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ARFGAP1 ADP ribosylation factor GTPase activating protein 1 [ Homo sapiens (human) ]

Gene ID: 55738, updated on 7-Apr-2024

Summary

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Official Symbol
ARFGAP1provided by HGNC
Official Full Name
ADP ribosylation factor GTPase activating protein 1provided by HGNC
Primary source
HGNC:HGNC:15852
See related
Ensembl:ENSG00000101199 MIM:608377; AllianceGenome:HGNC:15852
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
ARF1GAP; HRIHFB2281
Summary
The protein encoded by this gene is a GTPase-activating protein, which associates with the Golgi apparatus and which interacts with ADP-ribosylation factor 1. The encoded protein promotes hydrolysis of ADP-ribosylation factor 1-bound GTP and is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is required for the fusion of these vesicles with target compartments. The activity of this protein is stimulated by phosphoinosides and inhibited by phosphatidylcholine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
Expression
Ubiquitous expression in spleen (RPKM 11.8), testis (RPKM 11.1) and 25 other tissues See more
Orthologs
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Genomic context

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See ARFGAP1 in Genome Data Viewer
Location:
20q13.33
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63272813..63289790)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65078685..65095673)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61904165..61921142)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61879175-61880007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61880008-61880839 Neighboring gene sodium/potassium transporting ATPase interacting 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61883491-61883999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61885071-61885602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61885603-61886134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61889508-61890125 Neighboring gene uncharacterized LOC100192386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61891361-61891976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61915538-61916038 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr20:61922048-61922671 and GRCh37_chr20:61922672-61923296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61924431-61924932 Neighboring gene microRNA 4326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61924933-61925432 Neighboring gene collagen type XX alpha 1 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61952290-61952790 Neighboring gene RNA, U6 small nuclear 994, pseudogene

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. ArfGAP1 inhibits mTORC1 lysosomal localization and activation. Meng D, et al. EMBO J, 2021 Jun 15. PMID 33988249, Free PMC Article
  2. ArfGAP1 restricts Mycobacterium tuberculosis entry by controlling the actin cytoskeleton. Song OR, et al. EMBO Rep, 2018 Jan. PMID 29141986, Free PMC Article
  3. ARFGAP1 is dynamically associated with lipid droplets in hepatocytes. Gannon J, et al. PLoS One, 2014. PMID 25397679, Free PMC Article
  4. ArfGAP1 activity and COPI vesicle biogenesis. Beck R, et al. Traffic, 2009 Mar. PMID 19055691
  5. Kinetic analysis of Arf GAP1 indicates a regulatory role for coatomer. Luo R, et al. J Biol Chem, 2008 Aug 8. PMID 18541532, Free PMC Article

See all (92) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. C9orf72 Toxic Species Affect ArfGAP-1 Function.
    Title: C9orf72 Toxic Species Affect ArfGAP-1 Function.
  2. ArfGAP1 inhibits mTORC1 lysosomal localization and activation.
    Title: ArfGAP1 inhibits mTORC1 lysosomal localization and activation.
  3. ArfGAP1 acts as a GTPase-activating protein for human ADP-ribosylation factor-like 1 protein.
    Title: ArfGAP1 acts as a GTPase-activating protein for human ADP-ribosylation factor-like 1 protein.
  4. ArfGAP1 restricts Mycobacterium tuberculosis entry by controlling the actin cytoskeleton.
    Title: ArfGAP1 restricts Mycobacterium tuberculosis entry by controlling the actin cytoskeleton.
  5. ARFGAP1 is found associated with lipid droplets at steady state in some but not all hepatocytes.
    Title: ARFGAP1 is dynamically associated with lipid droplets in hepatocytes.
  6. ARFGAP1 is a host factor for Hepatitis C Virus RNA replication, and is hijacked by HCV NS5A to remove COPI cargo Sac1 from the site of HCV replication to maintain high levels of PI4P.
    Title: Hepatitis C virus NS5A hijacks ARFGAP1 to maintain a phosphatidylinositol 4-phosphate-enriched microenvironment.
  7. ArfGAP1 is identified as the first GTPase activating protein (GAP) for leucine-rich repeat kinase 2 (LRRK2).
    Title: ArfGAP1 is a GTPase activating protein for LRRK2: reciprocal regulation of ArfGAP1 by LRRK2.
  8. role of ARFGAP1 in AP-2-regulated endocytosis has mechanistic parallels with its roles in COPI transport, as both its GAP activity and coat function contribute to promoting AP-2 transport
    Title: ARFGAP1 promotes AP-2-dependent endocytosis.
  9. 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.
  10. catalytic amounts of Arf1GAP1 significantly reduce the yield of purified COPI vesicles
    Title: ArfGAP1 activity and COPI vesicle biogenesis.
Submit: New GeneRIF Correction See all GeneRIFs (15)

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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC39924

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of ARF protein signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in synapse IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ADP-ribosylation factor GTPase-activating protein 1
Names
ARF1-directed GTPase-activating protein

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_001281482.2 → NP_001268411.1  ADP-ribosylation factor GTPase-activating protein 1 isoform c

    See identical proteins and their annotated locations for NP_001268411.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the coding region, which results in a translational frameshift, compared to variant 2. The encoded isoform (c) has a shorter and distinct C-terminus, compared to isoform b.
    Source sequence(s)
    AA565406, BC000786, DC300118
    Consensus CDS
    CCDS63326.1
    UniProtKB/Swiss-Prot
    Q8N6T3
    Related
    ENSP00000359298.4, ENST00000370275.8
    Conserved Domains (1) summary
    pfam01412
    Location:7 → 114
    ArfGap; Putative GTPase activating protein for Arf

