PLD3 — 208 ClinVar variants
All ClinVar germline PLD3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 109 flagged for review →
4 Conflicting · 10 Benign · 8 Benign/Likely benign · 69 Likely benign · 117 Uncertain significance
Full PLD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 109
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 3
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
Predictors lean, ClinVar uncertain 77
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
PLD3 p.Arg375Trp
Uncertain significance
Multiple submitters
spinocerebellar ataxia 46
- PLD3 p.Arg413His Uncertain significance Multiple submitters
- PLD3 p.Arg424Ser Uncertain significance Multiple submitters
- PLD3 p.Arg457Gln Uncertain significance Multiple submitters
- PLD3 p.Arg488His Uncertain significance Multiple submitters
-
PLD3 p.Asn313Asp
Uncertain significance
Multiple submitters
spinocerebellar ataxia 46
- PLD3 p.Gln137Arg Uncertain significance Multiple submitters
- PLD3 p.Gly115Ser Uncertain significance Multiple submitters
- PLD3 p.Thr422Ala Uncertain significance Multiple submitters
- PLD3 p.Val199Ile Uncertain significance Multiple submitters
-
PLD3 p.Val399Met
Uncertain significance
Multiple submitters
spinocerebellar ataxia 46
- PLD3 p.Ala116Thr Uncertain significance Single submitter
- PLD3 p.Ala116Val Uncertain significance Single submitter
- PLD3 p.Ala164Thr Uncertain significance Single submitter
- PLD3 p.Ala179Thr Uncertain significance Single submitter
- PLD3 p.Ala18Thr Uncertain significance Single submitter
- PLD3 p.Ala28Gly Uncertain significance Single submitter
- PLD3 p.Ala28Val Uncertain significance Single submitter
- PLD3 p.Ala382Gly Uncertain significance Single submitter
- PLD3 p.Ala402Pro Uncertain significance Single submitter
- PLD3 p.Ala425Thr Uncertain significance Single submitter
- PLD3 p.Arg162Cys Uncertain significance Single submitter
- PLD3 p.Arg188His Uncertain significance Single submitter
- PLD3 p.Arg222His Uncertain significance Single submitter
- PLD3 p.Arg242Gln Uncertain significance Single submitter
- PLD3 p.Arg242Gly Uncertain significance Single submitter
- PLD3 p.Arg267Gln Uncertain significance Single submitter
- PLD3 p.Arg304His Uncertain significance Single submitter
- PLD3 p.Arg319Gln Uncertain significance Single submitter
- PLD3 p.Arg385His Uncertain significance Single submitter
- PLD3 p.Arg408Gly Uncertain significance Single submitter
- PLD3 p.Arg424His Uncertain significance Single submitter
- PLD3 p.Arg73His Uncertain significance Single submitter
- PLD3 p.Arg73Pro Uncertain significance Single submitter
- PLD3 p.Asn236Ser Uncertain significance Single submitter
- PLD3 p.Asn313Ser Uncertain significance Single submitter
- PLD3 p.Asn97Ser Uncertain significance Single submitter
- PLD3 p.Asp270Gly Uncertain significance Single submitter
- PLD3 p.Asp469Gly Uncertain significance Single submitter
- PLD3 p.Asp475Gly Uncertain significance Single submitter
- PLD3 p.Glu27Lys Uncertain significance Single submitter
- PLD3 p.Glu404Lys Uncertain significance Single submitter
- PLD3 p.Glu440Ala Uncertain significance Single submitter
- PLD3 p.Glu82Lys Uncertain significance Single submitter
- PLD3 p.Gly484Arg Uncertain significance Single submitter
-
PLD3 p.His201Leu
Uncertain significance
Single submitter
spinocerebellar ataxia 46
- PLD3 p.His339Tyr Uncertain significance Single submitter
- PLD3 p.His474Tyr Uncertain significance Single submitter
- PLD3 p.Ile26Thr Uncertain significance Single submitter
