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Aliases for ATPAF2 Gene

Aliases for ATPAF2 Gene

  • ATP Synthase Mitochondrial F1 Complex Assembly Factor 2 2 3 5
  • ATP12 Homolog 3 4
  • ATP12 3 4
  • ATP12p 3
  • LP3663 3
  • MC5DN1 3

External Ids for ATPAF2 Gene

Previous GeneCards Identifiers for ATPAF2 Gene

  • GC17M018166
  • GC17M019290
  • GC17M017861
  • GC17M018122
  • GC17M017863
  • GC17M017864
  • GC17M017918
  • GC17M017675
  • GC17M017881

Summaries for ATPAF2 Gene

Entrez Gene Summary for ATPAF2 Gene

  • This gene encodes an assembly factor for the F(1) component of the mitochondrial ATP synthase. This protein binds specifically to the F1 alpha subunit and is thought to prevent this subunit from forming nonproductive homooligomers during enzyme assembly. This gene is located within the Smith-Magenis syndrome region on chromosome 17. An alternatively spliced transcript variant has been described, but its biological validity has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for ATPAF2 Gene

ATPAF2 (ATP Synthase Mitochondrial F1 Complex Assembly Factor 2) is a Protein Coding gene. Diseases associated with ATPAF2 include Mitochondrial Complex V Deficiency, Nuclear Type 1 and Isolated Atp Synthase Deficiency.

UniProtKB/Swiss-Prot for ATPAF2 Gene

  • May play a role in the assembly of the F1 component of the mitochondrial ATP synthase (ATPase).

Gene Wiki entry for ATPAF2 Gene

Additional gene information for ATPAF2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATPAF2 Gene

Genomics for ATPAF2 Gene

GeneHancer (GH) Regulatory Elements for ATPAF2 Gene

Promoters and enhancers for ATPAF2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I018037 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 0.0 -17 3.9 HDGF PKNOX1 MLX ARID4B SIN3A ZNF2 ZBTB7B YY1 ZNF207 ZNF143 ATPAF2 GID4 FAM106A LOC100419436 TOM1L2 ZNF286B ENSG00000273018 ENSG00000264885 MPRIP-AS1 MPRIP
GH17I017833 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6.6 +200.8 200754 8.9 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 SP3 NFYC GC17P017838 SREBF1 ENSG00000264885 DRG2 SMCR8 RAI1 TOM1L2 TOP3A CCDC144B FOXO3B
GH17I017817 Promoter/Enhancer 2 Ensembl ENCODE dbSUPER 6.6 +216.2 216221 10.7 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 GC17M017823 GC17M017824 ENSG00000264885 LOC100419436 FAM106A DRG2 CCDC144B TOM1L2 ENSG00000197815 ZNF286B
GH17I017918 Enhancer 1.4 Ensembl ENCODE dbSUPER 8.8 +118.1 118054 5.6 PKNOX1 FOXA2 SIN3A FEZF1 ZNF2 ZNF48 ZNF121 GLIS2 ZNF213 ATF7 ENSG00000197815 TOM1L2 SMCR8 FOXO3B DRC3 DRG2 RAI1 RPL13P12 ACTG1P24 ATPAF2
GH17I017279 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 5.2 +758.3 758300 2.6 PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B E2F8 COPS3 PIR47486 PIR50772 FLCN NT5M DRG2 LOC644422 MPRIP-AS1 MPRIP FLII
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ATPAF2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ATPAF2 gene promoter:

Genomic Locations for ATPAF2 Gene

Genomic Locations for ATPAF2 Gene
61,801 bases
Minus strand

Genomic View for ATPAF2 Gene

Genes around ATPAF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATPAF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATPAF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATPAF2 Gene

Proteins for ATPAF2 Gene

  • Protein details for ATPAF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    ATP synthase mitochondrial F1 complex assembly factor 2
    Protein Accession:
    Secondary Accessions:
    • A6NDE5
    • A8K2J2
    • Q6XYC7

