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Aliases for ATL1 Gene

Aliases for ATL1 Gene

  • Atlastin GTPase 1 2 3 5
  • Guanine Nucleotide-Binding Protein 3 3 4
  • Brain-Specific GTP-Binding Protein 3 4
  • Spastic Paraplegia 3 Protein A 3 4
  • GTP-Binding Protein 3 3 4
  • SPG3A 3 4
  • GBP-3 3 4
  • HGBP3 3 4
  • GBP3 3 4
  • Spastic Paraplegia 3A (Autosomal Dominant) 2
  • Guanylate-Binding Protein 3 3
  • Atlastin-1 3
  • EC 3.6.5.- 4
  • Atlastin1 3
  • Atlastin 2
  • AD-FSP 3
  • HSN1D 3
  • FSP1 3
  • SPG3 3

External Ids for ATL1 Gene

Previous HGNC Symbols for ATL1 Gene

  • SPG3
  • SPG3A

Previous GeneCards Identifiers for ATL1 Gene

  • GC14P050097
  • GC14P050999
  • GC14P031125

Summaries for ATL1 Gene

Entrez Gene Summary for ATL1 Gene

  • The protein encoded by this gene is a GTPase and a Golgi body transmembrane protein. The encoded protein can form a homotetramer and has been shown to interact with spastin and with mitogen-activated protein kinase kinase kinase kinase 4. This protein may be involved in axonal maintenance as evidenced by the fact that defects in this gene are a cause of spastic paraplegia type 3. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for ATL1 Gene

ATL1 (Atlastin GTPase 1) is a Protein Coding gene. Diseases associated with ATL1 include Spastic Paraplegia 3A, Autosomal Dominant and Neuropathy, Hereditary Sensory, Type Id. Among its related pathways are Cytoskeletal Signaling. 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 ATL1 Gene

  • GTPase tethering membranes through formation of trans-homooligomers and mediating homotypic fusion of endoplasmic reticulum membranes. Functions in endoplasmic reticulum tubular network biogenesis. May also regulate Golgi biogenesis. May regulate axonal development.

Gene Wiki entry for ATL1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ATL1 Gene

Genomics for ATL1 Gene

Regulatory Elements for ATL1 Gene

Enhancers for ATL1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14F050607 0.8 FANTOM5 ENCODE 13.9 +75.9 75901 2.2 IKZF1 MAP4K5 ATL1 ABHD12B NIN TRIM9 RN7SL452P SNRPGP1
GH14F050599 0.9 FANTOM5 13.8 +67.4 67383 0.0 PRDM10 GABPA ATL1 MAP4K5 TRIM9 CDKL1 SNRPGP1 RN7SL452P
GH14F049851 0.5 ENCODE 13.8 -679.8 -679817 3.3 ARNT MLX CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 VCPKMT ATL1 POLE2 RHOQP1 RPS29 LRR1 NEMF RNU6-539P
GH14F049891 1.1 ENCODE 13.8 -636.7 -636749 8.9 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ATL1 POLE2 VCPKMT RPL36AL ARF6 RNU6-189P
GH14F050737 0.3 FANTOM5 11.8 +204.6 204628 0.1 HDGF PKNOX1 EBF1 POLR2A EED ETV6 CREM MAZ MTA2 CBFB ATL1 SAV1 CDKL1 MAP4K5 NIN GC14M050675 LOC105370489
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around ATL1 on UCSC Golden Path with GeneCards custom track

Promoters for ATL1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000417434 -609 3401 HDGF ATF1 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF48 ZNF2 GLIS2

Genomic Location for ATL1 Gene

Chromosome:
14
Start:
50,532,509 bp from pter
End:
50,633,068 bp from pter
Size:
100,560 bases
Orientation:
Plus strand

Genomic View for ATL1 Gene

Genes around ATL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATL1 Gene

Proteins for ATL1 Gene

  • Protein details for ATL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WXF7-ATLA1_HUMAN
    Recommended name:
    Atlastin-1
    Protein Accession:
    Q8WXF7
    Secondary Accessions:
    • A6NND5
    • A8K2C0
    • G5E9T1
    • O95890
    • Q69YH7
    • Q96FK0

