ATG4D — 96 ClinVar variants
All ClinVar germline ATG4D variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 86 flagged for review →
7 Pathogenic · 2 Conflicting · 1 Benign · 1 Benign/Likely benign · 6 Likely benign · 79 Uncertain significance
Full ATG4D gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 86
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 3
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
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ATG4D p.Ala295Asp
Pathogenic
No assertion criteria
spermatogenic failure 101
-
ATG4D p.Val273Ile
Pathogenic
No assertion criteria
spermatogenic failure 101
-
ATG4D p.Val395Met
Pathogenic
No assertion criteria
spermatogenic failure 101
Predictors agree, ClinVar conflicts 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
ATG4D p.Tyr280Cys
Conflicting
Single submitter
ATG4D-related neurodevelopmental condition
Predictors lean, ClinVar uncertain 41
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- ATG4D p.Ala421Thr Uncertain significance Single submitter
- ATG4D p.Ala448Pro Uncertain significance Single submitter
- ATG4D p.Ala448Thr Uncertain significance Single submitter
- ATG4D p.Arg12Trp Uncertain significance Single submitter
- ATG4D p.Arg193His Uncertain significance Single submitter
- ATG4D p.Arg231Gln Uncertain significance Single submitter
- ATG4D p.Arg29Gly Uncertain significance Single submitter
- ATG4D p.Arg424Gln Uncertain significance Single submitter
- ATG4D p.Arg459Gln Uncertain significance Single submitter
- ATG4D p.Arg465Leu Uncertain significance Single submitter
- ATG4D p.Asp165Glu Uncertain significance Single submitter
- ATG4D p.Gln208Arg Uncertain significance Single submitter
- ATG4D p.Glu170Lys Uncertain significance Single submitter
- ATG4D p.Glu178Gln Uncertain significance Single submitter
- ATG4D p.Glu311Gly Uncertain significance Single submitter
- ATG4D p.Glu311Lys Uncertain significance Single submitter
- ATG4D p.Glu328Lys Uncertain significance Single submitter
- ATG4D p.Gly173Ser Uncertain significance Single submitter
- ATG4D p.Gly236Glu Uncertain significance Single submitter
- ATG4D p.Gly346Ser Uncertain significance Single submitter
- ATG4D p.Gly38Ala Uncertain significance Single submitter
- ATG4D p.His377Arg Uncertain significance Single submitter
- ATG4D p.Ile333Val Uncertain significance Single submitter
- ATG4D p.Leu122Phe Uncertain significance Single submitter
- ATG4D p.Leu157His Uncertain significance Single submitter
- ATG4D p.Leu408His Uncertain significance Single submitter
- ATG4D p.Phe344Leu Uncertain significance Single submitter
- ATG4D p.Pro129Leu Uncertain significance Single submitter
- ATG4D p.Pro176Leu Uncertain significance Single submitter
- ATG4D p.Pro176Ser Uncertain significance Single submitter
- ATG4D p.Pro191Ser Uncertain significance Single submitter
- ATG4D p.Pro338Arg Uncertain significance Single submitter
- ATG4D p.Pro391Arg Uncertain significance Single submitter
- ATG4D p.Pro59Leu Uncertain significance Single submitter
- ATG4D p.Ser367Cys Uncertain significance Single submitter
- ATG4D p.Ser392Arg Uncertain significance Single submitter
- ATG4D p.Ser417Thr Uncertain significance Single submitter
- ATG4D p.Tyr101Cys Uncertain significance Single submitter
- ATG4D p.Val233Leu Uncertain significance Single submitter
- ATG4D p.Val266Ile Uncertain significance Single submitter
- ATG4D p.Val321Met Uncertain significance Single submitter
Predictors split 41
The independent predictors disagree with each other — read with care.
