ATP5F1D — 164 ClinVar variants
All ClinVar germline ATP5F1D variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 77 flagged for review →
2 Pathogenic · 3 Conflicting · 8 Benign · 58 Likely benign · 93 Uncertain significance
Full ATP5F1D gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 77
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.
-
ATP5F1D p.Asn160Ser
Conflicting
Single submitter
Inborn genetic diseases
Predictors lean, ClinVar uncertain 49
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
ATP5F1D p.Ala116Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Ala151Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Ala166Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Ala28Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Ala66Gly
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Arg150Gln
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Arg56Gln
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Asn51Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Asn54Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Gly92Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.His88Tyr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Lys136Glu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Met38Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Thr149Met
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Val16Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Val79Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
- ATP5F1D p.Ala108Thr Uncertain significance Single submitter
- ATP5F1D p.Ala137Asp Uncertain significance Single submitter
-
ATP5F1D p.Ala145Asp
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Ala25Val Uncertain significance Single submitter
- ATP5F1D p.Ala32Val Uncertain significance Single submitter
-
ATP5F1D p.Ala53Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
ATP5F1D p.Ala5Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
ATP5F1D p.Arg156Gln
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Arg156Leu Uncertain significance Single submitter
-
ATP5F1D p.Asn51Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
ATP5F1D p.Asn54Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
ATP5F1D p.Glu117Lys
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Glu135Lys Uncertain significance Single submitter
-
ATP5F1D p.Glu147Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Gly102Ser Uncertain significance Single submitter
- ATP5F1D p.Gly143Glu Uncertain significance Single submitter
- ATP5F1D p.Gly34Ser Uncertain significance Single submitter
-
ATP5F1D p.Gly65Glu
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.His73Pro Uncertain significance Single submitter
-
ATP5F1D p.Ile155Asn
Uncertain significance
Single submitter
Inborn genetic diseases
-
ATP5F1D p.Ile155Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Leu6Val Uncertain significance Single submitter
-
ATP5F1D p.Leu84Val
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Met124Thr Uncertain significance Single submitter
- ATP5F1D p.Phe42Cys Uncertain significance Single submitter
-
ATP5F1D p.Phe98Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
ATP5F1D p.Pro35Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Pro61Leu Uncertain significance Single submitter
- ATP5F1D p.Ser110Tyr Uncertain significance Single submitter
- ATP5F1D p.Ser33Pro Uncertain significance Single submitter
- ATP5F1D p.Thr62Met Uncertain significance Single submitter
- ATP5F1D p.Val112Met Uncertain significance Single submitter
- ATP5F1D p.Val60Met Uncertain significance Single submitter
Predictors split 27
The independent predictors disagree with each other — read with care.
-
ATP5F1D p.Ala27Asp
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Arg150Trp
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Ser33Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Thr121Met
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
ATP5F1D p.Val60Ala
Uncertain significance
Multiple submitters
Inborn genetic diseases
- ATP5F1D p.Ala71Val Uncertain significance Single submitter