- PLD3 p.Ile428Val Uncertain significance Single submitter
- PLD3 p.Leu10Val Uncertain significance Single submitter
- PLD3 p.Leu181Arg Uncertain significance Single submitter
-
PLD3 p.Leu244Val
Uncertain significance
Single submitter
spinocerebellar ataxia 46
-
PLD3 p.Leu308Pro
Uncertain significance
Single submitter
spinocerebellar ataxia 46
- PLD3 p.Leu333Val Uncertain significance Single submitter
- PLD3 p.Leu476Phe Uncertain significance Single submitter
- PLD3 p.Leu67Phe Uncertain significance Single submitter
- PLD3 p.Lys228Glu Uncertain significance Single submitter
- PLD3 p.Lys34Asn Uncertain significance Single submitter
- PLD3 p.Met54Thr Uncertain significance Single submitter
- PLD3 p.Pro173Thr Uncertain significance Single submitter
- PLD3 p.Pro17Leu Uncertain significance Single submitter
- PLD3 p.Pro410Leu Uncertain significance Single submitter
- PLD3 p.Pro471Arg Uncertain significance Single submitter
- PLD3 p.Pro74Ser Uncertain significance Single submitter
- PLD3 p.Ser169Thr Uncertain significance Single submitter
- PLD3 p.Ser216Thr Uncertain significance Single submitter
- PLD3 p.Ser294Thr Uncertain significance Single submitter
- PLD3 p.Thr210Ala Uncertain significance Single submitter
- PLD3 p.Thr245Asn Uncertain significance Single submitter
- PLD3 p.Thr55Ile Uncertain significance Single submitter
- PLD3 p.Trp60Leu Uncertain significance Single submitter
- PLD3 p.Tyr78His Uncertain significance Single submitter
- PLD3 p.Val161Ile Uncertain significance Single submitter
- PLD3 p.Val314Met Uncertain significance Single submitter
- PLD3 p.Val399Leu Uncertain significance Single submitter
- PLD3 p.Val39Ile Uncertain significance Single submitter
Predictors split 29
The independent predictors disagree with each other — read with care.
- PLD3 p.Ala114Val Uncertain significance Multiple submitters
- PLD3 p.Cys300Tyr Benign/Likely benign Multiple submitters
- PLD3 p.Ser391Pro Uncertain significance Multiple submitters
- PLD3 p.Val147Ala Uncertain significance Multiple submitters
- PLD3 p.Arg149Trp Uncertain significance Single submitter
- PLD3 p.Arg356His Uncertain significance Single submitter
- PLD3 p.Arg361His Uncertain significance Single submitter
- PLD3 p.Arg424Cys Likely benign Single submitter
- PLD3 p.Arg488Cys Uncertain significance Single submitter
- PLD3 p.Asn131Lys Uncertain significance Single submitter
- PLD3 p.Asn284Ser Conflicting Single submitter
- PLD3 p.Asn313Ile Uncertain significance Single submitter
- PLD3 p.Asn417Asp Uncertain significance Single submitter
- PLD3 p.Gln406Pro Uncertain significance Single submitter
- PLD3 p.Glu355Lys Uncertain significance Single submitter
- PLD3 p.Gly484Cys Uncertain significance Single submitter
- PLD3 p.Met192Ile Uncertain significance Single submitter
- PLD3 p.Met6Arg Uncertain significance Single submitter
- PLD3 p.Phe253Leu Uncertain significance Single submitter
- PLD3 p.Ser260Cys Uncertain significance Single submitter
- PLD3 p.Ser294Asn Uncertain significance Single submitter
- PLD3 p.Ser370Leu Uncertain significance Single submitter
- PLD3 p.Thr105Pro Uncertain significance Single submitter
- PLD3 p.Thr134Asn Uncertain significance Single submitter
- PLD3 p.Thr245Ile Uncertain significance Single submitter
- PLD3 p.Thr426Ala Uncertain significance Single submitter
- PLD3 p.Thr430Asn Uncertain significance Single submitter
- PLD3 p.Thr430Ser Uncertain significance Single submitter
-
PLD3 p.Met219Val
Uncertain significance
No assertion criteria
PLD3-related disorder
All PLD3 variants