- ATG4D p.Arg102Pro Uncertain significance Single submitter
- ATG4D p.Arg111Cys Uncertain significance Single submitter
- ATG4D p.Arg111Ser Uncertain significance Single submitter
- ATG4D p.Arg193Cys Uncertain significance Single submitter
- ATG4D p.Arg198His Uncertain significance Single submitter
- ATG4D p.Arg210His Uncertain significance Single submitter
- ATG4D p.Arg213Trp Uncertain significance Single submitter
- ATG4D p.Arg22Trp Uncertain significance Single submitter
- ATG4D p.Arg231Trp Uncertain significance Single submitter
- ATG4D p.Arg268Cys Uncertain significance Single submitter
- ATG4D p.Arg286Cys Uncertain significance Single submitter
- ATG4D p.Arg339Gln Uncertain significance Single submitter
- ATG4D p.Arg424Trp Uncertain significance Single submitter
- ATG4D p.Arg465Cys Uncertain significance Single submitter
- ATG4D p.Asn74Lys Uncertain significance Single submitter
- ATG4D p.Asp108Glu Uncertain significance Single submitter
- ATG4D p.Asp265Asn Uncertain significance Single submitter
- ATG4D p.Asp365Tyr Uncertain significance Single submitter
- ATG4D p.Asp370Asn Likely benign Single submitter
- ATG4D p.Asp437Gly Uncertain significance Single submitter
- ATG4D p.Cys320Gly Uncertain significance Single submitter
- ATG4D p.Gln110His Uncertain significance Single submitter
- ATG4D p.Gln201His Uncertain significance Single submitter
- ATG4D p.Glu58Val Uncertain significance Single submitter
- ATG4D p.Gly149Ser Uncertain significance Single submitter
- ATG4D p.Ile94Met Uncertain significance Single submitter
- ATG4D p.Leu136Met Uncertain significance Single submitter
- ATG4D p.Leu460Phe Uncertain significance Single submitter
- ATG4D p.Pro226Ala Uncertain significance Single submitter
- ATG4D p.Pro291Leu Uncertain significance Single submitter
- ATG4D p.Pro362Leu Uncertain significance Single submitter
- ATG4D p.Pro47Leu Likely benign Single submitter
- ATG4D p.Pro52Arg Uncertain significance Single submitter
- ATG4D p.Pro56Leu Uncertain significance Single submitter
- ATG4D p.Ser250Leu Uncertain significance Single submitter
-
ATG4D p.Ser89Asn
Conflicting
Single submitter
ATG4D-related neurodevelopmental condition
- ATG4D p.Thr267Ile Uncertain significance Single submitter
- ATG4D p.Thr379Ile Uncertain significance Single submitter
- ATG4D p.Thr451Ile Uncertain significance Single submitter
- ATG4D p.Val306Met Uncertain significance Single submitter
- ATG4D p.Val316Met Uncertain significance Single submitter
All ATG4D variants
Pathogenic 7
- p.Asp437fs Single submitter
- p.Ala295Asp No assertion criteria spermatogenic failure 101 ⚠
- p.Arg125Leu No assertion criteria spermatogenic failure 101
- p.Asp356Asn No assertion criteria ASHER
- p.Val273Ile No assertion criteria spermatogenic failure 101 ⚠
- p.Val395Met No assertion criteria spermatogenic failure 101 ⚠
- p.Val4_Ala8del No assertion criteria spermatogenic failure 101
Conflicting classifications of pathogenicity 2
- p.Ser89Asn Single submitter ATG4D-related neurodevelopmental condition ⚠
