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Aliases for AGAP1 Gene

Aliases for AGAP1 Gene

  • ArfGAP With GTPase Domain, Ankyrin Repeat And PH Domain 1 2 3 5
  • GTP-Binding And GTPase-Activating Protein 1 3 4
  • Centaurin, Gamma 2 2 3
  • Cnt-G2 3 4
  • CENTG2 3 4
  • AGAP-1 3 4
  • GGAP1 3 4
  • Arf GAP With GTP-Binding Protein-Like, ANK Repeat And PH Domains 1 3
  • Arf-GAP With GTPase, ANK Repeat And PH Domain-Containing Protein 1 3
  • Centaurin-Gamma-2 4
  • KIAA1099 4

External Ids for AGAP1 Gene

Previous HGNC Symbols for AGAP1 Gene

  • CENTG2

Previous GeneCards Identifiers for AGAP1 Gene

  • GC02P236068
  • GC02P236402
  • GC02P228413

Summaries for AGAP1 Gene

Entrez Gene Summary for AGAP1 Gene

  • This gene encodes a member of an ADP-ribosylation factor GTPase-activating protein family involved in membrane trafficking and cytoskeleton dynamics. This gene functions as a direct regulator of the adaptor-related protein complex 3 on endosomes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

GeneCards Summary for AGAP1 Gene

AGAP1 (ArfGAP With GTPase Domain, Ankyrin Repeat And PH Domain 1) is a Protein Coding gene. Diseases associated with AGAP1 include Retinitis Pigmentosa 13. Among its related pathways are Endocytosis. Gene Ontology (GO) annotations related to this gene include GTP binding and phospholipid binding. An important paralog of this gene is AGAP3.

UniProtKB/Swiss-Prot for AGAP1 Gene

  • GTPase-activating protein for ARF1 and, to a lesser extent, ARF5. Directly and specifically regulates the adapter protein 3 (AP-3)-dependent trafficking of proteins in the endosomal-lysosomal system.

Gene Wiki entry for AGAP1 Gene

Additional gene information for AGAP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for AGAP1 Gene

Genomics for AGAP1 Gene

GeneHancer (GH) Regulatory Elements for AGAP1 Gene

Promoters and enhancers for AGAP1 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
GH02J235492 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 653.4 +0.1 107 4.3 ARID4B SIN3A ZNF48 ETS1 ZNF143 MXD4 ZNF592 SSRP1 SETDB1 CTCF AGAP1 AGAP1-IT1
GH02J235541 Enhancer 1.2 Ensembl ENCODE 6.2 +49.5 49462 3.5 FOXA2 MLX ZFP64 ARID4B NEUROD1 SIN3A DMAP1 ZNF48 ETS1 YY1 AGAP1 AGAP1-IT1 PIR48120
GH02J236086 Enhancer 0.5 ENCODE 11.3 +593.1 593132 1.1 PCBP2 PKNOX1 NANOG BACH1 ETS1 RNU7-127P AGAP1 GC02P236082 PIR53345
GH02J235723 Enhancer 1 Ensembl ENCODE dbSUPER 5.5 +231.5 231527 3.5 CEBPB EP300 ZNF644 SREBF1 CEBPA HNF4A RCOR1 CHD2 AGAP1 PIR61578 GC02P235746 LOC105373943
GH02J235747 Enhancer 0.8 ENCODE dbSUPER 5.7 +254.5 254485 2.9 KLF1 MXI1 MAX KLF17 CEBPB EP300 ATF2 POLR2A RCOR1 ATF7 GC02P235753 PIR31689 PIR31730 PIR61585 LOC105373942 AGAP1 PIR48898
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around AGAP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the AGAP1 gene promoter:
  • AP-1
  • c-Jun
  • ATF-2
  • RSRFC4
  • E47
  • Tal-1
  • STAT5A

Genomic Locations for AGAP1 Gene

Genomic Locations for AGAP1 Gene
637,712 bases
Plus strand
637,712 bases
Plus strand

Genomic View for AGAP1 Gene

Genes around AGAP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AGAP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AGAP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AGAP1 Gene

Proteins for AGAP1 Gene

  • Protein details for AGAP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • B2RTX7
    • Q541S5
    • Q6P9D7
    • Q9NV93

