ATPAF2 — 231 ClinVar variants
All ClinVar germline ATPAF2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 109 flagged for review →
3 Likely pathogenic · 13 Conflicting · 16 Benign · 5 Benign/Likely benign · 63 Likely benign · 131 Uncertain significance
Full ATPAF2 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.
-
ATPAF2 p.Ala212Ser
Conflicting
Single submitter
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Arg227His Conflicting Single submitter
-
ATPAF2 p.Leu262Pro
Conflicting
Single submitter
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
Predictors lean, ClinVar uncertain 51
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
ATPAF2 p.Ala130Glu
Uncertain significance
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
-
ATPAF2 p.Ala268Thr
Uncertain significance
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Arg189Gln Uncertain significance Multiple submitters
- ATPAF2 p.Arg265Cys Uncertain significance Multiple submitters
- ATPAF2 p.Asn52Lys Uncertain significance Multiple submitters
- ATPAF2 p.Glu278Lys Uncertain significance Multiple submitters
- ATPAF2 p.Lys47Asn Uncertain significance Multiple submitters
- ATPAF2 p.Met106Thr Uncertain significance Multiple submitters
- ATPAF2 p.Met27Leu Uncertain significance Multiple submitters
- ATPAF2 p.Met27Thr Uncertain significance Multiple submitters
- ATPAF2 p.Thr105Ala Uncertain significance Multiple submitters
- ATPAF2 p.Val132Met Uncertain significance Multiple submitters
- ATPAF2 p.Ala197Thr Uncertain significance Single submitter
- ATPAF2 p.Ala212Val Uncertain significance Single submitter
- ATPAF2 p.Arg13Ser Uncertain significance Single submitter
- ATPAF2 p.Arg189Pro Uncertain significance Single submitter
- ATPAF2 p.Arg18Gln Uncertain significance Single submitter
- ATPAF2 p.Arg18Pro Uncertain significance Single submitter
- ATPAF2 p.Arg48Trp Uncertain significance Single submitter
- ATPAF2 p.Arg69Gly Uncertain significance Single submitter
- ATPAF2 p.Asn156Lys Uncertain significance Single submitter
-
ATPAF2 p.Asp138Asn
Uncertain significance
Single submitter
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Gln126His Uncertain significance Single submitter
- ATPAF2 p.Glu93Gln Uncertain significance Single submitter
- ATPAF2 p.Gly21Ala Uncertain significance Single submitter
- ATPAF2 p.Gly22Val Uncertain significance Single submitter
- ATPAF2 p.Gly249Ser Uncertain significance Single submitter
- ATPAF2 p.Ile140Val Uncertain significance Single submitter
- ATPAF2 p.Ile224Thr Uncertain significance Single submitter
- ATPAF2 p.Ile251Ser Uncertain significance Single submitter
- ATPAF2 p.Lys288Arg Uncertain significance Single submitter
- ATPAF2 p.Met106Val Uncertain significance Single submitter
- ATPAF2 p.Met180Ile Uncertain significance Single submitter
- ATPAF2 p.Met217Val Uncertain significance Single submitter
- ATPAF2 p.Met27Val Uncertain significance Single submitter
- ATPAF2 p.Pro34Arg Uncertain significance Single submitter
- ATPAF2 p.Pro43Ser Uncertain significance Single submitter
- ATPAF2 p.Pro82Arg Uncertain significance Single submitter
- ATPAF2 p.Ser24Gly Uncertain significance Single submitter
- ATPAF2 p.Ser54Thr Uncertain significance Single submitter
- ATPAF2 p.Ser83Arg Uncertain significance Single submitter
- ATPAF2 p.Thr177Ala Uncertain significance Single submitter
- ATPAF2 p.Trp158Arg Uncertain significance Single submitter
- ATPAF2 p.Tyr103Asn Uncertain significance Single submitter
- ATPAF2 p.Tyr142His Uncertain significance Single submitter
- ATPAF2 p.Tyr243Asn Uncertain significance Single submitter
-
ATPAF2 p.Val171Leu
Uncertain significance
Single submitter
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Val193Ile Uncertain significance Single submitter
- ATPAF2 p.Val193Leu Uncertain significance Single submitter
-
ATPAF2 p.Val234Met
Uncertain significance
Single submitter
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Val282Ile Uncertain significance Single submitter
Predictors split 55
The independent predictors disagree with each other — read with care.
