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

Gene ID: 5867, updated on 3-Nov-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
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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 (108) 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

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