Conflicting classifications of pathogenicity 4
- p.Arg351Gln Single submitter ⚠
- p.Arg375Gln Single submitter ⚠
- p.Asn160Lys Single submitter ⚠
- p.Asn284Ser Single submitter ⚠
Benign 10
- c.430-5C>G Multiple submitters
- p.Gly452Glu Multiple submitters
- p.Ile364= Multiple submitters
- c.430-15C>G Single submitter
- c.430-5C>T Single submitter
- c.550+11del Single submitter
- c.551-19C>T Single submitter
- p.Asp346= Single submitter
- p.Lys157= Single submitter
- p.Pro17= Single submitter
Benign/Likely benign 8
- c.430-4G>A Multiple submitters
- p.Ala442= Multiple submitters
- p.Cys300Tyr Multiple submitters ⚠
- p.Gly357= Multiple submitters
- p.Gly63Ser Multiple submitters
- p.Pro76Ala Multiple submitters
- p.Tyr354= Multiple submitters
- p.Val232Met Multiple submitters Alzheimer disease 19
Likely benign 69
- c.102+7G>A Multiple submitters
- c.678+16G>A Multiple submitters
- c.880-8G>A Multiple submitters
- p.Asp477Gly Multiple submitters
- p.Leu490Val Multiple submitters
- p.Thr136= Multiple submitters
- c.1019+12T>C Single submitter
- c.1019+15G>A Single submitter
- c.102+11T>G Single submitter
- c.102+17_102+22del Single submitter
- c.1020-13C>T Single submitter
- c.1020-8G>T Single submitter
- c.103-11C>T Single submitter
- c.103-17CCT[2] Single submitter
- c.1185+12C>T Single submitter
- c.1186-13C>T Single submitter
- c.1186-14C>A Single submitter
- c.1286-11T>C Single submitter
- c.245+12G>T Single submitter
- c.245+7G>T Single submitter
- c.246-4C>G Single submitter
- c.246-5C>A Single submitter
- c.246-5C>G Single submitter
- c.246-5C>T Single submitter
- c.27+15G>T Single submitter
- c.430-4G>T Single submitter
- c.550+10G>A Single submitter
- c.550+16A>G Single submitter
- c.551-13C>T Single submitter
- c.551-14C>T Single submitter
- c.678+10C>T Single submitter
- c.678+9_678+19del Single submitter
- c.880-13C>A Single submitter
- c.880-9C>T Single submitter
- p.Ala116= Single submitter
- p.Ala217= Single submitter
- p.Ala295= Single submitter
- p.Ala310= Single submitter
- p.Arg304= Single submitter
- p.Arg424Cys Single submitter ⚠
- p.Asn19Ser Single submitter
- p.Asn485= Single submitter
- p.Glu404= Single submitter
- p.Gly255= Single submitter
- p.Gly368= Single submitter
- p.Gly63= Single submitter
- p.Leu177= Single submitter
- p.Leu308= Single submitter
- p.Leu312= Single submitter
- p.Leu40= Single submitter
- p.Leu43= Single submitter
- p.Phe50= Single submitter
- p.Phe95= Single submitter
- p.Pro410= Single submitter
- p.Ser370= Single submitter
- p.Thr202= Single submitter
- p.Thr441= Single submitter
- p.Thr55= Single submitter
- p.Tyr213= Single submitter
- p.Tyr323= Single submitter
- p.Tyr411= Single submitter
- p.Tyr472= Single submitter
- p.Tyr62= Single submitter
- p.Val207= Single submitter
- p.Val232= Single submitter
- p.Val324Ile Single submitter
- p.Val326= Single submitter
- p.Glu15= No assertion criteria PLD3-related disorder
- p.Ile163Met No assertion criteria PLD3-related disorder
Uncertain significance 117
- p.Ala114Val Multiple submitters ⚠
- p.Arg375Trp Multiple submitters spinocerebellar ataxia 46 ⚠
- p.Arg413His Multiple submitters ⚠
- p.Arg424Ser Multiple submitters ⚠
- p.Arg457Gln Multiple submitters ⚠
- p.Arg488His Multiple submitters ⚠
- p.Asn313Asp Multiple submitters spinocerebellar ataxia 46 ⚠
- p.Gln137Arg Multiple submitters ⚠
- p.Gly115Ser Multiple submitters ⚠
- p.Ser391Pro Multiple submitters ⚠
- p.Thr422Ala Multiple submitters ⚠
- p.Val147Ala Multiple submitters ⚠
- p.Val199Ile Multiple submitters ⚠
