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    ARL6 ARF like GTPase 6 [ Homo sapiens (human) ]

    Gene ID: 84100, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ARL6provided by HGNC
    Official Full Name
    ARF like GTPase 6provided by HGNC
    Primary source
    HGNC:HGNC:13210
    See related
    Ensembl:ENSG00000113966 MIM:608845; AllianceGenome:HGNC:13210
    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
    BBS3; RP55
    Summary
    The protein encoded by this gene belongs to the ARF-like (ADP ribosylation factor-like) sub-family of the ARF family of GTP-binding proteins which are involved in regulation of intracellular traffic. Mutations in this gene are associated with Bardet-Biedl syndrome (BBS). A vision-specific transcript, encoding long isoform BBS3L, has been described (PMID: 20333246). [provided by RefSeq, Apr 2016]
    Expression
    Broad expression in testis (RPKM 2.3), brain (RPKM 1.6) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARL6 in Genome Data Viewer
    Location:
    3q11.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (97764521..97801242)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (100468299..100505006)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (97483365..97520086)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene EPH receptor A6 Neighboring gene TPTE2 pseudogene 7 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:97381594-97382192 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:97406521-97407050 Neighboring gene NANOG hESC enhancer GRCh37_chr3:97430329-97430833 Neighboring gene uncharacterized LOC124906256 Neighboring gene NANOG hESC enhancer GRCh37_chr3:97466009-97466510 Neighboring gene H3K27ac hESC enhancers GRCh37_chr3:97482933-97483434 and GRCh37_chr3:97483435-97483934 Neighboring gene uncharacterized LOC101929298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14552 Neighboring gene uncharacterized LOC105373994 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:97614773-97615564 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:97628706-97629296 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:97629297-97629886 Neighboring gene crystallin beta-gamma domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14553 Neighboring gene ribosomal oxygenase 2

    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. The Prognostic and Therapeutic Roles of ARL-6 Gene in Hepatocellular Carcinoma. Wang J, et al. Int J Med Sci, 2024. PMID 38169538, Free PMC Article
    2. New mutations in BBS genes in small consanguineous families with Bardet-Biedl syndrome: detection of candidate regions by homozygosity mapping. Pereiro I, et al. Mol Vis, 2010 Feb 1. PMID 20142850, Free PMC Article
    3. Biochemical characterization of missense mutations in the Arf/Arl-family small GTPase Arl6 causing Bardet-Biedl syndrome. Kobayashi T, et al. Biochem Biophys Res Commun, 2009 Apr 10. PMID 19236846
    4. Structure and activation mechanism of the BBSome membrane protein trafficking complex. Singh SK, et al. Elife, 2020 Jan 15. PMID 31939736, Free PMC Article
    5. High prevalence of Bardet-Biedl syndrome in La Réunion Island is due to a founder variant in ARL6/BBS3. Gouronc A, et al. Clin Genet, 2020 Aug. PMID 32361989