    Protein attributes for AGAP1 Gene

    857 amino acids
    Molecular mass:
    94470 Da
    Quaternary structure:
    • Homodimer. Interacts with several subunits of the AP-3 protein complex: AP3M1, AP3S1 and AP3S2. Interacts with GUCY1A3 and GUCY1B3.
    • Sequence=AAH60814.1; Type=Miscellaneous discrepancy; Note=A 4-nucleotides insertion of unknown origin disrupts the reading frame.; Evidence={ECO:0000305}; Sequence=BAA83051.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAA91862.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for AGAP1 Gene


neXtProt entry for AGAP1 Gene

Post-translational modifications for AGAP1 Gene

No data available for DME Specific Peptides for AGAP1 Gene

Domains & Families for AGAP1 Gene

Suggested Antigen Peptide Sequences for AGAP1 Gene

Graphical View of Domain Structure for InterPro Entry



  • The PH domain mediates AP-3 binding.
  • Belongs to the centaurin gamma-like family.
  • The PH domain mediates AP-3 binding.
  • Belongs to the centaurin gamma-like family.
genes like me logo Genes that share domains with AGAP1: view

Function for AGAP1 Gene

Molecular function for AGAP1 Gene

UniProtKB/Swiss-Prot Function:
GTPase-activating protein for ARF1 and, to a lesser extent, ARF5. Directly and specifically regulates the adapter protein 3 (AP-3)-dependent trafficking of proteins in the endosomal-lysosomal system.
UniProtKB/Swiss-Prot EnzymeRegulation:
GAP activity stimulated by phosphatidylinositol 3,4,5-trisphosphate (PIP3) and, to a lesser extent, by phosphatidylinositol 4,5-bisphosphate (PIP2). Phosphatidic acid potentiates PIP2 stimulation.

Phenotypes From GWAS Catalog for AGAP1 Gene

Gene Ontology (GO) - Molecular Function for AGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003924 GTPase activity IEA --
GO:0005096 GTPase activator activity IEA --
GO:0005515 protein binding IEA --
GO:0005525 GTP binding IEA --
GO:0005543 phospholipid binding IDA 18954304
genes like me logo Genes that share ontologies with AGAP1: view
genes like me logo Genes that share phenotypes with AGAP1: view

Animal Models for AGAP1 Gene

MGI Knock Outs for AGAP1:
  • Agap1 Agap1<tm1a(EUCOMM)Wtsi>

Animal Model Products

miRNA for AGAP1 Gene

miRTarBase miRNAs that target AGAP1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for AGAP1 Gene

Localization for AGAP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AGAP1 Gene

Cytoplasm. Note=Associates with the endocytic compartment.

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 AGAP1 gene
Compartment Confidence
nucleus 3
cytosol 3
golgi apparatus 1
endosome 1

Gene Ontology (GO) - Cellular Components for AGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IBA --
GO:0016020 membrane IBA --
GO:0043231 intracellular membrane-bounded organelle IBA --
genes like me logo Genes that share ontologies with AGAP1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for AGAP1 Gene

Pathways & Interactions for AGAP1 Gene

SuperPathways for AGAP1 Gene

SuperPathway Contained pathways
1 Endocytosis
genes like me logo Genes that share pathways with AGAP1: view

Pathways by source for AGAP1 Gene

1 KEGG pathway for AGAP1 Gene

Gene Ontology (GO) - Biological Process for AGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IBA --
GO:0032012 regulation of ARF protein signal transduction IBA --
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with AGAP1: view

