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    RAB4A RAB4A, member RAS oncogene family [ Homo sapiens (human) ]

    Gene ID: 5867, updated on 29-Oct-2024

    Summary

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    Official Symbol
    RAB4Aprovided by HGNC
    Official Full Name
    RAB4A, member RAS oncogene familyprovided by HGNC
    Primary source
    HGNC:HGNC:9781
    See related
    Ensembl:ENSG00000168118 MIM:179511; AllianceGenome:HGNC:9781
    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
    RAB4; HRES1; HRES-1; HRES-1/RAB4
    Summary
    This gene is a member of the largest group in the Ras superfamily of small GTPases, which regulate membrane trafficking. The encoded protein is associated with early endosomes and is involved in their sorting and recycling. The protein also plays a role in regulating the recycling of receptors from endosomes to the plasma membrane. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2012]
    Expression
    Ubiquitous expression in prostate (RPKM 22.3), heart (RPKM 17.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAB4A in Genome Data Viewer
    Location:
    1q42.13
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (229271111..229305894)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (228649787..228684556)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (229406858..229441641)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723935 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229388645-229389519 Neighboring gene uncharacterized LOC124904540 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:229389520-229390393 Neighboring gene transmembrane protein 78 Neighboring gene RAB4A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1926 Neighboring gene centriole, cilia and spindle associated protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229470989-229471498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1927 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1928 Neighboring gene Sharpr-MPRA regulatory region 13048 Neighboring gene MPRA-validated peak753 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:229516888-229517495 Neighboring gene RNA, U6 small nuclear 180, 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. Rab4 GTP/GDP modulates amiloride-sensitive sodium channel (ENaC) function in colonic epithelia. Saxena SK, et al. Biochem Biophys Res Commun, 2006 Feb 10. PMID 16389071
    2. Laminar Shear Stress Promotes Vascular Endothelial Cell Autophagy Through Upregulation with Rab4. Yao P, et al. DNA Cell Biol, 2016 Mar. PMID 26716952
    3. Cargo-mediated regulation of a rapid Rab4-dependent recycling pathway. Yudowski GA, et al. Mol Biol Cell, 2009 Jun. PMID 19369423, Free PMC Article
    4. Complex Rab4-Mediated Regulation of Endosomal Size and EGFR Activation. Tubbesing K, et al. Mol Cancer Res, 2020 May. PMID 32019812, Free PMC Article
    5. Regulation of CD4 expression via recycling by HRES-1/RAB4 controls susceptibility to HIV infection. Nagy G, et al. J Biol Chem, 2006 Nov 10. PMID 16935861

    See all (107) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ras-related Protein in Brain 4A (Rab4A) is Downregulated by miR-496 to inhibit the Progression of Gastric Cancer.
      Title: Ras-related Protein in Brain 4A (Rab4A) is Downregulated by miR-496 to inhibit the Progression of Gastric Cancer.
    2. Arf1-dependent LRBA recruitment to Rab4 endosomes is required for endolysosome homeostasis.
      Title: Arf1-dependent LRBA recruitment to Rab4 endosomes is required for endolysosome homeostasis.
    3. Receptor-mediated internalization promotes increased endosome size and number in a RAB4- and RAB5-dependent manner.
      Title: Receptor-mediated internalization promotes increased endosome size and number in a RAB4- and RAB5-dependent manner.
    4. RAB4A GTPase regulates epithelial-to-mesenchymal transition by modulating RAC1 activation.
      Title: RAB4A GTPase regulates epithelial-to-mesenchymal transition by modulating RAC1 activation.
    5. Agonist-activated glucagon receptors are deubiquitinated at early endosomes by two distinct deubiquitinases to facilitate Rab4a-dependent recycling.
      Title: Agonist-activated glucagon receptors are deubiquitinated at early endosomes by two distinct deubiquitinases to facilitate Rab4a-dependent recycling.
    6. Complex Rab4-Mediated Regulation of Endosomal Size and EGFR Activation.
      Title: Complex Rab4-Mediated Regulation of Endosomal Size and EGFR Activation.
    7. -type prostaglandin D synthase regulates the trafficking of the PGD2 DP1 receptor by interacting with the GTPase Rab4
      Title: L-type prostaglandin D synthase regulates the trafficking of the PGD(2) DP1 receptor by interacting with the GTPase Rab4.
    8. These findings bring attention to the effects of C-terminal carboxylmethylation on RAB GTPases and provide a rationale for targeting ICMT in the treatment of metastatic cancer
      Title: Isoprenylcysteine carboxylmethyltransferase function is essential for RAB4A-mediated integrin β3 recycling, cell migration and cancer metastasis.
    9. The results contradict the model of feedback activation of Rab5 and instead indicate that Rbpt5 is recruited by both Rabex5 recognizing ubiquitylated cargo and by Rab4 to activate Rab5 in a feed-forward manner.
      Title: Rabaptin5 is recruited to endosomes by Rab4 and Rabex5 to regulate endosome maturation.
    10. Rab4 expression is up-regulated by laminar shear stress, which contributed to improved vascular endothelial cell autophagy and function.
      Title: Laminar Shear Stress Promotes Vascular Endothelial Cell Autophagy Through Upregulation with Rab4.
    Submit: New GeneRIF Correction See all GeneRIFs (36)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9.
    EBI GWAS Catalog
    Linkage and association of successful aging to the 6q25 region in large Amish kindreds.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Expression of HRES-1/Rab4 is induced by HIV-1 Tat, which in turn down-regulates expression of CD4 and susceptibility to re-infection by HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables G protein activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GDP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GTP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activity 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 Rab protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in antigen processing and presentation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neurotransmitter receptor transport postsynaptic membrane to endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle-mediated transport in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasmic vesicle membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in early endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in insulin-responsive compartment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in postsynaptic recycling endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in recycling endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ras-related protein Rab-4A
    Names
    HTLV-1 related endogenous sequence
    NP_001258927.1
    NP_004569.2

    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_001271998.2 → NP_001258927.1  ras-related protein Rab-4A isoform 2

      See identical proteins and their annotated locations for NP_001258927.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AY585832, BC004309, BI546021, BX354553
      Consensus CDS
      CCDS73046.1
      UniProtKB/TrEMBL
      A0A087WYT5
      Related
      ENSP00000482077.1, ENST00000618010.4
      Conserved Domains (1) summary
      cl38936
      Location:5 → 69
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. NM_004578.4 → NP_004569.2  ras-related protein Rab-4A isoform 1

      See identical proteins and their annotated locations for NP_004569.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL162595, AY585832, BC004309, BI546021
      Consensus CDS
      CCDS31050.1
      UniProtKB/Swiss-Prot
      P20338, Q5T7P7, Q9BQ44
      UniProtKB/TrEMBL
      Q53GC2
      Related
      ENSP00000355651.4, ENST00000366690.5
      Conserved Domains (1) summary
      cd04113
      Location:14 → 174
      Rab4; Rab GTPase family 4 (Rab4)

    RNA

    1. NR_073545.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AY585832, BC002438, BC004309, BI828974, HY142709

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      229271111..229305894
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      228649787..228684556
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P20338.3 GenPept UniProtKB/Swiss-Prot:P20338

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
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