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    ARFGAP1 ARF GTPase activating protein 1 [ Homo sapiens (human) ]

    Gene ID: 55738, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ARFGAP1provided by HGNC
    Official Full Name
    ARF 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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63272813..63289790)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65078685..65095673)
    RS_2024_09 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 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. Expression, purification, and properties of ADP-ribosylation factor (ARF) GTPase activating protein-1. Huber I, et al. Methods Enzymol, 2001. PMID 11210549
    2. 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
    3. GAP control: regulating the regulators of small GTPases. Bernards A, et al. Trends Cell Biol, 2004 Jul. PMID 15246431
    4. ArfGAP1 activity and COPI vesicle biogenesis. Beck R, et al. Traffic, 2009 Mar. PMID 19055691
    5. ArfGAP1 inhibits mTORC1 lysosomal localization and activation. Meng D, et al. EMBO J, 2021 Jun 15. PMID 33988249, Free PMC Article

    See all (106) 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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    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
    ADP ribosylation factor GTPase activating protein 1
    ARF1-directed GTPase-activating protein

    NCBI Reference Sequences (RefSeq)

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    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.

    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_2024_08

    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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