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

Summary

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

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Structure and activation mechanism of the BBSome membrane protein trafficking complex.
Title: Structure and activation mechanism of the BBSome membrane protein trafficking complex.
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.
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.
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.
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.
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.
Arl6 is indispensable in cilia signaling but dispensable in ciliogenesis (Review).
Title: Molecular views of Arf-like small GTPases in cilia and ciliopathies.
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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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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 more info	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

NG_008119.2 RefSeqGene

Range

5008..41479

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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

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
NR_136595.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC110491, AL138043
NR_136597.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC110491, AL138043
NR_136598.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC110491, AL138043
NR_136600.3 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC110491, AL138043
NR_136601.3 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC110491, AL138043
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

97764521..97801242

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

RNA

XR_924186.4 RNA Sequence
XR_924185.4 RNA Sequence
XR_924188.4 RNA Sequence
XR_007095753.1 RNA Sequence
XR_924189.4 RNA Sequence
XR_924187.4 RNA Sequence
XR_001740321.3 RNA Sequence
XR_007095754.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

100468299..100505006

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

A8KA93, D3DN31, Q9H0F7
XM_054348083.1 → XP_054204058.1 ADP-ribosylation factor-like protein 6 isoform X2
XM_054348082.1 → XP_054204057.1 ADP-ribosylation factor-like protein 6 isoform X2