U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

ATL3 atlastin GTPase 3 [ Homo sapiens (human) ]

Gene ID: 25923, updated on 3-Nov-2024

Summary

Go to the top of the page Help
Official Symbol
ATL3provided by HGNC
Official Full Name
atlastin GTPase 3provided by HGNC
Primary source
HGNC:HGNC:24526
See related
Ensembl:ENSG00000184743 MIM:609369; AllianceGenome:HGNC:24526
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
HSN1F
Summary
This gene encodes a member of a family of dynamin-like, integral membrane GTPases. The encoded protein is required for the proper formation of the network of interconnected tubules of the endoplasmic reticulum. Mutations in this gene may be associated with hereditary sensory neuropathy type IF. Alternatively spliced transcript variants that encode distinct isoforms have been described. [provided by RefSeq, Feb 2014]
Expression
Ubiquitous expression in fat (RPKM 13.6), thyroid (RPKM 12.0) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See ATL3 in Genome Data Viewer
Location:
11q13.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (63624087..63671974, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (63613427..63661313, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (63391559..63439446, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3435 Neighboring gene CRISPRi-validated cis-regulatory element chr11.2897 Neighboring gene phospholipase A and acyltransferase 2 Neighboring gene uncharacterized LOC105369335 Neighboring gene phospholipase A and acyltransferase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63368875-63369376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63372619-63373384 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:63378198-63378707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63379461-63379961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3437 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:63398741-63399940 Neighboring gene inner mitochondrial membrane peptidase subunit 1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63438213-63438714 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63438715-63439214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3441 Neighboring gene reticulon 3 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:63529087-63529846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3443 Neighboring gene zinc finger translocation associated

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. A disease causing ATLASTIN 3 mutation affects multiple endoplasmic reticulum-related pathways. Behrendt L, et al. Cell Mol Life Sci, 2019 Apr. PMID 30666337, Free PMC Article
  2. Sensory neuropathy-causing mutations in ATL3 affect ER-mitochondria contact sites and impair axonal mitochondrial distribution. Krols M, et al. Hum Mol Genet, 2019 Feb 15. PMID 30339187, Free PMC Article
  3. Sensory-Neuropathy-Causing Mutations in ATL3 Cause Aberrant ER Membrane Tethering. Krols M, et al. Cell Rep, 2018 May 15. PMID 29768202
  4. ER remodeling by the large GTPase atlastin promotes vacuolar growth of Legionella pneumophila. Steiner B, et al. EMBO Rep, 2017 Oct. PMID 28835546, Free PMC Article
  5. Human atlastin-3 is a constitutive ER membrane fusion catalyst. Bryce S, et al. J Cell Biol, 2023 Jul 3. PMID 37102997, Free PMC Article

