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 de... See more...

Aliases for ATL3 Gene

Aliases for ATL3 Gene

  • Atlastin GTPase 3 2 3 5
  • Atlastin-3 3 4
  • DKFZP564J0863 2
  • EC 3.6.5.- 4
  • HSN1F 3
  • ATL3 5

External Ids for ATL3 Gene

Previous GeneCards Identifiers for ATL3 Gene

  • GC11M063154
  • GC11M063391
  • GC11M059725

Summaries for ATL3 Gene

Entrez Gene Summary for ATL3 Gene

  • 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]

GeneCards Summary for ATL3 Gene

ATL3 (Atlastin GTPase 3) is a Protein Coding gene. Diseases associated with ATL3 include Neuropathy, Hereditary Sensory, Type If and Hereditary Sensory And Autonomic Neuropathy Type 1. Gene Ontology (GO) annotations related to this gene include identical protein binding and GTPase activity. An important paralog of this gene is ATL2.

UniProtKB/Swiss-Prot Summary for ATL3 Gene

  • GTPase tethering membranes through formation of trans-homooligomers and mediating homotypic fusion of endoplasmic reticulum membranes. Functions in endoplasmic reticulum tubular network biogenesis (PubMed:18270207, PubMed:19665976, PubMed:27619977).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATL3 Gene

Genomics for ATL3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ATL3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J063665 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 616.9 +2.9 2866 6.6 RNF2 SP1 CREB1 CTCF HNRNPL TEAD4 SIX5 IKZF1 KDM1A BACH1 ATL3 PLAAT3 SPINDOC lnc-PLA2G16-2 piR-30667
GH11J063672 Promoter/Enhancer 0.6 Ensembl dbSUPER 600.7 -0.7 -727 0.2 NR2C2 ATL3 lnc-PLA2G16-2 RTN3
GH11J062838 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 23.3 +831.2 831173 5.2 ARHGAP35 SP1 HNRNPL CREB1 GATAD2A ZBTB33 ARID3A ATF7 PRDM10 REST WDR74 RF00004-024 RNU2-2P lnc-SLC3A2-5 lnc-SLC3A2-6 lnc-SLC3A2-7 CSKMT SNHG1 NXF1 INTS5
GH11J063760 Promoter/Enhancer 1.9 Ensembl ENCODE CraniofacialAtlas dbSUPER 25.3 -93.5 -93511 9.8 SP1 HNRNPL GATAD2A PRDM10 REST CTCF ZNF692 BACH1 JUND LARP7 ATL3 LOC105369332 NXF1 ENSG00000257086 WDR74 STX5 PLCB3 SNHG1 RTN3 C11orf95
GH11J063680 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 15.1 -10.4 -10429 4 ARHGAP35 SP1 CTCF TEAD4 PRDM10 ZNF512 IKZF1 KDM1A ZNF692 POLR2A RTN3 ATL3 IMMP1LP1 TAF6L RF00017-937 C11orf95
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATL3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATL3

Top Transcription factor binding sites by QIAGEN in the ATL3 gene promoter:
  • ATF6
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5

Genomic Locations for ATL3 Gene

Genomic Locations for ATL3 Gene
chr11:63,624,082-63,671,974
(GRCh38/hg38)
Size:
47,893 bases
Orientation:
Minus strand
chr11:63,391,559-63,439,393
(GRCh37/hg19)
Size:
47,835 bases
Orientation:
Minus strand

Genomic View for ATL3 Gene

Genes around ATL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATL3 Gene

Proteins for ATL3 Gene

  • Protein details for ATL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6DD88-ATLA3_HUMAN
    Recommended name:
    Atlastin-3
    Protein Accession:
    Q6DD88
    Secondary Accessions:
    • Q8N7W5
    • Q9H8Q5
    • Q9UFL1

    Protein attributes for ATL3 Gene

    Size:
    541 amino acids
    Molecular mass:
    60542 Da
    Quaternary structure:
    • Interacts with ZFYVE27 (PubMed:23969831).
    SequenceCaution:
    • Sequence=BAC05111.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ATL3 Gene

neXtProt entry for ATL3 Gene

Post-translational modifications for ATL3 Gene

  • Ubiquitination at Lys239 and Lys391
  • Modification sites at PhosphoSitePlus

Other Protein References for ATL3 Gene

No data available for DME Specific Peptides for ATL3 Gene

Domains & Families for ATL3 Gene

Gene Families for ATL3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for ATL3 Gene