    Protein attributes for ATPAF2 Gene

    289 amino acids
    Molecular mass:
    32772 Da
    Quaternary structure:
    • Interacts with ATP5A1.
    • Sequence=AAP34466.1; Type=Frameshift; Positions=87; Evidence={ECO:0000305};

neXtProt entry for ATPAF2 Gene

Post-translational modifications for ATPAF2 Gene

No Post-translational modifications

No data available for DME Specific Peptides for ATPAF2 Gene

Domains & Families for ATPAF2 Gene

Gene Families for ATPAF2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for ATPAF2 Gene

Suggested Antigen Peptide Sequences for ATPAF2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the ATP12 family.
  • Belongs to the ATP12 family.
genes like me logo Genes that share domains with ATPAF2: view

Function for ATPAF2 Gene

Molecular function for ATPAF2 Gene

UniProtKB/Swiss-Prot Function:
May play a role in the assembly of the F1 component of the mitochondrial ATP synthase (ATPase).

Phenotypes From GWAS Catalog for ATPAF2 Gene

Gene Ontology (GO) - Molecular Function for ATPAF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11410595
genes like me logo Genes that share ontologies with ATPAF2: view
genes like me logo Genes that share phenotypes with ATPAF2: view

Human Phenotype Ontology for ATPAF2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ATPAF2 Gene

MGI Knock Outs for ATPAF2:

Animal Model Products

miRNA for ATPAF2 Gene

miRTarBase miRNAs that target ATPAF2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for ATPAF2 Gene

Localization for ATPAF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATPAF2 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATPAF2 gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 4
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ATPAF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol IDA --
GO:0016607 nuclear speck IDA --
genes like me logo Genes that share ontologies with ATPAF2: view

Pathways & Interactions for ATPAF2 Gene

SuperPathways for ATPAF2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ATPAF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043461 proton-transporting ATP synthase complex assembly NAS,IEA 14757859
genes like me logo Genes that share ontologies with ATPAF2: view

No data available for Pathways by source and SIGNOR curated interactions for ATPAF2 Gene

Drugs & Compounds for ATPAF2 Gene

No Compound Related Data Available

Transcripts for ATPAF2 Gene

Unigene Clusters for ATPAF2 Gene

ATP synthase mitochondrial F1 complex assembly factor 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ATPAF2 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14
SP1: - - - - - - - -
SP2: - - - - - - -
SP3: - - -
SP5: - - - - - - - - - - - -
SP6: - - -
SP7: -

Relevant External Links for ATPAF2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ATPAF2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ATPAF2 Gene

Protein differential expression in normal tissues from HIPED for ATPAF2 Gene

This gene is overexpressed in Nasal epithelium (18.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ATPAF2 Gene

Protein tissue co-expression partners for ATPAF2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ATPAF2 Gene:


SOURCE GeneReport for Unigene cluster for ATPAF2 Gene:


mRNA Expression by UniProt/SwissProt for ATPAF2 Gene:

Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for ATPAF2 Gene

  • Liver(4.2)
  • Muscle(4.2)
  • Nervous system(2.9)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ATPAF2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • chin
  • ear
  • eye
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • skull
  • heart
  • heart valve
  • lung
  • liver
  • penis
  • testicle
  • urethra
  • peripheral nerve
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with ATPAF2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for ATPAF2 Gene

Orthologs for ATPAF2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATPAF2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ATPAF2 33 34
  • 99.54 (n)
(Canis familiaris)
Mammalia ATPAF2 33 34
  • 88.26 (n)
(Ornithorhynchus anatinus)
Mammalia ATPAF2 34
  • 87 (a)
(Rattus norvegicus)
Mammalia Atpaf2 33
  • 86.85 (n)
(Mus musculus)
Mammalia Atpaf2 33 16 34
  • 86.27 (n)
(Bos Taurus)
Mammalia ATPAF2 33 34
  • 85.88 (n)
(Monodelphis domestica)
Mammalia ATPAF2 34
  • 77 (a)
(Gallus gallus)
Aves ATPAF2 33 34
  • 74.85 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 76 (a)
-- 34
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia atpaf2 33
  • 72.82 (n)
MGC75949 33
(Danio rerio)
Actinopterygii atpaf2 33 34
  • 65.09 (n)
Dr.4726 33
fruit fly
(Drosophila melanogaster)
Insecta l(2)k14505 33 34
  • 53.59 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008876 33
  • 51.59 (n)
(Caenorhabditis elegans)
Secernentea CELE_Y116A8C.27 33
  • 42.22 (n)
Y116A8C.27 34
  • 28 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL140C 33
  • 43.07 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ATP12 33
  • 41 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A06259g 33
  • 38.99 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G40660 33
  • 42.86 (n)
(Oryza sativa)
Liliopsida Os07g0644000 33
  • 44.06 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU00676 33
  • 46.58 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3439 34
  • 41 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes atp12 33
  • 40.59 (n)
Species where no ortholog for ATPAF2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ATPAF2 Gene