  2. NM_001281483.2 → NP_001268412.1  ADP-ribosylation factor GTPase-activating protein 1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 2. The encoded isoform (d) has a shorter and distinct N-terminus, compared to isoform b.
    Source sequence(s)
    AA565406, AK296351, BC000786
    Consensus CDS
    CCDS63327.1
    UniProtKB/TrEMBL
    F8VWH9
    Related
    ENSP00000430500.1, ENST00000519604.5
    Conserved Domains (1) summary
    cl02464
    Location:4 → 61
    ArfGap; Putative GTPase activating protein for Arf

  3. NM_001281484.2 → NP_001268413.1  ADP-ribosylation factor GTPase-activating protein 1 isoform e

    See identical proteins and their annotated locations for NP_001268413.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two exons in the 5' and central coding region, and initiates translation at an alternate start codon, compared to variant 2. The encoded isoform (e) is shorter and has a distinct N-terminus, compared to isoform b.
    Source sequence(s)
    AA565406, AK303454, AK308161, BC000786, DC404137
    Consensus CDS
    CCDS63328.1
    UniProtKB/Swiss-Prot
    Q8N6T3
    Related
    ENSP00000443716.1, ENST00000519273.6

  4. NM_018209.4 → NP_060679.1  ADP-ribosylation factor GTPase-activating protein 1 isoform a

    See identical proteins and their annotated locations for NP_060679.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 2. The encoded isoform (a) is shorter, compared to isoform b.
    Source sequence(s)
    AA565406, AK223427, BC000786, BC028233, DC300118
    Consensus CDS
    CCDS13515.1
    UniProtKB/Swiss-Prot
    B7Z3U0, B7Z8H8, B7ZBI3, E1P5I9, E7EV62, Q6PK71, Q8N6T3, Q96KC4, Q96T02, Q9NSU3, Q9NVF6, Q9UIL0
    UniProtKB/TrEMBL
    Q53F62
    Related
    ENSP00000359306.4, ENST00000370283.9
    Conserved Domains (1) summary
    pfam01412
    Location:7 → 114
    ArfGap; Putative GTPase activating protein for Arf

  5. NM_175609.3 → NP_783202.1  ADP-ribosylation factor GTPase-activating protein 1 isoform b

    See identical proteins and their annotated locations for NP_783202.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (b).
    Source sequence(s)
    AA565406, BC011876, BC028233, DC300118
    Consensus CDS
    CCDS13516.1
    UniProtKB/TrEMBL
    Q53F62
    Related
    ENSP00000314615.3, ENST00000353546.7
    Conserved Domains (1) summary
    pfam01412
    Location:7 → 114
    ArfGap; Putative GTPase activating protein for Arf

RNA

  1. NR_104022.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate 5' exon structure, compared to variant 2. This variant is represented as non-coding because it lacks a large portion of the coding region, and does not encode a supported protein.
    Source sequence(s)
    AL121827
    Related
    ENST00000468975.6

  2. NR_104023.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) uses an alternate 5' exon structure, compared to variant 2. This variant is represented as non-coding because it lacks a large portion of the coding region, and does not encode a supported protein.
    Source sequence(s)
    AA565406, BC000786, BC127893, BQ717837

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63272813..63289790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047440287.1 → XP_047296243.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X2

    UniProtKB/Swiss-Prot
    B7Z3U0, B7Z8H8, B7ZBI3, E1P5I9, E7EV62, Q6PK71, Q8N6T3, Q96KC4, Q96T02, Q9NSU3, Q9NVF6, Q9UIL0

  2. XM_047440288.1 → XP_047296244.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X3

  3. XM_011528901.2 → XP_011527203.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X1

    UniProtKB/TrEMBL
    Q53F62
    Conserved Domains (1) summary
    pfam01412
    Location:7 → 114
    ArfGap; Putative GTPase activating protein for Arf

  4. XM_006723823.3 → XP_006723886.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X3

    See identical proteins and their annotated locations for XP_006723886.1

    UniProtKB/TrEMBL
    Q53F62
    Conserved Domains (1) summary
    pfam01412
    Location:7 → 114
    ArfGap; Putative GTPase activating protein for Arf

  5. XM_047440289.1 → XP_047296245.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X4

  6. XM_047440290.1 → XP_047296246.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X4

  7. XM_047440291.1 → XP_047296247.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X5

  8. XM_017027950.2 → XP_016883439.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X1

    UniProtKB/TrEMBL
    Q53F62
    Conserved Domains (1) summary
    pfam01412
    Location:7 → 114
    ArfGap; Putative GTPase activating protein for Arf

RNA

  1. XR_001754329.2 RNA Sequence

  2. XR_007067465.1 RNA Sequence

  3. XR_007067467.1 RNA Sequence

  4. XR_007067466.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65078685..65095673
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323682.1 → XP_054179657.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X3

  2. XM_054323680.1 → XP_054179655.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X2

    UniProtKB/Swiss-Prot
    B7Z3U0, B7Z8H8, B7ZBI3, E1P5I9, E7EV62, Q6PK71, Q8N6T3, Q96KC4, Q96T02, Q9NSU3, Q9NVF6, Q9UIL0

  3. XM_054323678.1 → XP_054179653.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X1

  4. XM_054323681.1 → XP_054179656.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X3

  5. XM_054323683.1 → XP_054179658.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X4

  6. XM_054323684.1 → XP_054179659.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X4

  7. XM_054323685.1 → XP_054179660.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X5

  8. XM_054323679.1 → XP_054179654.1  ADP-ribosylation factor GTPase-activating protein 1 isoform X1

RNA

  1. XR_008485273.1 RNA Sequence

  2. XR_008485274.1 RNA Sequence

  3. XR_008485276.1 RNA Sequence

  4. XR_008485275.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N6T3.2 GenPept UniProtKB/Swiss-Prot:Q8N6T3

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