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ARL3 ADP ribosylation factor like GTPase 3 [ Homo sapiens (human) ]

Gene ID: 403, updated on 7-Apr-2024

Summary

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Official Symbol
ARL3provided by HGNC
Official Full Name
ADP ribosylation factor like GTPase 3provided by HGNC
Primary source
HGNC:HGNC:694
See related
Ensembl:ENSG00000138175 MIM:604695; AllianceGenome:HGNC:694
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
RP83; ARFL3; JBTS35
Summary
Enables GDP binding activity; GTP binding activity; and microtubule binding activity. Involved in several processes, including cilium assembly; protein localization to cilium; and small GTPase mediated signal transduction. Acts upstream of or within post-Golgi vesicle-mediated transport. Located in several cellular components, including microtubule cytoskeleton; midbody; and photoreceptor connecting cilium. Implicated in Joubert syndrome and retinitis pigmentosa 83. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 13.2), kidney (RPKM 7.9) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
10q24.32
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (102673731..102714397, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (103559565..103600213, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (104433488..104474154, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2765 Neighboring gene hESC enhancers GRCh37_chr10:104402874-104403628 and GRCh37_chr10:104403629-104404384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3942 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:104405671-104405887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104408319-104409286 Neighboring gene uncharacterized LOC105378460 Neighboring gene TRIM8 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2769 Neighboring gene tripartite motif containing 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:104428852-104429454 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:104429455-104430056 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:104430057-104430658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104433562-104434111 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2771 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104474219-104474795 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104474796-104475371 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104488530-104489304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104489305-104490077 Neighboring gene sideroflexin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3949 Neighboring gene WW domain binding protein 1 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:104534833-104535364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:104535897-104536428 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:104536429-104536960 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104540708-104541208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104541209-104541709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3950 Neighboring gene RNA, U6 small nuclear 1231, 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. Homozygous Variant in ARL3 Causes Autosomal Recessive Cone Rod Dystrophy. Sheikh SA, et al. Invest Ophthalmol Vis Sci, 2019 Nov 1. PMID 31743939, Free PMC Article
  2. ARL3 is downregulated and acts as a prognostic biomarker in glioma. Wang Y, et al. J Transl Med, 2019 Jun 24. PMID 31234870, Free PMC Article
  3. Dominant ARL3-related retinitis pigmentosa. Holtan JP, et al. Ophthalmic Genet, 2019 Apr. PMID 30932721
  4. ARL3 subcellular localization and its suspected role in autophagy. Luo G, et al. Biochimie, 2018 Nov. PMID 30227171
  5. De Novo Occurrence of a Variant in ARL3 and Apparent Autosomal Dominant Transmission of Retinitis Pigmentosa. Strom SP, et al. PLoS One, 2016. PMID 26964041, Free PMC Article

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Mechanisms underlying morphological and functional changes of cilia in fibroblasts derived from patients bearing ARL3[T31A] and ARL3[T31A/C118F] mutations.
    Title: Mechanisms underlying morphological and functional changes of cilia in fibroblasts derived from patients bearing ARL3(T31A) and ARL3(T31A/C118F) mutations.
  2. Human Mutations in Arl3, a Small GTPase Involved in Lipidated Cargo Delivery to the Cilia, Cause Retinal Dystrophy.
    Title: Human Mutations in Arl3, a Small GTPase Involved in Lipidated Cargo Delivery to the Cilia, Cause Retinal Dystrophy.
  3. ARL3 activation requires the co-GEF BART and effector-mediated turnover.
    Title: ARL3 activation requires the co-GEF BART and effector-mediated turnover.
  4. Expression patterns of ciliopathy genes ARL3 and CEP120 reveal roles in multisystem development.
    Title: Expression patterns of ciliopathy genes ARL3 and CEP120 reveal roles in multisystem development.
  5. Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials.
    Title: Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials.
  6. Low ARL3 expression predicted poor prognosis and contributed to antiangiogenesis and the proportion of infiltrating immune cells in the GBM microenvironment. Thus, ARL3 may be a prognostic marker and therapeutic target for glioma.
    Title: ARL3 is downregulated and acts as a prognostic biomarker in glioma.
  7. Our study confirms that the ARL3 missense variant p.(Tyr90Cys) causes retinitis pigmentosa.
    Title: Dominant ARL3-related retinitis pigmentosa.
  8. Our study uncovers an additional cone rod dystrophy (CRD) gene and assigns the CRD phenotype to a variant of ARL3. The results imply that cargo transportation in photoreceptors as mediated by the ARL3 pathway is essential for cone and rod cell survival and vision in humans.
    Title: Homozygous Variant in ARL3 Causes Autosomal Recessive Cone Rod Dystrophy.
  9. We utilized a structure-based approach to pinpoint the binding interface to a strictly conserved cluster of residues on the surface of RP2 that spans both the C- and N-terminal domains of the protein, and which is structurally distinct from the ARL3-binding site.RP2 is a positive regulator of cell motility in vitro, recruiting OSTF1 to the cell membrane and preventing its interaction with the migration regulator Myo1E.
    Title: Characterization of a novel RP2-OSTF1 interaction and its implication for actin remodelling.
  10. ARL3 provides a potential hub in the network of proteins implicated in ciliopathies.
    Title: ARL3 Mutations Cause Joubert Syndrome by Disrupting Ciliary Protein Composition.
Submit: New GeneRIF Correction See all GeneRIFs (24)

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

Associated conditions

Description Tests
Joubert syndrome 35
MedGen: C4748442 OMIM: 618161 GeneReviews: Not available
Compare labs
Retinitis pigmentosa 83
MedGen: C4748536 OMIM: 618173 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
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

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 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 IEA
Inferred from Electronic Annotation
more info
  
enables magnesium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables microtubule binding 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 Golgi to plasma membrane transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intraciliary transport IEA
Inferred from Electronic Annotation
more info
  
involved_in kidney development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in mitotic cytokinesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in photoreceptor cell development ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within post-Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to ciliary membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein localization to cilium IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in small GTPase-mediated signal transduction IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
NOT located_in cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cilium TAS
Traceable Author Statement
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasmic microtubule IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
is_active_in microtubule cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in midbody IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in photoreceptor connecting cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in spindle microtubule IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ADP-ribosylation factor-like protein 3
Names
ADP-ribosylation factor-like 3
ARF-like 3

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_004311.4 → NP_004302.1  ADP-ribosylation factor-like protein 3

    See identical proteins and their annotated locations for NP_004302.1

    Status: REVIEWED

    Source sequence(s)
    AL391121
    Consensus CDS
    CCDS7538.1
    UniProtKB/Swiss-Prot
    B2R6C7, P36405, Q53X83, Q5JSM2
    Related
    ENSP00000260746.4, ENST00000260746.6
    Conserved Domains (1) summary
    cd04155
    Location:3 → 176
    Arl3; Arf-like 3 (Arl3) GTPase

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    102673731..102714397 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017016260.2 → XP_016871749.1  ADP-ribosylation factor-like protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B2R6C7, P36405, Q53X83, Q5JSM2
    Conserved Domains (1) summary
    cd04155
    Location:3 → 176
    Arl3; Arf-like 3 (Arl3) GTPase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    103559565..103600213 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054365942.1 → XP_054221917.1  ADP-ribosylation factor-like protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B2R6C7, P36405, Q53X83, Q5JSM2
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P36405.2 GenPept UniProtKB/Swiss-Prot:P36405

Gene LinkOut

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

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