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Prognostic and Therapeutic Roles of ARL-6 Gene in Hepatocellular Carcinoma.
      Title: The Prognostic and Therapeutic Roles of ARL-6 Gene in Hepatocellular Carcinoma.
    2. High prevalence of Bardet-Biedl syndrome in La Reunion Island is due to a founder variant in ARL6/BBS3.
      Title: High prevalence of Bardet-Biedl syndrome in La Réunion Island is due to a founder variant in ARL6/BBS3.
    3. Structure and activation mechanism of the BBSome membrane protein trafficking complex.
      Title: Structure and activation mechanism of the BBSome membrane protein trafficking complex.
    4. In the 64 BBS patients (44 males, 20 females) were studied, mutations were predominant in BBS10 and ARL6 genes; the c.272T>C; p.(I91T) mutation in ARL6 gene was a recurrent mutation
      Title: Screening for mutation hotspots in Bardet-Biedl syndrome patients from India.
    5. Mutations of the ARL6 gene cause Bardet-Biedl syndrome, a heterogeneous disorder that increases the risk of Hypertension and Diabetes mellitus.
      Title: Genome-Wide Gene-Sodium Interaction Analyses on Blood Pressure: The Genetic Epidemiology Network of Salt-Sensitivity Study.
    6. Elevated levels of serum ARL6 were able to discriminate between excessive alcohol users and controls.
      Title: Novel serum biomarkers for detection of excessive alcohol use.
    7. Results show that BBS1 and BBS3 regulates the ciliary traficking of PC1.
      Title: Bardet-Biedl syndrome proteins 1 and 3 regulate the ciliary trafficking of polycystic kidney disease 1 protein.
    8. The BBSome is a coat-like ciliary trafficking complex composed of proteins mutated in Bardet-Biedl syndrome. ARL6 E108A mutation prevents BBSome recruitment to cilia.
      Title: Structural basis for membrane targeting of the BBSome by ARL6.
    9. Arl6 is indispensable in cilia signaling but dispensable in ciliogenesis (Review).
      Title: Molecular views of Arf-like small GTPases in cilia and ciliopathies.
    10. Mutations identified in the present study extend the body of evidence implicating the genes ARL6 and BBS10 in causing Bardet-Biedl syndrome.
      Title: Novel homozygous mutations in the genes ARL6 and BBS10 underlying Bardet-Biedl syndrome.
    Submit: New GeneRIF Correction See all GeneRIFs (20)

    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

    EBI GWAS Catalog

    Description
    Genome-wide study of single-nucleotide polymorphisms associated with azoospermia and severe oligozoospermia.
    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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    Homology

    Clone Names

    • MGC32934

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phospholipid binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in determination of left/right symmetry ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in melanosome transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein localization to cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within protein localization to cilium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein polymerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein targeting to membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in axonemal microtubule ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in axoneme IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axoneme ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of membrane coat ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ADP-ribosylation factor-like protein 6
    Names
    ADP ribosylation factor like GTPase 6
    ARL6 interacting reticulophagy regulator 1
    Bardet-Biedl syndrome 3 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.

    Genomic

    1. NG_008119.2 RefSeqGene

      Range
      5008..41479
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001278293.3 → NP_001265222.1  ADP-ribosylation factor-like protein 6 isoform 1

      See identical proteins and their annotated locations for NP_001265222.1

      Status: REVIEWED

      Description
      Transcript Variant: Variants 1, 2 and 3 encode the same isoform (1).
      Source sequence(s)
      AC110491, AK292958, AL138043, BM464340, BM982145, BQ441226, BU183949
      Consensus CDS
      CCDS2928.1
      UniProtKB/Swiss-Prot
      A8KA93, D3DN31, Q9H0F7
      Related
      ENSP00000419619.1, ENST00000463745.6
      Conserved Domains (1) summary
      cd04157
      Location:19 → 180
      Arl6; Arf-like 6 (Arl6) GTPase

    2. NM_001323513.2 → NP_001310442.1  ADP-ribosylation factor-like protein 6 isoform BB3SL

      Status: REVIEWED

      Description
      Transcript Variant: Variant 5 encodes BBS3L, aka the long isoform, which is retina-specific and is required for visual function (PMID:20333246).
      Source sequence(s)
      AC110491, AL138043
      Consensus CDS
      CCDS93329.1
      UniProtKB/Swiss-Prot
      Q9H0F7
      Related
      ENSP00000488530.2, ENST00000631834.2
      Conserved Domains (1) summary
      cd04157
      Location:19 → 180
      Arl6; Arf-like 6 (Arl6) GTPase

    3. NM_001323514.2 → NP_001310443.1  ADP-ribosylation factor-like protein 6 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC110491, AL138043
      Conserved Domains (1) summary
      cd04157
      Location:19 → 159
      Arl6; Arf-like 6 (Arl6) GTPase