- ATPAF2 p.Ala267Thr Uncertain significance Multiple submitters
-
ATPAF2 p.Arg14Gly
Uncertain significance
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Arg189Trp Uncertain significance Multiple submitters
- ATPAF2 p.Arg238Cys Uncertain significance Multiple submitters
-
ATPAF2 p.Arg238His
Uncertain significance
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Arg263Gln Uncertain significance Multiple submitters
- ATPAF2 p.Arg265His Uncertain significance Multiple submitters
-
ATPAF2 p.Arg38Leu
Uncertain significance
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
-
ATPAF2 p.Arg3Lys
Uncertain significance
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Arg7Trp Uncertain significance Multiple submitters
-
ATPAF2 p.Glu84Lys
Uncertain significance
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
-
ATPAF2 p.Gly12Glu
Benign
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Gly170Ser Uncertain significance Multiple submitters
- ATPAF2 p.His274Arg Uncertain significance Multiple submitters
- ATPAF2 p.His274Tyr Uncertain significance Multiple submitters
- ATPAF2 p.Ile162Ser Uncertain significance Multiple submitters
- ATPAF2 p.Ser28Asn Uncertain significance Multiple submitters
- ATPAF2 p.Val151Met Uncertain significance Multiple submitters
-
ATPAF2 p.Val171Met
Benign/Likely benign
Multiple submitters
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Ala264Thr Uncertain significance Single submitter
- ATPAF2 p.Arg129Trp Uncertain significance Single submitter
-
ATPAF2 p.Arg189Gly
Conflicting
Single submitter
mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- ATPAF2 p.Arg227Cys Uncertain significance Single submitter
- ATPAF2 p.Arg263Trp Uncertain significance Single submitter
- ATPAF2 p.Asn250Tyr Uncertain significance Single submitter
- ATPAF2 p.Gln121Arg Uncertain significance Single submitter
- ATPAF2 p.Gln205Arg Uncertain significance Single submitter
- ATPAF2 p.Gln260Arg Uncertain significance Single submitter
- ATPAF2 p.Glu148Lys Uncertain significance Single submitter
- ATPAF2 p.Glu163Lys Uncertain significance Single submitter
- ATPAF2 p.Glu190Val Uncertain significance Single submitter
- ATPAF2 p.Glu231Gly Uncertain significance Single submitter
- ATPAF2 p.Glu45Ala Uncertain significance Single submitter
- ATPAF2 p.Gly269Ser Conflicting Single submitter
- ATPAF2 p.Gly58Asp Uncertain significance Single submitter
- ATPAF2 p.Ile207Thr Uncertain significance Single submitter
- ATPAF2 p.Leu127Val Uncertain significance Single submitter
- ATPAF2 p.Leu16Pro Uncertain significance Single submitter
- ATPAF2 p.Lys285Asn Uncertain significance Single submitter
- ATPAF2 p.Lys47Arg Uncertain significance Single submitter
- ATPAF2 p.Lys70Arg Uncertain significance Single submitter
- ATPAF2 p.Met217Thr Uncertain significance Single submitter
- ATPAF2 p.Phe209Leu Conflicting Single submitter
- ATPAF2 p.Pro43Leu Uncertain significance Single submitter
- ATPAF2 p.Ser35Phe Uncertain significance Single submitter
- ATPAF2 p.Ser4Asn Uncertain significance Single submitter
- ATPAF2 p.Ser54Ile Uncertain significance Single submitter
- ATPAF2 p.Thr100Ala Uncertain significance Single submitter
- ATPAF2 p.Thr120Asn Uncertain significance Single submitter
- ATPAF2 p.Thr139Asn Uncertain significance Single submitter
- ATPAF2 p.Thr139Ile Uncertain significance Single submitter
- ATPAF2 p.Thr149Ile Uncertain significance Single submitter
- ATPAF2 p.Tyr257Cys Uncertain significance Single submitter
- ATPAF2 p.Val193Phe Uncertain significance Single submitter
- ATPAF2 p.Val81Ile Conflicting Single submitter
All ATPAF2 variants
Likely pathogenic 3
- c.179-2A>G Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Glu146Ter Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Ile33fs Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
Conflicting classifications of pathogenicity 13
- c.133+1G>T Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.422+11T>C Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.732+6G>A Single submitter
- p.Ala212Ser Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Ala37= Single submitter
- p.Arg168= Single submitter
