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ARFGAP2 ARF GTPase activating protein 2 [ Homo sapiens (human) ]

Gene ID: 84364, updated on 3-Nov-2024

Summary

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Official Symbol
ARFGAP2provided by HGNC
Official Full Name
ARF GTPase activating protein 2provided by HGNC
Primary source
HGNC:HGNC:13504
See related
Ensembl:ENSG00000149182 MIM:606908; AllianceGenome:HGNC:13504
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IRZ; ZFP289; ZNF289; NBLA10535
Summary
Predicted to enable GTPase activator activity. Predicted to be involved in COPI coating of Golgi vesicle. Located in Golgi apparatus; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in skin (RPKM 24.0), brain (RPKM 23.0) and 25 other tissues See more
Orthologs
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Genomic context

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See ARFGAP2 in Genome Data Viewer
Location:
11p11.2
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47164301..47176879, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47321070..47333633, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47185852..47198430, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene centriolar satellite-associated tubulin polyglutamylase complex regulator 1 Neighboring gene uncharacterized LOC124902671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4687 Neighboring gene uncharacterized LOC124902672 Neighboring gene Sharpr-MPRA regulatory region 11477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3321 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47198949-47199530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:47207755-47208641 Neighboring gene protein kinase C and casein kinase substrate in neurons 3 Neighboring gene microRNA 6745 Neighboring gene ribosomal protein S20 pseudogene 26

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. ARFGAP2 and ARFGAP3 are essential for COPI coat assembly on the Golgi membrane of living cells. Kartberg F, et al. J Biol Chem, 2010 Nov 19. PMID 20858901, Free PMC Article
  2. Distinct role of subcomplexes of the COPI coat in the regulation of ArfGAP2 activity. Pevzner I, et al. Traffic, 2012 Jun. PMID 22375848
  3. Molecular cloning and characterization of a zinc finger protein involved in Id-1-stimulated mammary epithelial cell growth. Singh J, et al. J Biol Chem, 2001 Apr 13. PMID 11278321
  4. Two human ARFGAPs associated with COP-I-coated vesicles. Frigerio G, et al. Traffic, 2007 Nov. PMID 17760859, Free PMC Article
  5. Three homologous ArfGAPs participate in coat protein I-mediated transport. Saitoh A, et al. J Biol Chem, 2009 May 15. PMID 19299515, Free PMC Article

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. analysis of the distinct role of subcomplexes of the COPI coat in the regulation of ArfGAP2 activity
    Title: Distinct role of subcomplexes of the COPI coat in the regulation of ArfGAP2 activity.
  2. ARFGAP2 and ARFGAP3 are essential for COPI coat assembly on the Golgi membrane of living cells.
    Title: ARFGAP2 and ARFGAP3 are essential for COPI coat assembly on the Golgi membrane of living cells.
  3. ArfGAP1, ArfGAP2, and ArfGAP3 have overlapping roles in regulating COPI function in Golgi-to-ER retrograde transport.
    Title: Three homologous ArfGAPs participate in coat protein I-mediated transport.
  4. Differential roles of ArfGAP1, ArfGAP2, and ArfGAP3 in COPI trafficking
    Title: Differential roles of ArfGAP1, ArfGAP2, and ArfGAP3 in COPI trafficking.
  5. human ARFGAP2 and ARFGAP3 are associated with COP-I-coated vesicles and function in COP I traffic
    Title: Two human ARFGAPs associated with COP-I-coated vesicles.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies ARFGAP2, 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

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ14576, FLJ26000

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in COPI coating of Golgi vesicle 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 Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
ADP-ribosylation factor GTPase-activating protein 2
Names
ADP ribosylation factor GTPase activating protein 2
GTPase-activating protein ZNF289
zinc finger protein 289, ID1 regulated

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001242832.2 → NP_001229761.1  ADP-ribosylation factor GTPase-activating protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001229761.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AC090589
    Consensus CDS
    CCDS73283.1
    UniProtKB/TrEMBL
    G5E9L0
    Related
    ENSP00000400226.3, ENST00000426335.6
    Conserved Domains (2) summary
    PLN03114
    Location:1 → 443
    PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
    pfam01412
    Location:11 → 117
    ArfGap; Putative GTPase activating protein for Arf

  2. NM_001410995.1 → NP_001397924.1  ADP-ribosylation factor GTPase-activating protein 2 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC090589
    Consensus CDS
    CCDS91467.1
    UniProtKB/TrEMBL
    E9PN48
    Related
    ENSP00000434809.2, ENST00000525314.6

  3. NM_032389.6 → NP_115765.2  ADP-ribosylation factor GTPase-activating protein 2 isoform 1

    See identical proteins and their annotated locations for NP_115765.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC090589
    Consensus CDS
    CCDS7926.1
    UniProtKB/Swiss-Prot
    B4DX29, B7Z9M7, D3DQQ9, Q3LIF2, Q8N3I1, Q8N6H7, Q96SX7
    Related
    ENSP00000434442.1, ENST00000524782.6
    Conserved Domains (2) summary
    PLN03114
    Location:1 → 471
    PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
    cd09029
    Location:5 → 124
    ArfGap_ArfGap2; Arf1 GTPase-activating protein 2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    47164301..47176879 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017018413.2 → XP_016873902.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X4

    Conserved Domains (2) summary
    PLN03114
    Location:1 → 485
    PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
    cd09029
    Location:5 → 124
    ArfGap_ArfGap2; Arf1 GTPase-activating protein 2

  2. XM_005253167.2 → XP_005253224.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X2

    Conserved Domains (3) summary
    PLN03114
    Location:1 → 499
    PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
    pfam01412
    Location:11 → 117
    ArfGap; Putative GTPase activating protein for Arf
    cl23720
    Location:255 → 327
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

  3. XM_006718346.3 → XP_006718409.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X3

    Conserved Domains (3) summary
    PLN03114
    Location:1 → 496
    PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
    pfam01412
    Location:11 → 117
    ArfGap; Putative GTPase activating protein for Arf
    cl23720
    Location:252 → 324
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

  4. XM_005253166.3 → XP_005253223.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X1

    Conserved Domains (3) summary
    PLN03114
    Location:1 → 510
    PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
    pfam01412
    Location:11 → 117
    ArfGap; Putative GTPase activating protein for Arf
    cl23720
    Location:266 → 338
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    47321070..47333633 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370184.1 → XP_054226159.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X4

  2. XM_054370182.1 → XP_054226157.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X2

  3. XM_054370183.1 → XP_054226158.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X3

  4. XM_054370181.1 → XP_054226156.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N6H7.1 GenPept UniProtKB/Swiss-Prot:Q8N6H7

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