PNPLA3 — 150 ClinVar variants
All ClinVar germline PNPLA3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 76 flagged for review →
1 Conflicting · 13 Benign · 2 Benign/Likely benign · 27 Likely benign · 107 Uncertain significance
Full PNPLA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 76
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 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
Predictors lean, ClinVar uncertain 64
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
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PNPLA3 p.Arg79Gln
Uncertain significance
Multiple submitters
NAFLD1
-
PNPLA3 p.Asp136His
Uncertain significance
Multiple submitters
NAFLD1
-
PNPLA3 p.Ile237Met
Uncertain significance
Multiple submitters
NAFLD1
-
PNPLA3 p.Pro186His
Uncertain significance
Multiple submitters
NAFLD1
-
PNPLA3 p.Ser364Cys
Uncertain significance
Multiple submitters
NAFLD1
-
PNPLA3 p.Thr216Pro
Uncertain significance
Multiple submitters
NAFLD1
-
PNPLA3 p.Val162Met
Uncertain significance
Multiple submitters
NAFLD1
- PNPLA3 p.Ala25Glu Uncertain significance Single submitter
- PNPLA3 p.Ala40Val Uncertain significance Single submitter
- PNPLA3 p.Ala466Ser Uncertain significance Single submitter
- PNPLA3 p.Ala46Ser Uncertain significance Single submitter
- PNPLA3 p.Ala4Thr Uncertain significance Single submitter
- PNPLA3 p.Ala50Thr Uncertain significance Single submitter
-
PNPLA3 p.Ala76Thr
Uncertain significance
Single submitter
NAFLD1
- PNPLA3 p.Arg133Trp Uncertain significance Single submitter
- PNPLA3 p.Arg213Cys Uncertain significance Single submitter
- PNPLA3 p.Arg27Gly Uncertain significance Single submitter
- PNPLA3 p.Arg295Ser Uncertain significance Single submitter
-
PNPLA3 p.Arg306His
Uncertain significance
Single submitter
NAFLD1
-
PNPLA3 p.Arg447Gln
Uncertain significance
Single submitter
NAFLD1
- PNPLA3 p.Arg447Trp Uncertain significance Single submitter
- PNPLA3 p.Arg6Gly Uncertain significance Single submitter
- PNPLA3 p.Arg74Gln Uncertain significance Single submitter
- PNPLA3 p.Arg74Trp Uncertain significance Single submitter
-
PNPLA3 p.Arg79Trp
Uncertain significance
Single submitter
NAFLD1
- PNPLA3 p.Asn280Ile Uncertain significance Single submitter
- PNPLA3 p.Asn460Ser Uncertain significance Single submitter
- PNPLA3 p.Asp166Val Uncertain significance Single submitter
-
PNPLA3 p.Asp206Ala
Uncertain significance
Single submitter
NAFLD1
- PNPLA3 p.Asp313Asn Uncertain significance Single submitter
- PNPLA3 p.Asp318Val Uncertain significance Single submitter
- PNPLA3 p.Asp382Asn Uncertain significance Single submitter
-
PNPLA3 p.Cys28Arg
Uncertain significance
Single submitter
NAFLD1
-
PNPLA3 p.Cys99Arg
Uncertain significance
Single submitter
NAFLD1
- PNPLA3 p.Glu250Gly Uncertain significance Single submitter
- PNPLA3 p.Glu272Asp Uncertain significance Single submitter
- PNPLA3 p.Glu297Lys Uncertain significance Single submitter
- PNPLA3 p.Gly49Trp Uncertain significance Single submitter
- PNPLA3 p.Gly82Asp Uncertain significance Single submitter
- PNPLA3 p.His304Asp Uncertain significance Single submitter
- PNPLA3 p.His35Leu Uncertain significance Single submitter
- PNPLA3 p.Ile60Met Uncertain significance Single submitter
- PNPLA3 p.Leu142Phe Uncertain significance Single submitter
- PNPLA3 p.Leu310Arg Uncertain significance Single submitter
-
PNPLA3 p.Leu317Gln
Uncertain significance
Single submitter
NAFLD1
- PNPLA3 p.Leu36Ile Uncertain significance Single submitter
- PNPLA3 p.Leu51Ser Uncertain significance Single submitter
- PNPLA3 p.Leu72Val Uncertain significance Single submitter
- PNPLA3 p.Lys135Arg Uncertain significance Single submitter
- PNPLA3 p.Lys434Asn Uncertain significance Single submitter
- PNPLA3 p.Met269Ile Uncertain significance Single submitter
- PNPLA3 p.Met42Arg Uncertain significance Single submitter
- PNPLA3 p.Met42Val Uncertain significance Single submitter
- PNPLA3 p.Phe44Cys Uncertain significance Single submitter
- PNPLA3 p.Pro186Ser Uncertain significance Single submitter
-
PNPLA3 p.Pro446Leu
Uncertain significance
Single submitter
NAFLD1
- PNPLA3 p.Ser30Asn Uncertain significance Single submitter
- PNPLA3 p.Ser470Phe Uncertain significance Single submitter
- PNPLA3 p.Thr200Ala Uncertain significance Single submitter
-
PNPLA3 p.Thr200Met
Uncertain significance
Single submitter
NAFLD1
- PNPLA3 p.Thr445Ile Uncertain significance Single submitter
- PNPLA3 p.Tyr21Cys Uncertain significance Single submitter
- PNPLA3 p.Val127Ile Uncertain significance Single submitter
- PNPLA3 p.Val354Ile Uncertain significance Single submitter
Predictors split 11
The independent predictors disagree with each other — read with care.