No data available for SIGNOR curated interactions for AGAP1 Gene

Drugs & Compounds for AGAP1 Gene

(1) Drugs for AGAP1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0

(12) Additional Compounds for AGAP1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 1,2-Dipalmitoyl-3-sn-phosphatidic acid
  • 1,2-Dipalmitoyl-sn-glycerol-3-phosphate
  • 1,2-Dipalmitoyl-sn-glycerol-3-phosphoric acid
  • Dipalmitoyl phosphatidic acid
  • PA(32:0)
  • 1-Hexadecanoyl-2-(11Z-octadecenoyl)-sn-phosphatidic acid
  • 1-Palmitoyl-2-vaccenoyl-sn-glycero-3-phosphate
  • PA(16:0/18:1)
  • PA(16:0/18:1N7)
  • PA(16:0/18:1W7)
  • (2R)-1-(Palmitoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
  • 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphate
  • 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol 3-phosphate
  • 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-phosphatidic acid
  • PA(16:0/18:1)
  • 1-16:0-2-18:2-Phosphatidic acid
  • 1-Palmitoyl-2-linoleoyl-sn-glycero-3-phosphate
  • 16:0-18:2-PA
  • 2-Linoleoyl-1-palmitoyl-sn-glycero-3-phosphate
  • PA(16:0/18:2)
  • 2-Octadecanoyl-1-hexadecyl-sn-glycero-3-phosphate
  • PA(O-16:0/18:0)
genes like me logo Genes that share compounds with AGAP1: view

Transcripts for AGAP1 Gene

Unigene Clusters for AGAP1 Gene

ArfGAP with GTPase domain, ankyrin repeat and PH domain 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for AGAP1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14
SP1: - -
SP2: - -

Relevant External Links for AGAP1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for AGAP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AGAP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for AGAP1 Gene

This gene is overexpressed in Urine (33.0), Fetal Brain (13.0), and Brain (8.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for AGAP1 Gene

Protein tissue co-expression partners for AGAP1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of AGAP1 Gene:


SOURCE GeneReport for Unigene cluster for AGAP1 Gene:


mRNA Expression by UniProt/SwissProt for AGAP1 Gene:

Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for AGAP1 Gene

  • Nervous system(4.7)
  • Heart(4.1)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with AGAP1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for AGAP1 Gene

Orthologs for AGAP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for AGAP1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia AGAP1 34
  • 99 (a)
(Bos Taurus)
Mammalia AGAP1 34
  • 96 (a)
(Canis familiaris)
Mammalia AGAP1 34 33
  • 92.14 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 91 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 91 (a)
(Mus musculus)
Mammalia Agap1 16 34 33
  • 89.73 (n)
(Rattus norvegicus)
Mammalia Agap1 33
  • 87.89 (n)
(Gallus gallus)
Aves -- 34
  • 96 (a)
AGAP1 33
  • 84.99 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 91 (a)
-- 34
  • 66 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia agap1 33
  • 77.76 (n)
(Danio rerio)
Actinopterygii agap1 34 33
  • 78.16 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009160 33
  • 58.7 (n)
fruit fly
(Drosophila melanogaster)
Insecta cenG1A 34 33
  • 55.98 (n)
(Caenorhabditis elegans)
Secernentea cnt-2 34 33
  • 51.55 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
Cin.13853 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13853 33
Species where no ortholog for AGAP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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 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 AGAP1 Gene

Gene Tree for AGAP1 (if available)
Gene Tree for AGAP1 (if available)
Evolutionary constrained regions (ECRs) for AGAP1: view image

Paralogs for AGAP1 Gene

Paralogs for AGAP1 Gene

(26) SIMAP similar genes for AGAP1 Gene using alignment to 8 proteins:

  • C9J8Z2_HUMAN
  • H7C0A7_HUMAN
  • H7C211_HUMAN
  • H7C3T5_HUMAN Pseudogenes for AGAP1 Gene

genes like me logo Genes that share paralogs with AGAP1: view

Variants for AGAP1 Gene

Sequence variations from dbSNP and Humsavar for AGAP1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000004104 -- 235,534,446(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000016582 -- 235,824,191(+) T/C intron_variant
rs1000018030 -- 235,931,595(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000021552 -- 235,991,525(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000021746 -- 236,035,455(+) T/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for AGAP1 Gene