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A novel nonsense variant in the ATL3 gene is associated with disturbed pain sensitivity, numbness of distal limbs and muscle weakness.
    Title: A novel nonsense variant in the ATL3 gene is associated with disturbed pain sensitivity, numbness of distal limbs and muscle weakness.
  2. Human atlastin-3 is a constitutive ER membrane fusion catalyst.
    Title: Human atlastin-3 is a constitutive ER membrane fusion catalyst.
  3. Atlastin 2/3 regulate ER targeting of the ULK1 complex to initiate autophagy.
    Title: Atlastin 2/3 regulate ER targeting of the ULK1 complex to initiate autophagy.
  4. Rare mutations in ATL3, SPTLC2 and SCN9A explaining hereditary sensory neuropathy and congenital insensitivity to pain in a Brazilian cohort.
    Title: Rare mutations in ATL3, SPTLC2 and SCN9A explaining hereditary sensory neuropathy and congenital insensitivity to pain in a Brazilian cohort.
  5. ATL3 functions as a receptor for endoplasmic reticulum (ER)-phagy, promoting tubular ER degradation upon starvation. ATL3 specifically binds to GABARAP, but not LC3, subfamily proteins via 2 GABARAP interaction motifs (GIMs). ATL3-GABARAP interaction is essential for ATL3 to function in ER-phagy.
    Title: ATL3 Is a Tubular ER-Phagy Receptor for GABARAP-Mediated Selective Autophagy.
  6. the effects of ATL3 mutations on endoplasmic reticulum network organization go beyond a loss of fusion and shed light on neuropathies caused by atlastin defects.
    Title: Sensory-Neuropathy-Causing Mutations in ATL3 Cause Aberrant ER Membrane Tethering.
  7. the mitochondria in these cells display lowered motility, and the number of axonal mitochondria in neurons expressing disease-causing mutations in ATL3 is strongly decreased. These results underscore the functional interdependence of subcellular organelles in health and disease and show that disorders caused by ER-shaping defects are more complex than previously assumed.
    Title: Sensory neuropathy-causing mutations in ATL3 affect ER-mitochondria contact sites and impair axonal mitochondrial distribution.
  8. ATL3 Y192C delays endoplasmic reticulum-export by reducing the number of endoplasmic reticulum exit sites, reduces autophagy, fragments the Golgi and causes malformation of the nucleus. In cultured primary neurons, ATL3 Y192C does not localize to the growing axon, resulting in axon growth deficits.
    Title: A disease causing ATLASTIN 3 mutation affects multiple endoplasmic reticulum-related pathways.
  9. study reports that Sey1/Atl3 and Rtn4 localize to early Legionella-containing vacuoles (LCV) and are critical for pathogen vacuole formation; Sey1/Atl3-dependent ER remodeling contributes to LCV maturation and intracellular replication of L. pneumophila
    Title: ER remodeling by the large GTPase atlastin promotes vacuolar growth of Legionella pneumophila.
  10. These results suggest that the three ATLs have different capacities to mediate endoplasmic reticulum fusion, with ATL1 being the strongest and ATL3 being the weakest.
    Title: Human atlastin GTPases mediate differentiated fusion of endoplasmic reticulum membranes.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

Go to the top of the page Help

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
Neuropathy, hereditary sensory, type 1F
MedGen: C3810194 OMIM: 615632 GeneReviews: Not available
Compare labs

Variation

Go to the top of the page Help

See Variation Viewer (GRCh37.p13)

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • DKFZp564J0863

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables identical protein 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 organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endoplasmic reticulum organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
NOT involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of endoplasmic reticulum tubular network organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein homooligomerization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein homooligomerization IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum tubular network IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum tubular network membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
atlastin-3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_033985.1 RefSeqGene

    Range
    5599..52888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001290048.2 → NP_001276977.1  atlastin-3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon compared to variant 1. The encoded protein (isoform 2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK301910, AP000753, BC077727, DC394729
    Consensus CDS
    CCDS73309.1
    UniProtKB/TrEMBL
    B4DXC4, F5H6I7
    Related
    ENSP00000437593.1, ENST00000538786.1
    Conserved Domains (1) summary
    cl38936
    Location:19 → 287
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. NM_015459.5 → NP_056274.3  atlastin-3 isoform 1

    See identical proteins and their annotated locations for NP_056274.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
    Source sequence(s)
    AP000753, BC077727
    Consensus CDS
    CCDS41663.1
    UniProtKB/Swiss-Prot
    Q6DD88, Q8N7W5, Q9H8Q5, Q9UFL1
    UniProtKB/TrEMBL
    B4DXC4
    Related
    ENSP00000381844.3, ENST00000398868.8
    Conserved Domains (1) summary
    cl21455
    Location:37 → 305
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    63624087..63671974 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426725.1 → XP_047282681.1  atlastin-3 isoform X2

  2. XM_006718493.2 → XP_006718556.1  atlastin-3 isoform X1

    UniProtKB/TrEMBL
    B4DXC4
    Conserved Domains (1) summary
    cl21455
    Location:37 → 286
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    63613427..63661313 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368354.1 → XP_054224329.1  atlastin-3 isoform X2

  2. XM_054368353.1 → XP_054224328.1  atlastin-3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6DD88.1 GenPept UniProtKB/Swiss-Prot:Q6DD88

Gene LinkOut

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

Other Literature Sources
Chemical Information
Molecular Biology Databases
Research Materials
Tools