Gene Tree for ATPAF2 (if available)
Gene Tree for ATPAF2 (if available)

Paralogs for ATPAF2 Gene

No data available for Paralogs for ATPAF2 Gene

Variants for ATPAF2 Gene

Sequence variations from dbSNP and Humsavar for ATPAF2 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1015124277 uncertain-significance, Mitochondrial Complex V (ATP Synthase) Deficiency, Nuclear Type 18,039,014(-) C/A 5_prime_UTR_variant, non_coding_transcript_variant
rs104894554 pathogenic, Nuclearly-encoded mitochondrial complex V (ATP synthase) deficiency 1, Mitochondrial complex V deficiency, nuclear 1 (MC5DN1) [MIM:604273] 18,028,276(-) A/T coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs117739515 likely-benign, Mitochondrial Complex V (ATP Synthase) Deficiency, Nuclear Type 18,018,419(-) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant, non_coding_transcript_variant
rs141020107 uncertain-significance, Mitochondrial Complex V (ATP Synthase) Deficiency, Nuclear Type 18,021,221(-) C/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs143241583 uncertain-significance, not provided, Mitochondrial Complex V (ATP Synthase) Deficiency, Nuclear Type, not specified 18,038,974(-) G/A/C 5_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for ATPAF2 Gene

Variant ID Type Subtype PubMed ID
nsv510701 CNV deletion 20534489
nsv499114 OTHER inversion 21111241
nsv155 OTHER inversion 15895083

Variation tolerance for ATPAF2 Gene

Residual Variation Intolerance Score: 60% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.01; 37.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATPAF2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATPAF2 Gene

Disorders for ATPAF2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for ATPAF2 Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mitochondrial complex v deficiency, nuclear type 1
  • mc5dn1
isolated atp synthase deficiency
  • isolated mitochondrial respiratory chain complex v deficiency
mitochondrial complex v deficiency
  • complex 5 mitochondrial respiratory chain deficiency
3-methylglutaconic aciduria
  • 3-methyl glutaconic aciduria
- elite association - COSMIC cancer census association via MalaCards


  • Mitochondrial complex V deficiency, nuclear 1 (MC5DN1) [MIM:604273]: A mitochondrial disorder with heterogeneous clinical manifestations including dysmorphic features, psychomotor retardation, hypotonia, growth retardation, cardiomyopathy, enlarged liver, hypoplastic kidneys and elevated lactate levels in urine, plasma and cerebrospinal fluid. {ECO:0000269 PubMed:14757859}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for ATPAF2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ATPAF2: view

No data available for Genatlas for ATPAF2 Gene

Publications for ATPAF2 Gene

  1. Atp11p and Atp12p are assembly factors for the F(1)-ATPase in human mitochondria. (PMID: 11410595) Wang ZG … Ackerman SH (The Journal of biological chemistry 2001) 2 3 4 58
  2. Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk. (PMID: 20167577) Reynolds CA … Prince JA (Human molecular genetics 2010) 3 44 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Respiratory chain complex V deficiency due to a mutation in the assembly gene ATP12. (PMID: 14757859) De Meirleir L … Van Coster R (Journal of medical genetics 2004) 3 4 58

Products for ATPAF2 Gene

Sources for ATPAF2 Gene

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