- p.Arg189Gly Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Arg227His Single submitter ⚠
- p.Gly269Ser Single submitter ⚠
- p.Leu116= Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Leu262Pro Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Phe209Leu Single submitter ⚠
- p.Val81Ile Single submitter ⚠
Benign 16
- c.422+206T>A Multiple submitters
- c.616+103A>G Multiple submitters
- c.616+156A>G Multiple submitters
- c.616+191T>C Multiple submitters
- c.733-161G>A Multiple submitters
- c.*165C>T Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*20C>G Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Gln246= Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Gly12Glu Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- c.178+28_178+29dup Single submitter
- c.179-72T>C Single submitter
- c.503+269C>T Single submitter
- c.616+237T>G Single submitter
- c.733-280C>T Single submitter
- c.*130T>C Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*456T>C Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
Benign/Likely benign 5
- c.422+15G>A Multiple submitters
- c.-147G>A Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Ala233= Multiple submitters
- p.Glu241Gly Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Val171Met Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
Likely benign 63
- c.324+11C>T Multiple submitters
- c.732+301C>A Multiple submitters
- p.Ala131= Multiple submitters
- c.133+274G>C Single submitter
- c.134-20T>A Single submitter
- c.134-271del Single submitter
- c.134-4dup Single submitter
- c.134-6T>C Single submitter
- c.178+17_178+18del Single submitter
- c.178+19del Single submitter
- c.178+7G>A Single submitter
- c.179-10A>G Single submitter
- c.179-15A>G Single submitter
- c.324+13_324+14del Single submitter
- c.324+15G>A Single submitter
- c.324+20A>T Single submitter
- c.325-216C>G Single submitter
- c.422+20G>A Single submitter
- c.503+16C>T Single submitter
- c.504-256G>A Single submitter
- c.504-265C>T Single submitter
- c.504-51G>T Single submitter
- c.616+18T>C Single submitter
- c.616+19G>A Single submitter
- c.616+20T>C Single submitter
- c.617-9T>G Single submitter
- c.732+17C>G Single submitter
- c.733-11C>T Single submitter
- c.733-125C>T Single submitter
- c.733-200T>C Single submitter
- c.733-215G>A Single submitter
- c.733-317A>C Single submitter
- c.-107G>A Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Ala25= Single submitter
- p.Ala268= Single submitter
- p.Arg143= Single submitter
- p.Arg238= Single submitter
- p.Glu163= Single submitter
- p.Gly170= Single submitter
- p.Gly249= Single submitter
- p.Gly61= Single submitter
- p.Ile161= Single submitter
- p.Ile224Met Single submitter
- p.Ile251Val Single submitter
- p.Leu196= Single submitter
- p.Leu214= Single submitter
- p.Leu223= Single submitter
- p.Leu226= Single submitter
- p.Leu235= Single submitter
- p.Leu78= Single submitter
- p.Lys133= Single submitter
- p.Pro147= Single submitter
- p.Pro182= Single submitter
- p.Pro23Leu Single submitter
- p.Ser277= Single submitter
- p.Thr109= Single submitter
- p.Thr110= Single submitter
- p.Thr266= Single submitter
- p.Thr80= Single submitter
- p.Tyr142= Single submitter
- p.Tyr169= Single submitter
- p.Tyr199= Single submitter
- p.Val210= Single submitter
Uncertain significance 131
- c.-90C>A Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*132C>T Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Ala130Glu Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Ala267Thr Multiple submitters ⚠
- p.Ala268Thr Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Arg14Gly Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Arg189Gln Multiple submitters ⚠
- p.Arg189Trp Multiple submitters ⚠
- p.Arg238Cys Multiple submitters ⚠
- p.Arg238His Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Arg263Gln Multiple submitters ⚠
- p.Arg265Cys Multiple submitters ⚠
- p.Arg265His Multiple submitters ⚠
- p.Arg38Leu Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Arg3Lys Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Arg7Trp Multiple submitters ⚠
- p.Asn52Lys Multiple submitters ⚠
- p.Glu278Lys Multiple submitters ⚠
- p.Glu84Lys Multiple submitters mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Gly170Ser Multiple submitters ⚠