Variant ID Type Subtype PubMed ID
dgv4191n100 CNV gain 25217958
esv1000874 CNV insertion 20482838
esv1341911 CNV insertion 17803354
esv1723837 CNV insertion 17803354
esv22988 CNV loss 19812545
dgv2364e59 CNV duplication 20981092
dgv2363e59 CNV tandem duplication 20981092
dgv2178n106 CNV deletion 24896259
dgv2177n106 CNV deletion 24896259
nsv999839 CNV gain 25217958
nsv979188 CNV duplication 23825009
nsv961575 CNV duplication 23825009
nsv954221 CNV deletion 24416366
nsv834575 CNV gain 17160897
nsv821922 CNV gain 20364138
nsv821919 CNV gain 20364138
nsv584721 CNV loss 21841781
nsv584720 CNV loss 21841781
nsv527654 CNV gain 19592680
nsv524185 CNV loss 19592680
nsv522224 CNV gain 19592680
nsv460141 CNV loss 19166990
nsv214308 CNV insertion 16902084
nsv213603 CNV deletion 16902084
nsv1147547 CNV insertion 26484159
nsv1143972 CNV deletion 24896259
nsv1142982 CNV tandem duplication 24896259
nsv1131562 CNV deletion 24896259
nsv1123441 CNV deletion 24896259
nsv1072504 CNV deletion 25765185
nsv1072503 CNV deletion 25765185
nsv1072083 CNV deletion 25765185
nsv1072082 CNV deletion 25765185
nsv1009153 CNV loss 25217958
nsv1007000 CNV gain 25217958
nsv1000252 CNV loss 25217958
esv3594720 CNV loss 21293372
esv3594719 CNV loss 21293372
esv3594717 CNV loss 21293372
esv3594716 CNV loss 21293372
esv3594715 CNV loss 21293372
esv3594713 CNV loss 21293372
esv3594712 CNV loss 21293372
esv3584379 CNV loss 25503493
esv3575341 CNV gain 25503493
esv3561212 CNV deletion 23714750
esv3561209 CNV deletion 23714750
esv3439920 CNV insertion 20981092
esv3429143 CNV duplication 20981092
esv33938 CNV loss 17666407
esv275222 CNV loss 21479260
esv2751845 CNV gain 17911159
esv2721700 CNV deletion 23290073
esv2721699 CNV deletion 23290073
esv2721698 CNV deletion 23290073
esv2721697 CNV deletion 23290073
esv2721693 CNV deletion 23290073
esv2721692 CNV deletion 23290073
esv2721691 CNV deletion 23290073
esv2721690 CNV deletion 23290073
esv2721689 CNV deletion 23290073
esv2721688 CNV deletion 23290073
esv2721687 CNV deletion 23290073
esv2675448 CNV deletion 23128226
esv2670324 CNV deletion 23128226
esv2661531 CNV deletion 23128226
esv2659699 CNV deletion 23128226
esv2647729 CNV insertion 19546169
esv2521379 CNV deletion 19546169
esv25019 CNV loss 19812545
esv24255 CNV loss 19812545
esv2424821 CNV deletion 19546169

Variation tolerance for AGAP1 Gene

Residual Variation Intolerance Score: 9.78% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.99; 80.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for AGAP1 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AGAP1 Gene

Disorders for AGAP1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for AGAP1 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 13
  • rp13
- elite association - COSMIC cancer census association via MalaCards
Search AGAP1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for AGAP1

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 AGAP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for AGAP1 Gene

Publications for AGAP1 Gene

  1. The Arf GAPs AGAP1 and AGAP2 distinguish between the adaptor protein complexes AP-1 and AP-3. (PMID: 16079295) Nie Z … Randazzo PA (Journal of cell science 2005) 3 4 22 58
  2. Evaluation of the chromosome 2q37.3 gene CENTG2 as an autism susceptibility gene. (PMID: 15892143) Wassink TH … Sheffield VC (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2005) 3 4 22 58
  3. AGAP1, a novel binding partner of nitric oxide-sensitive guanylyl cyclase. (PMID: 15381706) Meurer S … Gross S (The Journal of biological chemistry 2004) 3 4 22 58
  4. AGAP1, an endosome-associated, phosphoinositide-dependent ADP-ribosylation factor GTPase-activating protein that affects actin cytoskeleton. (PMID: 12388557) Nie Z … Randazzo PA (The Journal of biological chemistry 2002) 3 4 22 58
  5. Genome-wide association study identifies five new schizophrenia loci. (PMID: 21926974) Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium (Nature genetics 2011) 3 44 58

Products for AGAP1 Gene

Sources for AGAP1 Gene

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