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Aliases for APAF1 Gene

Aliases for APAF1 Gene

  • Apoptotic Peptidase Activating Factor 1 2 3 5
  • APAF-1 3 4
  • Apoptotic Protease-Activating Factor 1 3
  • Apoptotic Peptidase Activating Factor 2
  • Apoptotic Protease Activating Factor 2
  • KIAA0413 4
  • CED4 3

External Ids for APAF1 Gene

Previous GeneCards Identifiers for APAF1 Gene

  • GC12P098489
  • GC12P099542
  • GC12P098971
  • GC12P097541
  • GC12P099039
  • GC12P096100

Summaries for APAF1 Gene

Entrez Gene Summary for APAF1 Gene

  • This gene encodes a cytoplasmic protein that initiates apoptosis. This protein contains several copies of the WD-40 domain, a caspase recruitment domain (CARD), and an ATPase domain (NB-ARC). Upon binding cytochrome c and dATP, this protein forms an oligomeric apoptosome. The apoptosome binds and cleaves caspase 9 preproprotein, releasing its mature, activated form. Activated caspase 9 stimulates the subsequent caspase cascade that commits the cell to apoptosis. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for APAF1 Gene

APAF1 (Apoptotic Peptidase Activating Factor 1) is a Protein Coding gene. Diseases associated with APAF1 include Dystrophinopathies and Alzheimer Disease Mitochondrial. Among its related pathways are TNFR1 Pathway and Nanomaterial induced apoptosis. GO annotations related to this gene include identical protein binding and ADP binding. An important paralog of this gene is TEP1.

UniProtKB/Swiss-Prot for APAF1 Gene

  • Oligomeric Apaf-1 mediates the cytochrome c-dependent autocatalytic activation of pro-caspase-9 (Apaf-3), leading to the activation of caspase-3 and apoptosis. This activation requires ATP. Isoform 6 is less effective in inducing apoptosis.

Gene Wiki entry for APAF1 Gene

Additional gene information for APAF1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APAF1 Gene

Genomics for APAF1 Gene

Regulatory Elements for APAF1 Gene

Enhancers for APAF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H098592 1.1 ENCODE 11.1 -50.6 -50626 4.3 PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ZNF207 TMPO SLC25A3 IKBIP APAF1 TMPO-AS1 GC12M098595
GH12H098612 1 Ensembl ENCODE 12.1 -32.2 -32175 1 HDGF ZNF687 NR2F1 TRIM22 ELF1 EBF1 DPF2 ZNF592 ZNF217 ZNF692 IKBIP APAF1 GC12M098601
GH12H098605 0.9 Ensembl ENCODE 12.1 -38.1 -38068 2.3 CTCF ZNF654 CEBPB MAX RAD21 BCL6B CEBPA SMC3 BCL6 IKBIP APAF1 SLC25A3 GC12M098602 GC12M098601
GH12H098532 0.9 ENCODE 10 -111.6 -111564 1.8 HDAC1 PKNOX1 ARNT RAD21 ZNF766 ZNF143 ATF7 SMARCA5 CEBPB ZEB2 RNU4-41P LINC02453 SNORA53 APAF1 IKBIP SLC9A7P1 GC12M098524 GC12M098549
GH12H098618 0.5 Ensembl 17.8 -25.9 -25925 1.2 ZNF121 POLR2A CEBPB EP300 MYC SLC25A3 APAF1 IKBIP PPIAP8 GC12M098601
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around APAF1 on UCSC Golden Path with GeneCards custom track

Promoters for APAF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000056141 159 3801 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 ZNF416 ZNF143

Genomic Locations for APAF1 Gene

Genomic Locations for APAF1 Gene
90,293 bases
Plus strand

Genomic View for APAF1 Gene

Genes around APAF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APAF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APAF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for APAF1 Gene

Proteins for APAF1 Gene

  • Protein details for APAF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Apoptotic protease-activating factor 1
    Protein Accession:
    Secondary Accessions:
    • B2RMX8
    • O43297
    • Q7Z438
    • Q9BXZ6
    • Q9UBZ5
    • Q9UGN8
    • Q9UGN9
    • Q9UGP0
    • Q9UJ58
    • Q9UJ59
    • Q9UJ60
    • Q9UJ61
    • Q9UJ62
    • Q9UJ63
    • Q9UJ64
    • Q9UJ65
    • Q9UJ66
    • Q9UJ67
    • Q9UNC9