- p.His274Arg Multiple submitters ⚠
- p.His274Tyr Multiple submitters ⚠
- p.Ile162Ser Multiple submitters ⚠
- p.Lys47Asn Multiple submitters ⚠
- p.Met106Thr Multiple submitters ⚠
- p.Met27Leu Multiple submitters ⚠
- p.Met27Thr Multiple submitters ⚠
- p.Phe134del Multiple submitters
- p.Ser28Asn Multiple submitters ⚠
- p.Thr105Ala Multiple submitters ⚠
- p.Val132Met Multiple submitters ⚠
- p.Val151Met Multiple submitters ⚠
- c.177_178+4dup Single submitter
- c.179-12T>G Single submitter
- c.503+5G>C Single submitter
- c.616+3A>T Single submitter
- c.732+5G>A Single submitter
- c.-1G>T Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*108C>T Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*137C>T Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*138G>A Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*194C>A Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*250C>T Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*26G>C Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*337T>C Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*378A>T Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*485G>A Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*526C>T Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- c.*54C>T Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Ala197Thr Single submitter ⚠
- p.Ala212Val Single submitter ⚠
- p.Ala264Thr Single submitter ⚠
- p.Arg129Trp Single submitter ⚠
- p.Arg13Ser Single submitter ⚠
- p.Arg189Pro Single submitter ⚠
- p.Arg18Gln Single submitter ⚠
- p.Arg18Pro Single submitter ⚠
- p.Arg227Cys Single submitter ⚠
- p.Arg263Trp Single submitter ⚠
- p.Arg48Trp Single submitter ⚠
- p.Arg69Gly Single submitter ⚠
- p.Asn113_Thr114insAsn Single submitter
- p.Asn156Lys Single submitter ⚠
- p.Asn250Tyr Single submitter ⚠
- p.Asp138Asn Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Gln121Arg Single submitter ⚠
- p.Gln126His Single submitter ⚠
- p.Gln205Arg Single submitter ⚠
- p.Gln260Arg Single submitter ⚠
- p.Gln260Ter Single submitter
- p.Glu148Lys Single submitter ⚠
- p.Glu163Lys Single submitter ⚠
- p.Glu190Val Single submitter ⚠
- p.Glu231Gly Single submitter ⚠
- p.Glu241fs Single submitter
- p.Glu45Ala Single submitter ⚠
- p.Glu93Gln Single submitter ⚠
- p.Gly21Ala Single submitter ⚠
- p.Gly22Val Single submitter ⚠
- p.Gly249Ser Single submitter ⚠
- p.Gly58Asp Single submitter ⚠
- p.His68fs Single submitter
- p.Ile140Val Single submitter ⚠
- p.Ile207Thr Single submitter ⚠
- p.Ile224Thr Single submitter ⚠
- p.Ile251Ser Single submitter ⚠
- p.Leu127Val Single submitter ⚠
- p.Leu16Pro Single submitter ⚠
- p.Leu6Pro Single submitter
- p.Lys285Asn Single submitter ⚠
- p.Lys288= Single submitter
- p.Lys288Arg Single submitter ⚠
- p.Lys47Arg Single submitter ⚠
- p.Lys70Arg Single submitter ⚠
- p.Met106Val Single submitter ⚠
- p.Met180Ile Single submitter ⚠
- p.Met217Thr Single submitter ⚠
- p.Met217Val Single submitter ⚠
- p.Met27Val Single submitter ⚠
- p.Pro160= Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1
- p.Pro34Arg Single submitter ⚠
- p.Pro43Leu Single submitter ⚠
- p.Pro43Ser Single submitter ⚠
- p.Pro82Arg Single submitter ⚠
- p.Ser24Gly Single submitter ⚠
- p.Ser35Phe Single submitter ⚠
- p.Ser4Asn Single submitter ⚠
- p.Ser54Ile Single submitter ⚠
- p.Ser54Thr Single submitter ⚠
- p.Ser83Arg Single submitter ⚠
- p.Thr100Ala Single submitter ⚠
- p.Thr120Asn Single submitter ⚠
- p.Thr139Asn Single submitter ⚠
- p.Thr139Ile Single submitter ⚠
- p.Thr149Ile Single submitter ⚠
- p.Thr177Ala Single submitter ⚠
- p.Thr281fs Single submitter
- p.Thr44= Single submitter
- p.Trp158Arg Single submitter ⚠
- p.Trp94Ter Single submitter
- p.Tyr103Asn Single submitter ⚠
- p.Tyr142His Single submitter ⚠
- p.Tyr243Asn Single submitter ⚠
- p.Tyr257Cys Single submitter ⚠
- p.Val171Leu Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Val193Ile Single submitter ⚠
- p.Val193Leu Single submitter ⚠
- p.Val193Phe Single submitter ⚠
- p.Val234Met Single submitter mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 ⚠
- p.Val282Ile Single submitter ⚠
- p.Ter290Arg No assertion criteria microcephaly