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AGAP1 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 [ Homo sapiens (human) ]

Gene ID: 116987, updated on 4-Feb-2024

Summary

Official Symbol
AGAP1provided by HGNC
Official Full Name
ArfGAP with GTPase domain, ankyrin repeat and PH domain 1provided by HGNC
Primary source
HGNC:HGNC:16922
See related
Ensembl:ENSG00000157985 MIM:608651; AllianceGenome:HGNC:16922
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GGAP1; AGAP-1; CENTG2; cnt-g2
Summary
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]
Expression
Broad expression in brain (RPKM 11.1), colon (RPKM 5.1) and 23 other tissues See more
Orthologs
NEW
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Try the new Transcript table

Genomic context

See AGAP1 in Genome Data Viewer
Location:
2q37.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (235494043..236131793)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (235983538..236621510)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (236402687..237040437)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373940 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:236182269-236182836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236233641-236234543 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:236255926-236257125 Neighboring gene uncharacterized LOC105373941 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:236302767-236303966 Neighboring gene CRISPRi-validated cis-regulatory element chr2.7130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236403941-236404814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236409110-236409715 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236413687-236414193 Neighboring gene AGAP1 intronic transcript 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236475811-236476311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236494510-236495010 Neighboring gene trinucleotide repeat containing 17 Neighboring gene Sharpr-MPRA regulatory region 15430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236505422-236506274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236539863-236540736 Neighboring gene Sharpr-MPRA regulatory region 12909 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236567081-236567736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236599338-236599838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236599839-236600339 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:236617362-236618561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236632223-236632790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236632791-236633358 Neighboring gene uncharacterized LOC105373942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236696882-236697382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236701667-236702167 Neighboring gene Sharpr-MPRA regulatory region 1374 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:236735809-236737008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236757968-236758468 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:236763280-236764479 Neighboring gene VISTA enhancer hs521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236784736-236785236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236785237-236785737 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236801538-236802038 Neighboring gene NANOG hESC enhancer GRCh37_chr2:236812532-236813067 Neighboring gene NANOG hESC enhancer GRCh37_chr2:236813068-236813602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236814296-236814796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236814797-236815297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236842540-236843040 Neighboring gene thymosin beta 10 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236843041-236843541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236859019-236859518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236863470-236863970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236881395-236881894 Neighboring gene uncharacterized LOC124907999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236908700-236909590 Neighboring gene Sharpr-MPRA regulatory region 6211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236921919-236922882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236934624-236935124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236936185-236936684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236943445-236944014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236950015-236950927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236950928-236951839 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236953845-236954624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236955459-236955962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236954625-236955404 Neighboring gene VISTA enhancer hs921 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236970128-236970759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236970760-236971390 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:236979819-236980320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236982603-236983103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236984110-236984614 Neighboring gene RNA, U7 small nuclear 127 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236991437-236991936 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236995415-236996056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237014597-237015120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237015121-237015644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:237017217-237017740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237017741-237018264 Neighboring gene RNA, 7SL, cytoplasmic 204, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237028027-237028769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237028770-237029512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237035362-237035872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237037456-237038393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237044810-237045310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237045311-237045811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237064500-237065288 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:237067303-237068123 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:237068124-237068944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:237068945-237069764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237069765-237070586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:237070587-237071406 Neighboring gene VISTA enhancer hs249 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:237072227-237073046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:237075208-237076160 Neighboring gene uncharacterized LOC124906126 Neighboring gene GBX2 and ASB18 antisense RNA 1 Neighboring gene gastrulation brain homeobox 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Related articles in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
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EBI GWAS Catalog
Genome-wide association study identifies five new schizophrenia loci.
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HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies AGAP1, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA1099, MGC71657

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTP binding IEA
Inferred from Electronic Annotation
more info
 
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables phospholipid binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in activation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
Names
Arf GAP with GTP-binding protein-like, ANK repeat and PH domains 1
GTP-binding and GTPase-activating protein 1
centaurin, gamma 2
NP_001032208.1
NP_001231817.1
NP_001399051.1
NP_055729.2

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_030314.1 RefSeqGene

    Range
    4955..642705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001037131.3NP_001032208.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001032208.1

    Status: REVIEWED

    Source sequence(s)
    AC012305, AC019047, AK001722, AY033765, BC060814, BC140856, BC167153, CA446024
    Consensus CDS
    CCDS33408.1
    UniProtKB/Swiss-Prot
    B2RTX7, Q541S5, Q6P9D7, Q9NV93, Q9UPQ3
    UniProtKB/TrEMBL
    H7C211
    Related
    ENSP00000307634.7, ENST00000304032.13
    Conserved Domains (8) summary
    cd04103
    Location:72229
    Centaurin_gamma; Centaurin gamma (CENTG) GTPase
    smart00173
    Location:73235
    RAS; Ras subfamily of RAS small GTPases
    cd00204
    Location:736825
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:344592
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    pfam00169
    Location:347411
    PH; PH domain
    pfam01412
    Location:611725
    ArfGap; Putative GTPase activating protein for Arf
    pfam12796
    Location:736826
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:768799
    ANK; ANK repeat [structural motif]
  2. NM_001244888.2NP_001231817.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the allele encoded by the GRCh38 reference genome and encodes isoform 3.
    Source sequence(s)
    AC012305, AC064874, BC060814, BC167157
    Consensus CDS
    CCDS58756.1
    UniProtKB/Swiss-Prot
    Q9UPQ3
    UniProtKB/TrEMBL
    B2RZG9
    Related
    ENSP00000387174.1, ENST00000409457.5
    Conserved Domains (2) summary
    cd04103
    Location:72229
    Centaurin_gamma; Centaurin gamma (CENTG) GTPase
    smart00173
    Location:73235
    RAS; Ras subfamily of RAS small GTPases
  3. NM_001412122.1NP_001399051.1  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses the same exon combination as variant 3 but represents the allele encoded by the T2T-CHM13v2.0 genome assembly. It encodes isoform 4 which is shorter and has a distinct C-terminus, compared to isoform 3.
    Source sequence(s)
    CP068276
  4. NM_014914.5NP_055729.2  arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC012305, AC019047, AF413078, AK001722, AY033765, BC060814, BC140856, CA446024
    Consensus CDS
    CCDS2514.1
    UniProtKB/TrEMBL
    B2RZG9
    Related
    ENSP00000338378.5, ENST00000336665.9
    Conserved Domains (8) summary
    cd04103
    Location:72229
    Centaurin_gamma; Centaurin gamma (CENTG) GTPase
    smart00173
    Location:73235
    RAS; Ras subfamily of RAS small GTPases
    cd00204
    Location:683772
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd01250
    Location:344539
    PH_AGAP; Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain
    pfam00169
    Location:347411
    PH; PH domain
    pfam01412
    Location:558672
    ArfGap; Putative GTPase activating protein for Arf
    pfam12796
    Location:683773
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:715746
    ANK; ANK repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    235494043..236131793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    235983538..236621510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)