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Aliases for APAF1 Gene

Aliases for APAF1 Gene

  • Apoptotic Peptidase Activating Factor 1 2 3
  • APAF-1 3 4
  • 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 nephronophthisis 13 and cranioectodermal dysplasia 4. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and ERK Signaling. GO annotations related to this gene include identical protein binding and ADP binding. An important paralog of this gene is WDR3.

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

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

Genomics for APAF1 Gene

Regulatory Elements for APAF1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for APAF1 Gene

98,645,141 bp from pter
98,735,433 bp from pter
90,293 bases
Plus strand

Genomic View for APAF1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for APAF1 Gene at MOPED

Post-translational modifications for APAF1 Gene

  • Ubiquitination at Lys 809
  • Modification sites at PhosphoSitePlus

Antibody Products

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

No data available for DME Specific Peptides for APAF1 Gene

Domains & Families for APAF1 Gene

Suggested Antigen Peptide Sequences for APAF1 Gene

Graphical View of Domain Structure for InterPro Entry



  • The CARD domain mediates interaction with APIP
  • Contains 15 WD repeats.
  • 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).
  • Contains 1 CARD domain.
  • Contains 1 NB-ARC domain.
  • Contains 15 WD repeats.
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.

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 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

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for APAF1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , 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

Jensen Localization Image for APAF1 Gene COMPARTMENTS Subcellular localization image for APAF1 gene
Compartment Confidence
cytosol 5
extracellular 5
mitochondrion 3
golgi apparatus 2
nucleus 2
endoplasmic reticulum 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for APAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005829 cytosol TAS --
GO:0043293 apoptosome TAS 18309324
GO:0070062 extracellular exosome IDA 19056867
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

PCR Array Products

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 --
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process IDA 21827945
GO:0007275 multicellular organismal development --
genes like me logo Genes that share ontologies with APAF1: view

Drugs & Compounds for APAF1 Gene

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine triphosphate Approved Nutra Target 0
Bortezomib Approved, Experimental, Investigational Pharma Proteosome and NF-kappaB inhibitor, Other, Proteasome inhibitors 758
Celecoxib Approved, Investigational Pharma Inhibition, Inhibitor Selective cyclooxygenase-2 (COX-2) inhibitor 395
Cisplatin Approved Pharma Inhibits DNA synthesis,chemotherapy drug, Platinum, Potent pro-apoptotic anticancer agent; activates caspase-3 2437
Cytarabine Approved, Investigational Pharma 995

(19) Additional Compounds for APAF1 Gene - From: NovoSeek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Antagonist, Gating inhibitor 58-64-0
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:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for APAF1

Flow Cytometry Products

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 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, MOPED, and MaxQB for APAF1 Gene

SOURCE GeneReport for Unigene cluster for APAF1 Gene Hs.552567

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
genes like me logo Genes that share expression patterns with APAF1: view

Protein tissue co-expression partners for APAF1 Gene

- Elite partner

Primer Products

In Situ Assay Products

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 36
  • 99 (a)
APAF1 35
  • 99.63 (n)
  • 99.44 (a)
(Ornithorhynchus anatinus)
Mammalia APAF1 36
  • 81 (a)
(Mus musculus)
Mammalia Apaf1 36
  • 87 (a)
Apaf1 16
Apaf1 35
  • 86 (n)
  • 87.42 (a)
(Monodelphis domestica)
Mammalia APAF1 36
  • 80 (a)
(Canis familiaris)
Mammalia APAF1 36
  • 87 (a)
APAF1 35
  • 91.77 (n)
  • 91.03 (a)
(Bos Taurus)
Mammalia APAF1 36
  • 90 (a)
APAF1 35
  • 90.81 (n)
  • 90.46 (a)
(Rattus norvegicus)
Mammalia Apaf1 35
  • 85.36 (n)
  • 87.42 (a)
(Gallus gallus)
Aves APAF1 36
  • 70 (a)
APAF1 35
  • 72.4 (n)
  • 70.04 (a)
(Anolis carolinensis)
Reptilia APAF1 36
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia apaf1 35
  • 67.19 (n)
  • 66.46 (a)
(Danio rerio)
Actinopterygii apaf1 36
  • 54 (a)
apaf1 35
  • 59.54 (n)
  • 55.5 (a)
-- 35
fruit fly
(Drosophila melanogaster)
Insecta CG30116 36
  • 10 (a)
(Caenorhabditis elegans)
Secernentea qui-1 36
  • 8 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DIP2 36
  • 15 (a)
Species with no ortholog for APAF1:
  • 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 MAF
rs919699 -- 98,690,548(-) CAGAA(C/T)TTGGA intron-variant
rs1007573 -- 98,698,843(-) AATAC(C/T)GTAAA intron-variant
rs1148446 -- 98,727,690(-) gtgct(A/G)ggatt intron-variant
rs1195707 -- 98,672,437(-) ctgta(A/G)tccca intron-variant
rs1195708 -- 98,672,416(-) aggcc(A/G)aggca intron-variant

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

Variant ID Type Subtype PubMed ID
nsv832496 CNV Gain 17160897
esv2746267 CNV Deletion 23290073
nsv455696 CNV Loss 19166990
nsv844 CNV Insertion 18451855

Variation tolerance for APAF1 Gene

Residual Variation Intolerance Score: 10.92% 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

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APAF1 Gene

Disorders for APAF1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for APAF1 Gene - From: OMIM, DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
nephronophthisis 13
  • nphp13
cranioectodermal dysplasia 4
  • sensenbrenner syndrome 4
short-rib thoracic dysplasia 5 with or without polydactyly
  • asphyxiating thoracic dystrophy 5
senior-loken syndrome 8
  • slsn8
  • dystrophinopathy
- elite association
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. Novel small molecules relieve prothymosin alpha-mediated inhibition of apoptosome formation by blocking its interaction with Apaf-1. (PMID: 20121050) Qi X. … Du F. (Biochemistry 2010) 23 67
  2. Comparative proteomics analysis of caspase-9-protein complexes in untreated and cytochrome c/dATP stimulated lysates of NSCLC cells. (PMID: 19118655) Checinska A. … Jimenez C.R. (J. Proteomics 2009) 23 67
  3. Oxidative modification of caspase-9 facilitates its activation via disulfide-mediated interaction with Apaf-1. (PMID: 19238172) Zuo Y. … Yi J. (Cell Res. 2009) 23 67
  4. Effects of 5-Aza-CdR on the proliferation of human breast cancer cell line MCF-7 and on the expression of Apaf-1 gene. (PMID: 19662370) Xiong H. … Chen Y. (J. Huazhong Univ. Sci. Technol. Med. Sci. 2009) 23 67
  5. [Apoptotic protease activating factor 1 inducing apoptosis and related anti-tumor therapy -- review]. (PMID: 19236791) He L.L. … Zhang P.T. (Zhongguo Shi Yan Xue Ye Xue Za Zhi 2009) 23 67

Products for APAF1 Gene

Sources for APAF1 Gene

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