    Protein attributes for ATL1 Gene

    Size:
    558 amino acids
    Molecular mass:
    63544 Da
    Quaternary structure:
    • Monomer as apoprotein and in the GDP-bound form. Homodimer in the GTP-bound form. Interacts (via N-terminal region) with MAP4K4 (via CNH regulatory domain). Interacts with REEP5, RTN3 and RTN4 (via the transmembrane region). Interacts with SPAST; interaction is direct. May interact with TMED2. Interacts with REEP1. Interacts with CPT1C. Interacts with ARL6IP1 (By similarity). Interacts with ZFYVE27 (PubMed:23969831).
    SequenceCaution:
    • Sequence=AAD20047.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAK51160.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ATL1 Gene

    Alternative splice isoforms for ATL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATL1 Gene

Post-translational modifications for ATL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for ATL1 (atlastin)
  • Abcam antibodies for ATL1

No data available for DME Specific Peptides for ATL1 Gene

Domains & Families for ATL1 Gene

Protein Domains for ATL1 Gene

Suggested Antigen Peptide Sequences for ATL1 Gene

Graphical View of Domain Structure for InterPro Entry

Q8WXF7

UniProtKB/Swiss-Prot:

ATLA1_HUMAN :
  • Contains 1 GB1/RHD3-type G (guanine nucleotide-binding) domain.
  • Belongs to the TRAFAC class dynamin-like GTPase superfamily. GB1/RHD3-type GTPase family. GB1 subfamily.
Domain:
  • Contains 1 GB1/RHD3-type G (guanine nucleotide-binding) domain.
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 ATL1: view

No data available for Gene Families for ATL1 Gene

Function for ATL1 Gene

Molecular function for ATL1 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. May also regulate Golgi biogenesis. May regulate axonal development.

Enzyme Numbers (IUBMB) for ATL1 Gene

Gene Ontology (GO) - Molecular Function for ATL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003924 GTPase activity IEA,IDA 14506257
GO:0005515 protein binding IPI 16815977
GO:0005525 GTP binding IEA,ISS --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with ATL1: view
genes like me logo Genes that share phenotypes with ATL1: view

Human Phenotype Ontology for ATL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ATL1 Gene

MGI Knock Outs for ATL1:

Animal Model Products

miRNA for ATL1 Gene

miRTarBase miRNAs that target ATL1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for ATL1 Gene

Localization for ATL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATL1 Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein. Cell projection, axon. Note=Localizes to endoplasmic reticulum tubular network. {ECO:0000250 UniProtKB:Q8BH66}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for ATL1 Gene COMPARTMENTS Subcellular localization image for ATL1 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
cytoskeleton 1
cytosol 1
endosome 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for ATL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000137 Golgi cis cisterna ISS --
GO:0000139 Golgi membrane IEA --
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IDA 19665976
GO:0005789 endoplasmic reticulum membrane ISS --
genes like me logo Genes that share ontologies with ATL1: view

Pathways & Interactions for ATL1 Gene

SuperPathways for ATL1 Gene

SuperPathway Contained pathways
1 Cytoskeletal Signaling
genes like me logo Genes that share pathways with ATL1: view

Pathways by source for ATL1 Gene

1 Cell Signaling Technology pathway for ATL1 Gene

Gene Ontology (GO) - Biological Process for ATL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007029 endoplasmic reticulum organization IDA 19665976
GO:0007409 axonogenesis ISS --
GO:0051260 protein homooligomerization IDA 14506257
genes like me logo Genes that share ontologies with ATL1: view

No data available for SIGNOR curated interactions for ATL1 Gene

Transcripts for ATL1 Gene

Unigene Clusters for ATL1 Gene

Atlastin GTPase 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ATL1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c · 3d · 3e ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - -
SP2: - - - -
SP3: - - -
SP4: - -
SP5:
SP6:

Relevant External Links for ATL1 Gene

GeneLoc Exon Structure for
ATL1
ECgene alternative splicing isoforms for
ATL1

Expression for ATL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATL1 Gene

mRNA differential expression in normal tissues according to GTEx for ATL1 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x5.3), Brain - Anterior cingulate cortex (BA24) (x4.6), and Brain - Cortex (x4.2).