- PNPLA3 p.Arg247Thr Uncertain significance Single submitter
- PNPLA3 p.Arg95Gln Uncertain significance Single submitter
- PNPLA3 p.Asp39Tyr Uncertain significance Single submitter
- PNPLA3 p.Glu31Lys Uncertain significance Single submitter
- PNPLA3 p.Gly112Ser Uncertain significance Single submitter
- PNPLA3 p.Gly115Asp Uncertain significance Single submitter
- PNPLA3 p.Gly55Asp Uncertain significance Single submitter
- PNPLA3 p.Gly59Ala Uncertain significance Single submitter
- PNPLA3 p.Pro229Leu Uncertain significance Single submitter
- PNPLA3 p.Pro34Arg Uncertain significance Single submitter
- PNPLA3 p.Thr395Pro Uncertain significance Single submitter
All PNPLA3 variants
Conflicting classifications of pathogenicity 1
- p.Lys434Glu Single submitter NAFLD1 ⚠
Benign 13
- c.187+12G>A Multiple submitters NAFLD1
- c.*429T>C Multiple submitters NAFLD1
- c.*63C>T Multiple submitters NAFLD1
- c.*707T>C Multiple submitters NAFLD1
- c.*747T>A Multiple submitters NAFLD1
- c.*889A>G Multiple submitters NAFLD1
- p.Cys99Gly Multiple submitters NAFLD1
- p.Gly115Cys Multiple submitters NAFLD1
- p.Phe187= Multiple submitters NAFLD1
- p.Pro149= Multiple submitters NAFLD1
- p.Ser453Arg Multiple submitters NAFLD1
- c.*393G>C Single submitter NAFLD1
- p.Val227Ile Single submitter
Likely benign 27
- c.980-15A>C Multiple submitters NAFLD1
- c.-111G>A Multiple submitters NAFLD1
- c.-112A>T Multiple submitters NAFLD1
- c.-168C>A Multiple submitters NAFLD1
- c.-40C>G Multiple submitters NAFLD1
- c.*1090A>G Multiple submitters NAFLD1
- c.*626A>G Multiple submitters NAFLD1
- p.Glu331Gly Multiple submitters NAFLD1
- p.Ser453Ile Multiple submitters NAFLD1
- p.Tyr220Cys Multiple submitters NAFLD1
- c.1112+14G>A Single submitter NAFLD1
- c.*275C>T Single submitter NAFLD1
- p.Ala325Thr Single submitter
- p.Arg240Gln Single submitter
- p.Cys101Tyr Single submitter
- p.Glu267Asp Single submitter
- p.Glu288Lys Single submitter NAFLD1
- p.Gly124= Single submitter
- p.His32Arg Single submitter
- p.Ile83= Single submitter NAFLD1
- p.Leu43Phe Single submitter
- p.Leu72= Single submitter NAFLD1
- p.Met399Thr Single submitter
- p.Phe17= Single submitter
- p.Ser9= Single submitter
- p.Val143Ile Single submitter
- p.Val173Ile Single submitter
Uncertain significance 107
- c.697-4A>T Multiple submitters NAFLD1
- p.Arg79Gln Multiple submitters NAFLD1 ⚠
- p.Asp136His Multiple submitters NAFLD1 ⚠
- p.Ile237Met Multiple submitters NAFLD1 ⚠
- p.Pro186His Multiple submitters NAFLD1 ⚠
- p.Ser364Cys Multiple submitters NAFLD1 ⚠
- p.Thr216Pro Multiple submitters NAFLD1 ⚠
- p.Val162Met Multiple submitters NAFLD1 ⚠
- p.Val165Ala Multiple submitters NAFLD1
- c.1112+13G>T Single submitter NAFLD1
- c.696+12G>A Single submitter NAFLD1
- c.697-5C>A Single submitter NAFLD1
- c.980-14A>C Single submitter NAFLD1
- c.-108T>C Single submitter NAFLD1
- c.-131C>G Single submitter NAFLD1
- c.-180C>T Single submitter NAFLD1
- c.-44C>G Single submitter NAFLD1
- c.-69T>C Single submitter NAFLD1
- c.*1068C>T Single submitter NAFLD1