- ATP5F1D p.Arg14Cys Uncertain significance Single submitter
-
ATP5F1D p.Arg20Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Arg20Pro Uncertain significance Single submitter
-
ATP5F1D p.Arg8Cys
Uncertain significance
Single submitter
Inborn genetic diseases
-
ATP5F1D p.Arg9Cys
Conflicting
Single submitter
mitochondrial complex V (ATP synthase) deficiency, nuclear type 5
- ATP5F1D p.Arg9Pro Uncertain significance Single submitter
- ATP5F1D p.Asn160Thr Uncertain significance Single submitter
- ATP5F1D p.Asp123Gly Uncertain significance Single submitter
- ATP5F1D p.Asp146Asn Uncertain significance Single submitter
- ATP5F1D p.Asp91Gly Uncertain significance Single submitter
- ATP5F1D p.Gly52Cys Uncertain significance Single submitter
- ATP5F1D p.Lys131Asn Uncertain significance Single submitter
- ATP5F1D p.Met38Ile Uncertain significance Single submitter
- ATP5F1D p.Phe50Leu Conflicting Single submitter
- ATP5F1D p.Pro29Leu Uncertain significance Single submitter
-
ATP5F1D p.Ser39Phe
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Thr93Ile Uncertain significance Single submitter
-
ATP5F1D p.Val106Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Val112Leu Uncertain significance Single submitter
-
ATP5F1D p.Val48Met
Uncertain significance
Single submitter
Inborn genetic diseases
- ATP5F1D p.Val79Ala Uncertain significance Single submitter
All ATP5F1D variants
Pathogenic 2
- p.Pro82Leu No assertion criteria mitochondrial complex V (ATP synthase) deficiency, nuclear type 5
- p.Val106Gly No assertion criteria mitochondrial complex V (ATP synthase) deficiency, nuclear type 5
Conflicting classifications of pathogenicity 3
- p.Arg9Cys Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 5 ⚠
- p.Asn160Ser Single submitter Inborn genetic diseases ⚠
- p.Phe50Leu Single submitter ⚠
Benign 8
- c.141+58C>T Multiple submitters
- c.384+16G>C Multiple submitters
- p.Ile104= Multiple submitters
- c.296-15G>A Single submitter
- c.385-19G>A Single submitter
- p.Met124Val Single submitter
- p.Thr144= Single submitter
- p.Val87= Single submitter
Likely benign 58
- p.Asp126= Multiple submitters
- p.Met38Val Multiple submitters
- p.Pro61= Multiple submitters
- c.141+9G>C Single submitter
- c.142-16A>G Single submitter
- c.142-20C>A Single submitter
- c.295+20G>A Single submitter
- c.296-16C>T Single submitter
- c.296-17C>G Single submitter
- c.296-5C>T Single submitter
- c.296-6C>T Single submitter
- c.296-7C>A Single submitter
- c.384+16G>A Single submitter
- c.384+19C>T Single submitter
- c.385-15C>T Single submitter
- c.385-19G>C Single submitter
- c.385-20C>T Single submitter
- c.385-8C>T Single submitter
- p.Ala105Thr Single submitter Inborn genetic diseases
- p.Ala108= Single submitter
- p.Ala116= Single submitter
- p.Ala119= Single submitter
- p.Ala139= Single submitter
- p.Ala21= Single submitter
- p.Ala23= Single submitter
- p.Arg156= Single submitter
- p.Arg17= Single submitter
- p.Asn160= Single submitter
- p.Asn54= Single submitter
- p.Asp146= Single submitter
- p.Gln138= Single submitter
- p.Gln154= Single submitter
- p.Gln37= Single submitter
- p.Gln57Arg Single submitter
- p.Gly83= Single submitter
- p.Gly92= Single submitter
- p.Leu122= Single submitter
- p.Leu127= Single submitter
- p.Leu134= Single submitter
- p.Leu141= Single submitter
- p.Leu15= Single submitter
- p.Leu163= Single submitter
- p.Leu167= Single submitter
- p.Leu77= Single submitter
- p.Phe49= Single submitter
- p.Pro10= Single submitter
- p.Pro3= Single submitter
- p.Pro45= Single submitter
- p.Ser101= Single submitter
- p.Ser111= Single submitter
- p.Ser39= Single submitter
- p.Thr121= Single submitter
- p.Thr149= Single submitter
- p.Thr62= Single submitter
- p.Thr94= Single submitter
- c.141+6G>C No assertion criteria ATP5F1D-related disorder
- c.-10C>T No assertion criteria ATP5F1D-related disorder
- p.Ala105= No assertion criteria ATP5F1D-related disorder
Uncertain significance 93
- p.Ala116Thr Multiple submitters Inborn genetic diseases ⚠
- p.Ala151Val Multiple submitters Inborn genetic diseases ⚠
