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

Gene ID: 84100, updated on 2-Nov-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
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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

Associated conditions

Description Tests
Bardet-Biedl syndrome 1
MedGen: C2936862 OMIM: 209900 GeneReviews: Bardet-Biedl Syndrome Overview
not available
Bardet-Biedl syndrome 3
MedGen: C1859564 OMIM: 600151 GeneReviews: Bardet-Biedl Syndrome Overview
not available
Retinitis pigmentosa
MedGen: C0035334 OMIM: 268000 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
not available
Retinitis pigmentosa 55
MedGen: C3150808 OMIM: 613575 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
not available

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)

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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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

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