- p.Val399Met Multiple submitters spinocerebellar ataxia 46 ⚠
- c.27+3A>G Single submitter
- c.550+3G>A Single submitter
- p.Ala116Thr Single submitter ⚠
- p.Ala116Val Single submitter ⚠
- p.Ala164Thr Single submitter ⚠
- p.Ala179Thr Single submitter ⚠
- p.Ala18Thr Single submitter ⚠
- p.Ala28Gly Single submitter ⚠
- p.Ala28Val Single submitter ⚠
- p.Ala382Gly Single submitter ⚠
- p.Ala402Pro Single submitter ⚠
- p.Ala425Thr Single submitter ⚠
- p.Arg149Trp Single submitter ⚠
- p.Arg162Cys Single submitter ⚠
- p.Arg188His Single submitter ⚠
- p.Arg222His Single submitter ⚠
- p.Arg242Gln Single submitter ⚠
- p.Arg242Gly Single submitter ⚠
- p.Arg267Gln Single submitter ⚠
- p.Arg304His Single submitter ⚠
- p.Arg319Gln Single submitter ⚠
- p.Arg356His Single submitter ⚠
- p.Arg361Cys Single submitter
- p.Arg361His Single submitter ⚠
- p.Arg385His Single submitter ⚠
- p.Arg408Gly Single submitter ⚠
- p.Arg424His Single submitter ⚠
- p.Arg457Trp Single submitter
- p.Arg488Cys Single submitter ⚠
- p.Arg73His Single submitter ⚠
- p.Arg73Pro Single submitter ⚠
- p.Asn131Lys Single submitter ⚠
- p.Asn236Ser Single submitter ⚠
- p.Asn313Ile Single submitter ⚠
- p.Asn313Ser Single submitter ⚠
- p.Asn417Asp Single submitter ⚠
- p.Asn417del Single submitter
- p.Asn97Ser Single submitter ⚠
- p.Asp270Gly Single submitter ⚠
- p.Asp469Gly Single submitter ⚠
- p.Asp475Gly Single submitter ⚠
- p.Gln406Pro Single submitter ⚠
- p.Glu27Lys Single submitter ⚠
- p.Glu355Lys Single submitter ⚠
- p.Glu404Lys Single submitter ⚠
- p.Glu440Ala Single submitter ⚠
- p.Glu82Lys Single submitter ⚠
- p.Glu9fs Single submitter
- p.Gly484Arg Single submitter ⚠
- p.Gly484Cys Single submitter ⚠
- p.His201Leu Single submitter spinocerebellar ataxia 46 ⚠
- p.His339Tyr Single submitter ⚠
- p.His474Tyr Single submitter ⚠
- p.Ile26Thr Single submitter ⚠
- p.Ile428Val Single submitter ⚠
- p.Leu10Val Single submitter ⚠
- p.Leu181Arg Single submitter ⚠
- p.Leu244Val Single submitter spinocerebellar ataxia 46 ⚠
- p.Leu299fs Single submitter
- p.Leu308Pro Single submitter spinocerebellar ataxia 46 ⚠
- p.Leu333Val Single submitter ⚠
- p.Leu476Phe Single submitter ⚠
- p.Leu67Phe Single submitter ⚠
- p.Lys228Glu Single submitter ⚠
- p.Lys34= Single submitter
- p.Lys34Asn Single submitter ⚠
- p.Met192Ile Single submitter ⚠
- p.Met54Thr Single submitter ⚠
- p.Met6Arg Single submitter ⚠
- p.Phe253Leu Single submitter ⚠
- p.Pro173Thr Single submitter ⚠
- p.Pro17Leu Single submitter ⚠
- p.Pro278Ala Single submitter
- p.Pro410Leu Single submitter ⚠
- p.Pro471Arg Single submitter ⚠
- p.Pro74Ser Single submitter ⚠
- p.Ser169Thr Single submitter ⚠
- p.Ser183= Single submitter
- p.Ser216Thr Single submitter ⚠
- p.Ser260Cys Single submitter ⚠
- p.Ser294Asn Single submitter ⚠
- p.Ser294Thr Single submitter ⚠
- p.Ser370Leu Single submitter ⚠
- p.Thr105Pro Single submitter ⚠
- p.Thr134Asn Single submitter ⚠
- p.Thr210Ala Single submitter ⚠
- p.Thr245Asn Single submitter ⚠
- p.Thr245Ile Single submitter ⚠
- p.Thr305Ala Single submitter
- p.Thr426Ala Single submitter ⚠
- p.Thr430Asn Single submitter ⚠
- p.Thr430Ser Single submitter ⚠
- p.Thr55Ile Single submitter ⚠
- p.Trp205Ter Single submitter spinocerebellar ataxia 46
- p.Trp60Leu Single submitter ⚠
- p.Tyr251Phe Single submitter
- p.Tyr78His Single submitter ⚠
- p.Val159Met Single submitter
- p.Val161Ile Single submitter ⚠
- p.Val314Met Single submitter ⚠
- p.Val399Leu Single submitter ⚠
- p.Val39Ile Single submitter ⚠
- p.Met219Val No assertion criteria PLD3-related disorder ⚠