- p.Ala166Ser Multiple submitters Inborn genetic diseases ⚠
- p.Ala27Asp Multiple submitters Inborn genetic diseases ⚠
- p.Ala28Val Multiple submitters Inborn genetic diseases ⚠
- p.Ala66Gly Multiple submitters Inborn genetic diseases ⚠
- p.Arg150Gln Multiple submitters Inborn genetic diseases ⚠
- p.Arg150Trp Multiple submitters Inborn genetic diseases ⚠
- p.Arg56Gln Multiple submitters Inborn genetic diseases ⚠
- p.Asn51Ser Multiple submitters Inborn genetic diseases ⚠
- p.Asn54Thr Multiple submitters Inborn genetic diseases ⚠
- p.Glu161Lys Multiple submitters Inborn genetic diseases
- p.Gly92Arg Multiple submitters Inborn genetic diseases ⚠
- p.His88Tyr Multiple submitters Inborn genetic diseases ⚠
- p.Lys136Glu Multiple submitters Inborn genetic diseases ⚠
- p.Met38Leu Multiple submitters Inborn genetic diseases ⚠
- p.Ser33Cys Multiple submitters Inborn genetic diseases ⚠
- p.Thr121Met Multiple submitters Inborn genetic diseases ⚠
- p.Thr149Met Multiple submitters Inborn genetic diseases ⚠
- p.Tyr97Ter Multiple submitters
- p.Val16Leu Multiple submitters Inborn genetic diseases ⚠
- p.Val60Ala Multiple submitters Inborn genetic diseases ⚠
- p.Val79Ile Multiple submitters Inborn genetic diseases ⚠
- c.141+4C>A Single submitter
- c.295+5G>T Single submitter
- c.384+3G>A Single submitter
- c.*3G>A Single submitter ATP5F1D-related disorder
- p.Ala108Thr Single submitter ⚠
- p.Ala119Thr Single submitter Inborn genetic diseases
- p.Ala137Asp Single submitter ⚠
- p.Ala145Asp Single submitter Inborn genetic diseases ⚠
- p.Ala25Val Single submitter ⚠
- p.Ala26_Ala27insTyrAlaGluAlaAla Single submitter
- p.Ala28_Pro29insAla Single submitter
- p.Ala32Val Single submitter ⚠
- p.Ala5_Leu6insAlaMetLeuProAlaAla Single submitter Inborn genetic diseases
- p.Ala53Val Single submitter Inborn genetic diseases ⚠
- p.Ala5Thr Single submitter Inborn genetic diseases ⚠
- p.Ala71Val Single submitter ⚠
- p.Arg14Cys Single submitter ⚠
- p.Arg156Gln Single submitter Inborn genetic diseases ⚠
- p.Arg156Leu Single submitter ⚠
- p.Arg156Ter Single submitter
- p.Arg20Cys Single submitter Inborn genetic diseases ⚠
- p.Arg20Pro Single submitter ⚠
- p.Arg8Cys Single submitter Inborn genetic diseases ⚠
- p.Arg9Pro Single submitter ⚠
- p.Asn160Thr Single submitter ⚠
- p.Asn51Thr Single submitter Inborn genetic diseases ⚠
- p.Asn54Ser Single submitter Inborn genetic diseases ⚠
- p.Asp123Gly Single submitter ⚠
- p.Asp146Asn Single submitter ⚠
- p.Asp91Gly Single submitter ⚠
- p.Gln113fs Single submitter
- p.Gln154Ter Single submitter
- p.Glu117Lys Single submitter Inborn genetic diseases ⚠
- p.Glu117Ter Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 5
- p.Glu135Lys Single submitter ⚠
- p.Glu147Ala Single submitter Inborn genetic diseases ⚠
- p.Glu147del Single submitter
- p.Gly102Ser Single submitter ⚠
- p.Gly143Glu Single submitter ⚠
- p.Gly34Ser Single submitter ⚠
- p.Gly52Cys Single submitter ⚠
- p.Gly65Glu Single submitter Inborn genetic diseases ⚠
- p.His73Pro Single submitter ⚠
- p.Ile155Asn Single submitter Inborn genetic diseases ⚠
- p.Ile155Ser Single submitter Inborn genetic diseases ⚠
- p.Leu63Met Single submitter
- p.Leu6Val Single submitter ⚠
- p.Leu77fs Single submitter
- p.Leu84Val Single submitter Inborn genetic diseases ⚠
- p.Lys131Asn Single submitter ⚠
- p.Met124Thr Single submitter ⚠
- p.Met38Ile Single submitter ⚠
- p.Phe42Cys Single submitter ⚠
- p.Phe98= Single submitter
- p.Phe98Leu Single submitter Inborn genetic diseases ⚠
- p.Pro29Leu Single submitter ⚠
- p.Pro35Ala Single submitter Inborn genetic diseases ⚠
- p.Pro61Leu Single submitter ⚠
- p.Ser110Tyr Single submitter ⚠
- p.Ser111Leu Single submitter
- p.Ser33Pro Single submitter ⚠
- p.Ser39Phe Single submitter Inborn genetic diseases ⚠
- p.Thr62Met Single submitter ⚠
- p.Thr93Ile Single submitter ⚠
- p.Val106Ala Single submitter Inborn genetic diseases ⚠
- p.Val112Leu Single submitter ⚠
- p.Val112Met Single submitter ⚠
- p.Val48Met Single submitter Inborn genetic diseases ⚠
- p.Val60Met Single submitter ⚠
- p.Val79Ala Single submitter ⚠