Suggested Antigen Peptide Sequences for ATL3 Gene

GenScript: Design optimal peptide antigens:
  • Atlastin-3 (ATLA3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6DD88

UniProtKB/Swiss-Prot:

ATLA3_HUMAN :
  • Belongs to the TRAFAC class dynamin-like GTPase superfamily. GB1/RHD3-type GTPase family. GB1 subfamily.
Family:
  • Belongs to the TRAFAC class dynamin-like GTPase superfamily. GB1/RHD3-type GTPase family. GB1 subfamily.
genes like me logo Genes that share domains with ATL3: view

Function for ATL3 Gene

Molecular function for ATL3 Gene

UniProtKB/Swiss-Prot Function:
GTPase tethering membranes through formation of trans-homooligomers and mediating homotypic fusion of endoplasmic reticulum membranes. Functions in endoplasmic reticulum tubular network biogenesis (PubMed:18270207, PubMed:19665976, PubMed:27619977).

Enzyme Numbers (IUBMB) for ATL3 Gene

Gene Ontology (GO) - Molecular Function for ATL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003924 GTPase activity IEA,NAS 18270207
GO:0005515 protein binding IPI 23969831
GO:0005525 GTP binding IEA,IBA 21873635
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with ATL3: view
genes like me logo Genes that share phenotypes with ATL3: view

Human Phenotype Ontology for ATL3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for ATL3 Gene

miRTarBase miRNAs that target ATL3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATL3

No data available for Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for ATL3 Gene

Localization for ATL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATL3 Gene

Endoplasmic reticulum membrane. Multi-pass membrane protein. Note=Localizes to endoplasmic reticulum tubules and accumulates in punctuate structures corresponding to 3-way junctions, which represent crossing-points at which the tubules build a polygonal network. {ECO:0000269 PubMed:23969831, ECO:0000269 PubMed:24459106, ECO:0000269 PubMed:27619977}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATL3 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 3
peroxisome 2
cytoskeleton 1
mitochondrion 1
nucleus 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA 18270207
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA,IDA 18270207
GO:0071782 endoplasmic reticulum tubular network IDA 23969831
genes like me logo Genes that share ontologies with ATL3: view

Pathways & Interactions for ATL3 Gene

PathCards logo

SuperPathways for ATL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ATL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006888 NOT ER to Golgi vesicle-mediated transport IMP 18270207
GO:0007029 endoplasmic reticulum organization IBA,IMP 18270207
GO:0007030 Golgi organization IMP 18270207
GO:0051260 protein homooligomerization IBA,IDA 18270207
GO:1903373 positive regulation of endoplasmic reticulum tubular network organization IMP 27619977
genes like me logo Genes that share ontologies with ATL3: view

No data available for Pathways by source and SIGNOR curated interactions for ATL3 Gene

Drugs & Compounds for ATL3 Gene

No Compound Related Data Available

Transcripts for ATL3 Gene

mRNA/cDNA for ATL3 Gene

2 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATL3

Alternative Splicing Database (ASD) splice patterns (SP) for ATL3 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1: -
SP2: - -
SP3: - - - -
SP4:

Relevant External Links for ATL3 Gene

GeneLoc Exon Structure for
ATL3

Expression for ATL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATL3 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATL3 Gene



Protein tissue co-expression partners for ATL3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATL3

SOURCE GeneReport for Unigene cluster for ATL3 Gene:

Hs.356719

mRNA Expression by UniProt/SwissProt for ATL3 Gene:

Q6DD88-ATLA3_HUMAN
Tissue specificity: Expressed in the central nervous system and in dorsal root ganglia neurons. Expressed in peripheral tissues (at protein level).