    Protein attributes for APAF1 Gene

    1248 amino acids
    Molecular mass:
    141840 Da
    Quaternary structure:
    • Monomer. Oligomerizes to a heptameric ring, known as the apoptosome, upon binding of cytochrome c and dATP. Oligomeric Apaf-1 and pro-caspase-9 bind to each other via their respective NH2-terminal CARD domains and consecutively mature caspase-9 is released from the complex. Pro-caspase-3 is recruited into the Apaf-1-pro-caspase-9 complex via interaction with pro-caspase-9. Interacts with APIP. Interacts (via CARD and NACHT domains) with NAIP/BIRC1 (via NACHT domain).
    • Physiological concentrations of calcium ions negatively affect the assembly of apoptosome by inhibiting nucleotide exchange in the monomeric form.
    • Sequence=AAK28401.1; Type=Frameshift; Positions=108; Evidence={ECO:0000305}; Sequence=BAA24843.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for APAF1 Gene

    Alternative splice isoforms for APAF1 Gene

neXtProt entry for APAF1 Gene

Post-translational modifications for APAF1 Gene

  • Ubiquitination at Lys809
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for APAF1 (APAF)
  • Abcam antibodies for APAF1

No data available for DME Specific Peptides for APAF1 Gene

Domains & Families for APAF1 Gene

Gene Families for APAF1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for APAF1 Gene

Graphical View of Domain Structure for InterPro Entry



  • The CARD domain mediates interaction with APIP.
  • The CARD domain mediates interaction with APIP.
  • The monomeric form is autoinhibited in a closed conformation through a bound ADP at the nucleotide binding site. Exchange of ADP for ATP and binding of cytochrome c trigger a large conformational change where the first WD repeat region swings out, allowing the NB-ARC domain to rotate and expose the contact areas for oligomerization (By similarity).
genes like me logo Genes that share domains with APAF1: view

Function for APAF1 Gene

Molecular function for APAF1 Gene

GENATLAS Biochemistry:
cytoplasmic scaffolding apoptotic protease activating factor 1,89kDa,forming a ternary complex ATP,datp dependent with cytochrome C1 and the initiator of apoptosis caspase 9,not inhibited by binding to BCL2
UniProtKB/Swiss-Prot Function:
Oligomeric Apaf-1 mediates the cytochrome c-dependent autocatalytic activation of pro-caspase-9 (Apaf-3), leading to the activation of caspase-3 and apoptosis. This activation requires ATP. Isoform 6 is less effective in inducing apoptosis.
UniProtKB/Swiss-Prot Induction:
By E2F and p53/TP53 in apoptotic neurons.

Phenotypes From GWAS Catalog for APAF1 Gene

Gene Ontology (GO) - Molecular Function for APAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding TAS 10383829
GO:0005515 protein binding IPI 9267021
GO:0005524 ATP binding IEA --
GO:0008656 cysteine-type endopeptidase activator activity involved in apoptotic process NAS,TAS 15009102
GO:0031072 heat shock protein binding IEA --
genes like me logo Genes that share ontologies with APAF1: view
genes like me logo Genes that share phenotypes with APAF1: view

Animal Models for APAF1 Gene

MGI Knock Outs for APAF1:

Animal Model Products

Clone Products

  • Addgene plasmids for APAF1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for APAF1 Gene

Localization for APAF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for APAF1 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 APAF1 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
mitochondrion 3
golgi apparatus 2
plasma membrane 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for APAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0034774 secretory granule lumen TAS --
genes like me logo Genes that share ontologies with APAF1: view

Pathways & Interactions for APAF1 Gene

genes like me logo Genes that share pathways with APAF1: view

SIGNOR curated interactions for APAF1 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for APAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEA --
GO:0001843 neural tube closure IEA --
GO:0006915 apoptotic process TAS 9753320
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process IDA 21827945
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with APAF1: view

Drugs & Compounds for APAF1 Gene

(23) Drugs for APAF1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
dATP Experimental Pharma Full agonist, Agonist 0
ATP Nutra Agonist, Target 0

(18) Additional Compounds for APAF1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with APAF1: view

Transcripts for APAF1 Gene

Unigene Clusters for APAF1 Gene

Apoptotic peptidase activating factor 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for APAF1

Alternative Splicing Database (ASD) splice patterns (SP) for APAF1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b
SP1: - - - - - - - -

Relevant External Links for APAF1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for APAF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for APAF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for APAF1 Gene

This gene is overexpressed in Whole Blood (x4.9).

Protein differential expression in normal tissues from HIPED for APAF1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (25.4) and Lymph node (11.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for APAF1 Gene

Protein tissue co-expression partners for APAF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of APAF1 Gene:


SOURCE GeneReport for Unigene cluster for APAF1 Gene:


mRNA Expression by UniProt/SwissProt for APAF1 Gene:

Tissue specificity: Ubiquitous. Highest levels of expression in adult spleen and peripheral blood leukocytes, and in fetal brain, kidney and lung. Isoform 1 is expressed in heart, kidney and liver.