    4. NM_032146.5 → NP_115522.1  ADP-ribosylation factor-like protein 6 isoform 1

      See identical proteins and their annotated locations for NP_115522.1

      Status: REVIEWED

      Description
      Transcript Variant: Variants 1, 2 and 3 encode the same isoform (1).
      Source sequence(s)
      AC110491, AK292958, AL136815, AL138043, BG722744, BM464340, BM982145, BQ441226, BU183949, DC323603
      Consensus CDS
      CCDS2928.1
      UniProtKB/Swiss-Prot
      A8KA93, D3DN31, Q9H0F7
      Related
      ENSP00000337722.2, ENST00000335979.6
      Conserved Domains (1) summary
      cd04157
      Location:19 → 180
      Arl6; Arf-like 6 (Arl6) GTPase

    5. NM_177976.3 → NP_816931.1  ADP-ribosylation factor-like protein 6 isoform 1

      See identical proteins and their annotated locations for NP_816931.1

      Status: REVIEWED

      Description
      Transcript Variant: Variants 1, 2 and 3 encode the same isoform (1).
      Source sequence(s)
      AC110491, AK292958, AL136815, AL138043, BM464340, BM705017, BM982145, BQ441226, BU183949, DC323603
      Consensus CDS
      CCDS2928.1
      UniProtKB/Swiss-Prot
      A8KA93, D3DN31, Q9H0F7
      Related
      ENSP00000418740.2, ENST00000462412.3
      Conserved Domains (1) summary
      cd04157
      Location:19 → 180
      Arl6; Arf-like 6 (Arl6) GTPase

    RNA

    1. NR_103511.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and contains an alternate 3' terminal exon, compared to variant 3. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 3, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL138043, BC024239

    2. NR_136595.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC110491, AL138043

    3. NR_136597.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC110491, AL138043

    4. NR_136598.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC110491, AL138043

    5. NR_136600.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC110491, AL138043

    6. NR_136601.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC110491, AL138043

    7. NR_136602.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC110491, AL138043

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      97764521..97801242
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007311.3 → XP_016862800.1  ADP-ribosylation factor-like protein 6 isoform X1

      UniProtKB/Swiss-Prot
      A8KA93, D3DN31, Q9H0F7
      Conserved Domains (1) summary
      cd04157
      Location:19 → 180
      Arl6; Arf-like 6 (Arl6) GTPase

    2. XM_017007312.3 → XP_016862801.1  ADP-ribosylation factor-like protein 6 isoform X2

      Conserved Domains (1) summary
      cd04157
      Location:19 → 159
      Arl6; Arf-like 6 (Arl6) GTPase

    3. XM_047449062.1 → XP_047305018.1  ADP-ribosylation factor-like protein 6 isoform X2

    RNA

    1. XR_924186.4 RNA Sequence

    2. XR_924185.4 RNA Sequence

    3. XR_924188.4 RNA Sequence

    4. XR_007095753.1 RNA Sequence

    5. XR_924189.4 RNA Sequence

    6. XR_924187.4 RNA Sequence

    7. XR_001740321.3 RNA Sequence

    8. XR_007095754.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      100468299..100505006
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348081.1 → XP_054204056.1  ADP-ribosylation factor-like protein 6 isoform X1

      UniProtKB/Swiss-Prot
      A8KA93, D3DN31, Q9H0F7

    2. XM_054348083.1 → XP_054204058.1  ADP-ribosylation factor-like protein 6 isoform X2

    3. XM_054348082.1 → XP_054204057.1  ADP-ribosylation factor-like protein 6 isoform X2

    RNA

    1. XR_008486834.1 RNA Sequence

    2. XR_008486832.1 RNA Sequence

    3. XR_008486833.1 RNA Sequence

    4. XR_008486835.1 RNA Sequence

    5. XR_008486838.1 RNA Sequence

    6. XR_008486836.1 RNA Sequence

    7. XR_008486837.1 RNA Sequence

    8. XR_008486839.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H0F7.1 GenPept UniProtKB/Swiss-Prot:Q9H0F7

    Gene LinkOut

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

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