Evidence on tissue expression from TISSUES for ATL3 Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Pancreas(4.2)
  • Kidney(2.2)
  • Skin(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ATL3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with ATL3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein differential expression in normal tissues for ATL3 Gene

Orthologs for ATL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ATL3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ATL3 30 31
  • 99.74 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ATL3 30 31
  • 91.5 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ATL3 30 31
  • 90.7 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Atl3 30 17 31
  • 90.02 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 90 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Atl3 30
  • 89.4 (n)
Oppossum
(Monodelphis domestica)
Mammalia ATL3 31
  • 76 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ATL3 31
  • 73 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia atl3 30
  • 70.57 (n)
Zebrafish
(Danio rerio)
Actinopterygii atl3 30 31
  • 67.14 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8856 30
Fruit Fly
(Drosophila melanogaster)
Insecta atl 31
  • 50 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea atln-1 31
  • 50 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 42 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.1135 30
Species where no ortholog for ATL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for ATL3 Gene

ENSEMBL:
Gene Tree for ATL3 (if available)
TreeFam:
Gene Tree for ATL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATL3: view image

Paralogs for ATL3 Gene

Paralogs for ATL3 Gene

(3) SIMAP similar genes for ATL3 Gene using alignment to 4 proteins:

  • ATLA3_HUMAN
  • C9JUU1_HUMAN
  • F5GWF8_HUMAN
  • F5H6I7_HUMAN
genes like me logo Genes that share paralogs with ATL3: view

Variants for ATL3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATL3 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
639122 Uncertain Significance: Hereditary sensory neuropathy type IF 63,631,104(-) T/A MISSENSE_VARIANT
640627 Uncertain Significance: Hereditary sensory neuropathy type IF 63,631,076(-) TCCG/T INFRAME_DELETION
641805 Uncertain Significance: Hereditary sensory neuropathy type IF 63,644,228(-) GG/AA MISSENSE_VARIANT
643677 Uncertain Significance: Hereditary sensory neuropathy type IF 63,631,189(-) T/C MISSENSE_VARIANT
644572 Uncertain Significance: Hereditary sensory neuropathy type IF 63,658,762(-) T/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for ATL3 Gene

Structural Variations from Database of Genomic Variants (DGV) for ATL3 Gene

Variant ID Type Subtype PubMed ID
nsv353 CNV deletion 18451855
nsv832183 CNV loss 17160897

Variation tolerance for ATL3 Gene

Residual Variation Intolerance Score: 45.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.28; 70.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATL3 Gene

Human Gene Mutation Database (HGMD)
ATL3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATL3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATL3 Gene

Disorders for ATL3 Gene

MalaCards: The human disease database

(9) MalaCards diseases for ATL3 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
neuropathy, hereditary sensory, type if
  • hsn1f
hereditary sensory and autonomic neuropathy type 1
  • hsan1
hereditary sensory neuropathy
  • familial dysautonomia, type ii
neuropathy
  • peripheral neuropathy
spastic paraplegia 3a
  • spastic paraplegia 3, autosomal dominant
- elite association - COSMIC cancer census association via MalaCards
Search ATL3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

ATLA3_HUMAN
  • Neuropathy, hereditary sensory, 1F (HSN1F) [MIM:615632]: An autosomal dominant sensory neuropathy affecting the lower limbs. Distal sensory impairment becomes apparent during the second or third decade of life, resulting in painless ulceration of the feet with poor healing, which can progress to osteomyelitis, bone destruction, and amputation. There is no autonomic involvement, spasticity, or cognitive impairment. {ECO:0000269 PubMed:24459106}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with ATL3: view

No data available for Genatlas for ATL3 Gene

Publications for ATL3 Gene

  1. Atlastin GTPases are required for Golgi apparatus and ER morphogenesis. (PMID: 18270207) Rismanchi N … Blackstone C (Human molecular genetics 2008) 2 3 4
  2. Cooperation of the ER-shaping proteins atlastin, lunapark, and reticulons to generate a tubular membrane network. (PMID: 27619977) Wang S … Rapoport TA (eLife 2016) 3 4
  3. Sensory neuropathy with bone destruction due to a mutation in the membrane-shaping atlastin GTPase 3. (PMID: 24459106) Kornak U … Kurth I (Brain : a journal of neurology 2014) 3 4
  4. Protrudin binds atlastins and endoplasmic reticulum-shaping proteins and regulates network formation. (PMID: 23969831) Chang J … Blackstone C (Proceedings of the National Academy of Sciences of the United States of America 2013) 3 4
  5. A class of dynamin-like GTPases involved in the generation of the tubular ER network. (PMID: 19665976) Hu J … Blackstone C (Cell 2009) 3 4

Products for ATL3 Gene

  • Signalway Proteins for ATL3

Sources for ATL3 Gene