Evidence on tissue expression from TISSUES for APAF1 Gene

  • Nervous system(4.5)
  • Blood(4.4)
  • Heart(4.4)
  • Kidney(4.4)
  • Intestine(2.1)
  • Lung(2)
genes like me logo Genes that share expression patterns with APAF1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for APAF1 Gene

Orthologs for APAF1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for APAF1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia APAF1 33 34
  • 99.63 (n)
(Canis familiaris)
Mammalia APAF1 33 34
  • 91.77 (n)
(Bos Taurus)
Mammalia APAF1 33 34
  • 90.81 (n)
(Mus musculus)
Mammalia Apaf1 33 16 34
  • 86 (n)
(Rattus norvegicus)
Mammalia Apaf1 33
  • 85.36 (n)
(Ornithorhynchus anatinus)
Mammalia APAF1 34
  • 81 (a)
(Monodelphis domestica)
Mammalia APAF1 34
  • 80 (a)
(Gallus gallus)
Aves APAF1 33 34
  • 72.4 (n)
(Anolis carolinensis)
Reptilia APAF1 34
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia apaf1 33
  • 67.19 (n)
(Danio rerio)
Actinopterygii apaf1 33 34
  • 59.54 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta CG30116 34
  • 10 (a)
(Caenorhabditis elegans)
Secernentea qui-1 34
  • 8 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DIP2 34
  • 15 (a)
Species where no ortholog for APAF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for APAF1 Gene

Gene Tree for APAF1 (if available)
Gene Tree for APAF1 (if available)

Paralogs for APAF1 Gene

Paralogs for APAF1 Gene

(3) SIMAP similar genes for APAF1 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with APAF1: view

Variants for APAF1 Gene

Sequence variations from dbSNP and Humsavar for APAF1 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1000021515 -- 98,656,810(+) GGTGG(G/T)CGTTG intron-variant
rs1000047211 -- 98,649,500(+) GTCCT(A/G)TGTGA nc-transcript-variant, reference, synonymous-codon
rs1000086190 -- 98,677,657(+) GAAAT(A/G)ACAGA intron-variant
rs1000173660 -- 98,658,582(+) AGTCT(A/G)ACTTC intron-variant
rs1000197856 -- 98,658,219(+) GTATA(G/T)TCTAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for APAF1 Gene

Variant ID Type Subtype PubMed ID
nsv844 CNV insertion 18451855
nsv832496 CNV gain 17160897
nsv559920 CNV loss 21841781
nsv559919 CNV loss 21841781
nsv559918 CNV loss 21841781
nsv455696 CNV loss 19166990
nsv1051515 CNV gain 25217958
esv2746267 CNV deletion 23290073

Variation tolerance for APAF1 Gene

Residual Variation Intolerance Score: 10.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.49; 55.27% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for APAF1 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 APAF1 Gene

Disorders for APAF1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for APAF1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
  • dystrophinopathy
alzheimer disease mitochondrial
  • ad-mt
rectal neoplasm
  • neoplasm of rectum
lung cancer
  • lung cancer, protection against
lateral sclerosis
  • adult-onset primary lateral sclerosis
- elite association - COSMIC cancer census association via MalaCards
Search APAF1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for APAF1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with APAF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for APAF1 Gene

Publications for APAF1 Gene

  1. Allelic imbalance of 12q22-23 associated with APAF-1 locus correlates with poor disease outcome in cutaneous melanoma. (PMID: 15026369) Fujimoto A … Hoon DS (Cancer research 2004) 3 22 45 60
  2. APAF-1-ALT, a novel alternative splicing form of APAF-1, potentially causes impeded ability of undergoing DNA damage-induced apoptosis in the LNCaP human prostate cancer cell line. (PMID: 12804598) Ogawa T … Furukawa T (Biochemical and biophysical research communications 2003) 3 4 22 60
  3. Cytochrome c and dATP-mediated oligomerization of Apaf-1 is a prerequisite for procaspase-9 activation. (PMID: 10364241) Saleh A … Alnemri ES (The Journal of biological chemistry 1999) 3 4 22 60
  4. Role of cytochrome c and dATP/ATP hydrolysis in Apaf-1-mediated caspase-9 activation and apoptosis. (PMID: 10393175) Hu Y … Núñez G (The EMBO journal 1999) 3 4 22 60
  5. Three new types of Apaf-1 in mammalian cells. (PMID: 10441496) Hahn C … Stein H (Biochemical and biophysical research communications 1999) 3 4 22 60

Products for APAF1 Gene

  • Addgene plasmids for APAF1

Sources for APAF1 Gene

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