- p.Tyr280Cys Single submitter ATG4D-related neurodevelopmental condition ⚠
Benign 1
- p.Pro305= Multiple submitters
Benign/Likely benign 1
- p.Ala259= Multiple submitters
Likely benign 6
- p.Ala154= Single submitter
- p.Asp370Asn Single submitter ⚠
- p.Leu179Pro Single submitter
- p.Met172Thr Single submitter
- p.Pro47Leu Single submitter ⚠
- p.Tyr347= Single submitter
Uncertain significance 79
- p.Ala421Thr Single submitter ⚠
- p.Ala448Pro Single submitter ⚠
- p.Ala448Thr Single submitter ⚠
- p.Arg102Pro Single submitter ⚠
- p.Arg111Cys Single submitter ⚠
- p.Arg111Ser Single submitter ⚠
- p.Arg12Trp Single submitter ⚠
- p.Arg193Cys Single submitter ⚠
- p.Arg193His Single submitter ⚠
- p.Arg198His Single submitter ⚠
- p.Arg210His Single submitter ⚠
- p.Arg213Trp Single submitter ⚠
- p.Arg22Trp Single submitter ⚠
- p.Arg231Gln Single submitter ⚠
- p.Arg231Trp Single submitter ⚠
- p.Arg268Cys Single submitter ⚠
- p.Arg286Cys Single submitter ⚠
- p.Arg29Gly Single submitter ⚠
- p.Arg339Gln Single submitter ⚠
- p.Arg424Gln Single submitter ⚠
- p.Arg424Trp Single submitter ⚠
- p.Arg459Gln Single submitter ⚠
- p.Arg465Cys Single submitter ⚠
- p.Arg465Leu Single submitter ⚠
- p.Asn74Lys Single submitter ⚠
- p.Asp108Glu Single submitter ⚠
- p.Asp165Glu Single submitter ⚠
- p.Asp265Asn Single submitter ⚠
- p.Asp365Tyr Single submitter ⚠
- p.Asp437Gly Single submitter ⚠
- p.Cys320Gly Single submitter ⚠
- p.Gln110His Single submitter ⚠
- p.Gln201His Single submitter ⚠
- p.Gln208Arg Single submitter ⚠
- p.Glu170Lys Single submitter ⚠
- p.Glu178Gln Single submitter ⚠
- p.Glu311Gly Single submitter ⚠
- p.Glu311Lys Single submitter ⚠
- p.Glu328Lys Single submitter ⚠
- p.Glu58Val Single submitter ⚠
- p.Gly149Ser Single submitter ⚠
- p.Gly173Ser Single submitter ⚠
- p.Gly236Glu Single submitter ⚠
- p.Gly346Ser Single submitter ⚠
- p.Gly38Ala Single submitter ⚠
- p.His377Arg Single submitter ⚠
- p.Ile333Val Single submitter ⚠
- p.Ile94Met Single submitter ⚠
- p.Leu122Phe Single submitter ⚠
- p.Leu136Met Single submitter ⚠
- p.Leu157His Single submitter ⚠
- p.Leu408His Single submitter ⚠
- p.Leu460Phe Single submitter ⚠
- p.Phe344Leu Single submitter ⚠
- p.Pro129Leu Single submitter ⚠
- p.Pro176Leu Single submitter ⚠
- p.Pro176Ser Single submitter ⚠
- p.Pro191Ser Single submitter ⚠
- p.Pro226Ala Single submitter ⚠
- p.Pro291Leu Single submitter ⚠
- p.Pro338Arg Single submitter ⚠
- p.Pro362Leu Single submitter ⚠
- p.Pro391Arg Single submitter ⚠
- p.Pro52Arg Single submitter ⚠
- p.Pro56Leu Single submitter ⚠
- p.Pro59Leu Single submitter ⚠
- p.Ser250Leu Single submitter ⚠
- p.Ser367Cys Single submitter ⚠
- p.Ser392Arg Single submitter ⚠
- p.Ser417Thr Single submitter ⚠
- p.Thr267Ile Single submitter ⚠
- p.Thr379Ile Single submitter ⚠
- p.Thr451Ile Single submitter ⚠
- p.Tyr101Cys Single submitter ⚠
- p.Val233Leu Single submitter ⚠
- p.Val266Ile Single submitter ⚠
- p.Val306Met Single submitter ⚠
- p.Val316Met Single submitter ⚠
- p.Val321Met Single submitter ⚠