutral lipid storage myopathy
  • p.Pro467= Single submitter neutral lipid storage myopathy
  • p.Pro471= Single submitter neutral lipid storage myopathy
  • p.Pro86= Single submitter neutral lipid storage myopathy
  • p.Ser11= Single submitter neutral lipid storage myopathy
  • p.Ser145= Single submitter neutral lipid storage myopathy
  • p.Ser223= Single submitter
  • p.Ser281= Single submitter neutral lipid storage myopathy
  • p.Ser344= Single submitter neutral lipid storage myopathy
  • p.Ser347= Single submitter neutral lipid storage myopathy
  • p.Ser372= Single submitter neutral lipid storage myopathy
  • p.Ser404= Single submitter neutral lipid storage myopathy
  • p.Ser428= Single submitter
  • p.Ser476= Single submitter neutral lipid storage myopathy
  • p.Thr181= Single submitter neutral lipid storage myopathy
  • p.Thr321= Single submitter neutral lipid storage myopathy
  • p.Thr349= Single submitter neutral lipid storage myopathy
  • p.Thr450= Single submitter neutral lipid storage myopathy
  • p.Tyr151= Single submitter neutral lipid storage myopathy
  • p.Tyr176= Single submitter neutral lipid storage myopathy
  • p.Tyr376= Single submitter neutral lipid storage myopathy
  • p.Val121= Single submitter neutral lipid storage myopathy
  • p.Val127= Single submitter neutral lipid storage myopathy
  • p.Val184= Single submitter neutral lipid storage myopathy
  • p.Val20= Single submitter neutral lipid storage myopathy
  • p.Val313= Single submitter neutral lipid storage myopathy
  • p.Val328= Single submitter neutral lipid storage myopathy
  • p.Val57= Single submitter neutral lipid storage myopathy

Uncertain significance 284