ATL3 atlastin GTPase 3 [Homo sapiens (human)] - Gene

Summary

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
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Genomic context

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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Human atlastin-3 is a constitutive ER membrane fusion catalyst.
Title: Human atlastin-3 is a constitutive ER membrane fusion catalyst.
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.
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.
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.
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.
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.
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.
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.
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

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

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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Markers

A006Q18 (e-PCR)
- UniSTS:36125

D8S2279 (e-PCR)
- UniSTS:473907

L18426 (e-PCR)
- UniSTS:34648

D1S1423 (e-PCR)
- UniSTS:149619

RH12215 (e-PCR)
- UniSTS:61109

G27556 (e-PCR)
- UniSTS:66278

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 more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: atlastin-3

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_033985.1 RefSeqGene

Range

5599..52888

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

63624087..63671974 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B4DXC4
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