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Aliases for ATL3 Gene

Aliases for ATL3 Gene

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

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 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).

Additional gene information for ATL3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATL3 Gene

Genomics for ATL3 Gene

GeneHancer (GH) Regulatory Elements for ATL3 Gene

Promoters and enhancers for ATL3 Gene
GeneHancer (GH) Identifier GH Type GH
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 2.2 EPDnew Ensembl ENCODE dbSUPER 667 +2.9 2875 6.6 HDGF SIN3A YY1 ZNF766 CBX5 E2F8 ZNF207 ZNF143 FOS DEK ATL3 NXF1 LOC105369332 PLCB3 STX5 IMMP1LP1 TMEM179B UBXN1 PLA2G16 SPINDOC
GH11J063673 Enhancer 0.9 ENCODE dbSUPER 650.7 -1.8 -1779 1.3 BCOR FOXA2 CEBPG ZNF316 ATF7 TRIM24 GATAD2A L3MBTL2 FOXA3 HLF ATL3 GC11M063550
GH11J062838 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 23.3 +831.1 831128 4.8 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 WDR74 GC11M062842 RNU2-2P NXF1 CSKMT INTS5 SNHG1 UBXN1 MTA2 GANAB
GH11J063760 Promoter/Enhancer 1.9 Ensembl ENCODE dbSUPER 25.3 -93.5 -93486 9.8 FOXA2 ARID4B SIN3A DMAP1 ZNF48 YY1 ETS1 GLIS2 ZNF143 ZFP91 ATL3 LOC105369332 NXF1 ENSG00000257086 WDR74 STX5 PLCB3 SNHG1 RTN3 GC11M063761
GH11J063680 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 15.1 -10.1 -10109 3.4 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 GC11M063550 RTN3 NXF1 ATL3 IMMP1LP1 TAF6L LOC105369332 PLCB3 STX5 TMEM179B
- 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 UCSC Golden Path with GeneCards custom track

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
47,893 bases
Minus strand
47,835 bases
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:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q8N7W5
    • Q9H8Q5
    • Q9UFL1

    Protein attributes for ATL3 Gene

    541 amino acids
    Molecular mass:
    60542 Da
    Quaternary structure:
    • Interacts with ZFYVE27 (PubMed:23969831).
    • 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 Lys391 and Lys239
  • 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

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:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the TRAFAC class dynamin-like GTPase superfamily. GB1/RHD3-type GTPase family. GB1 subfamily.
  • 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:0003924 GTPase activity IEA,NAS 18270207
GO:0005515 protein binding IPI 23969831
GO:0005525 GTP binding IEA --
GO:0016787 hydrolase activity IEA --
GO:0042802 identical protein binding IDA 18270207
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

miRNA for ATL3 Gene

miRTarBase miRNAs that target ATL3

Clone Products

  • Addgene plasmids 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

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
golgi apparatus 2

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 HDA,IEA 19946888
GO:0016021 integral component of membrane IDA,IEA 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

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 IMP 18270207
GO:0007030 Golgi organization IMP 18270207
GO:0051260 protein homooligomerization 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

Unigene Clusters for ATL3 Gene

Atlastin GTPase 3:
Representative Sequences:

Clone Products

  • Addgene plasmids 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: - - - -

Relevant External Links for ATL3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ATL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of ATL3 Gene:


SOURCE GeneReport for Unigene cluster for ATL3 Gene:


mRNA Expression by UniProt/SwissProt for ATL3 Gene:

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(4.7)
  • Liver(4.3)
  • Pancreas(4.2)

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

Germ Layers:
  • ectoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • 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
  • 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
(Pan troglodytes)
Mammalia ATL3 34 33
  • 99.74 (n)
(Canis familiaris)
Mammalia ATL3 34 33
  • 91.5 (n)
(Bos Taurus)
Mammalia ATL3 34 33
  • 90.7 (n)
(Mus musculus)
Mammalia Atl3 16 34 33
  • 90.02 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 90 (a)
-- 34
  • 82 (a)
(Rattus norvegicus)
Mammalia Atl3 33
  • 89.4 (n)
(Monodelphis domestica)
Mammalia ATL3 34
  • 76 (a)
(Anolis carolinensis)
Reptilia ATL3 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia atl3 33
  • 70.57 (n)
(Danio rerio)
Actinopterygii atl3 34 33
  • 67.14 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8856 33
fruit fly
(Drosophila melanogaster)
Insecta atl 34
  • 50 (a)
(Caenorhabditis elegans)
Secernentea atln-1 34
  • 50 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 42 (a)
Cin.1135 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1135 33
Species where no ortholog for ATL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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

Gene Tree for ATL3 (if available)
Gene Tree for ATL3 (if available)
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:

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

Variants for ATL3 Gene

Sequence variations from dbSNP and Humsavar for ATL3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs112847445 benign, Hereditary sensory neuropathy type IF 63,631,078(-) C/T coding_sequence_variant, missense_variant
rs151040560 benign, Hereditary sensory neuropathy type IF 63,644,238(-) A/G coding_sequence_variant, synonymous_variant
rs17158455 benign, Hereditary sensory neuropathy type IF 63,631,205(-) T/C coding_sequence_variant, synonymous_variant
rs189119869 benign, Hereditary sensory neuropathy type IF 63,631,145(-) T/C/G coding_sequence_variant, synonymous_variant
rs200026815 likely-benign, Hereditary sensory neuropathy type IF 63,631,058(-) G/A coding_sequence_variant, synonymous_variant

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

(6) MalaCards diseases for ATL3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, 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
spastic paraplegia 3a
  • spastic paraplegia 3, autosomal dominant
  • peripheral neuropathy
- elite association - COSMIC cancer census association via MalaCards
Search ATL3 in MalaCards View complete list of genes associated with diseases


  • 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.

Additional Disease Information for ATL3

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 58
  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 58
  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 58
  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 58
  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 58

Products for ATL3 Gene

  • Addgene plasmids for ATL3

Sources for ATL3 Gene

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