- c.*1076C>T Single submitter NAFLD1
- c.*1175A>C Single submitter NAFLD1
- c.*141T>G Single submitter NAFLD1
- c.*176G>A Single submitter NAFLD1
- c.*19T>G Single submitter NAFLD1
- c.*222G>A Single submitter NAFLD1
- c.*346G>A Single submitter NAFLD1
- c.*448C>T Single submitter NAFLD1
- c.*71T>G Single submitter NAFLD1
- c.*760T>C Single submitter NAFLD1
- c.*812A>G Single submitter NAFLD1
- c.*918G>A Single submitter NAFLD1
- c.*960T>G Single submitter NAFLD1
- c.*987_*989dup Single submitter
- c.*990T>A Single submitter NAFLD1
- p.Ala25Glu Single submitter ⚠
- p.Ala40Val Single submitter ⚠
- p.Ala466Ser Single submitter ⚠
- p.Ala46Ser Single submitter ⚠
- p.Ala4Thr Single submitter ⚠
- p.Ala50Thr Single submitter ⚠
- p.Ala76Thr Single submitter NAFLD1 ⚠
- p.Arg133Trp Single submitter ⚠
- p.Arg213Cys Single submitter ⚠
- p.Arg247Thr Single submitter ⚠
- p.Arg27Gly Single submitter ⚠
- p.Arg295Ser Single submitter ⚠
- p.Arg306His Single submitter NAFLD1 ⚠
- p.Arg447Gln Single submitter NAFLD1 ⚠
- p.Arg447Trp Single submitter ⚠
- p.Arg6Gly Single submitter ⚠
- p.Arg74Gln Single submitter ⚠
- p.Arg74Trp Single submitter ⚠
- p.Arg79Trp Single submitter NAFLD1 ⚠
- p.Arg95Gln Single submitter ⚠
- p.Asn280Ile Single submitter ⚠
- p.Asn460Ser Single submitter ⚠
- p.Asp166Val Single submitter ⚠
- p.Asp206Ala Single submitter NAFLD1 ⚠
- p.Asp313Asn Single submitter ⚠
- p.Asp318Val Single submitter ⚠
- p.Asp382Asn Single submitter ⚠
- p.Asp39Tyr Single submitter ⚠
- p.Cys28Arg Single submitter NAFLD1 ⚠
- p.Cys99Arg Single submitter NAFLD1 ⚠
- p.Glu250Gly Single submitter ⚠
- p.Glu272Asp Single submitter ⚠
- p.Glu297Lys Single submitter ⚠
- p.Glu31Lys Single submitter ⚠
- p.Gly112Ser Single submitter ⚠
- p.Gly115Asp Single submitter ⚠
- p.Gly49Trp Single submitter ⚠
- p.Gly55Asp Single submitter ⚠
- p.Gly59Ala Single submitter ⚠
- p.Gly82Asp Single submitter ⚠
- p.His22fs Single submitter
- p.His304Asp Single submitter ⚠
- p.His35Leu Single submitter ⚠
- p.Ile60Met Single submitter ⚠
- p.Leu142Phe Single submitter ⚠
- p.Leu310Arg Single submitter ⚠
- p.Leu317Gln Single submitter NAFLD1 ⚠
- p.Leu36Ile Single submitter ⚠
- p.Leu51Ser Single submitter ⚠
- p.Leu72Val Single submitter ⚠
- p.Lys135Arg Single submitter ⚠
- p.Lys434Asn Single submitter ⚠
- p.Met269Ile Single submitter ⚠
- p.Met42Arg Single submitter ⚠
- p.Met42Val Single submitter ⚠
- p.Phe44Cys Single submitter ⚠
- p.Pro186Ser Single submitter ⚠
- p.Pro229Leu Single submitter ⚠
- p.Pro34Arg Single submitter ⚠
- p.Pro403= Single submitter NAFLD1
- p.Pro446= Single submitter NAFLD1
- p.Pro446Leu Single submitter NAFLD1 ⚠
- p.Pro473= Single submitter NAFLD1
- p.Ser30Asn Single submitter ⚠
- p.Ser470Phe Single submitter ⚠
- p.Thr200Ala Single submitter ⚠
- p.Thr200Met Single submitter NAFLD1 ⚠
- p.Thr395Pro Single submitter ⚠
- p.Thr445Ile Single submitter ⚠
- p.Tyr21Cys Single submitter ⚠
- p.Val127Ile Single submitter ⚠
- p.Val138= Single submitter NAFLD1
- p.Val354Ile Single submitter ⚠