Protein differential expression in normal tissues from HIPED for ATL1 Gene

This gene is overexpressed in Frontal cortex (17.8), Brain (10.1), Fetal Brain (9.4), Spinal cord (7.0), and Peripheral blood mononuclear cells (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ATL1 Gene



Protein tissue co-expression partners for ATL1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ATL1 Gene:

ATL1

SOURCE GeneReport for Unigene cluster for ATL1 Gene:

Hs.584905

mRNA Expression by UniProt/SwissProt for ATL1 Gene:

Q8WXF7-ATLA1_HUMAN
Tissue specificity: Expressed predominantly in the adult and fetal central nervous system. Measurable expression in all tissues examined, although expression in adult brain is at least 50-fold higher than in other tissues. Detected predominantly in pyramidal neurons in the cerebral cortex and the hippocampus of the brain. Expressed in upper and lower motor neurons (at protein level).
genes like me logo Genes that share expression patterns with ATL1: view

Primer Products

Orthologs for ATL1 Gene

This gene was present in the common ancestor of animals.

Orthologs for ATL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ATL1 34 35
  • 99.7 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ATL1 35
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ATL1 34 35
  • 95.4 (n)
cow
(Bos Taurus)
Mammalia ATL1 34 35
  • 94.44 (n)
oppossum
(Monodelphis domestica)
Mammalia ATL1 35
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Atl1 34
  • 90.98 (n)
mouse
(Mus musculus)
Mammalia Atl1 34 16 35
  • 90.74 (n)
chicken
(Gallus gallus)
Aves ATL1 34 35
  • 80.98 (n)
lizard
(Anolis carolinensis)
Reptilia ATL1 35
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atl1 34
  • 80 (n)
zebrafish
(Danio rerio)
Actinopterygii atl1 34 35
  • 72.04 (n)
fruit fly
(Drosophila melanogaster)
Insecta atl 35
  • 53 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea atln-1 35
  • 49 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 41 (a)
OneToMany
Species where no ortholog for ATL1 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 ATL1 Gene

ENSEMBL:
Gene Tree for ATL1 (if available)
TreeFam:
Gene Tree for ATL1 (if available)

Paralogs for ATL1 Gene

Variants for ATL1 Gene

Sequence variations from dbSNP and Humsavar for ATL1 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs119476046 Spastic paraplegia 3, autosomal dominant (SPG3) [MIM:182600], Pathogenic 50,613,343(+) AAAAA(C/T)GCCTC reference, missense
rs119476047 Spastic paraplegia 3, autosomal dominant (SPG3) [MIM:182600], Pathogenic 50,614,425(+) CCATT(A/C)CTGTT reference, missense
rs119476048 Spastic paraplegia 3, autosomal dominant (SPG3) [MIM:182600], Pathogenic 50,614,422(+) CATCC(A/G)TTCCT reference, missense
rs119476049 Spastic paraplegia 3, autosomal dominant (SPG3) [MIM:182600], Pathogenic 50,613,278(+) TGTTC(A/G)AGACT reference, missense
rs119476050 Spastic paraplegia 3, autosomal dominant (SPG3) [MIM:182600], Pathogenic 50,628,154(+) TTAGC(C/T)GGCGT reference, missense

Structural Variations from Database of Genomic Variants (DGV) for ATL1 Gene

Variant ID Type Subtype PubMed ID
esv2663828 CNV deletion 23128226
esv2665685 CNV deletion 23128226
esv2666565 CNV deletion 23128226
esv3351061 CNV insertion 20981092
esv3551543 CNV deletion 23714750
esv3581192 CNV loss 25503493
esv3634482 CNV loss 21293372
esv3634483 CNV loss 21293372
esv3634484 CNV loss 21293372
nsv1039493 CNV gain 25217958
nsv1273 CNV deletion 18451855
nsv1274 CNV insertion 18451855
nsv474501 CNV novel sequence insertion 20440878
nsv564839 CNV loss 21841781
nsv826949 CNV gain 20364138
nsv974474 CNV duplication 23825009
nsv976339 CNV duplication 23825009

Variation tolerance for ATL1 Gene

Residual Variation Intolerance Score: 11.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.46; 10.06% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ATL1 Gene

Human Gene Mutation Database (HGMD)
ATL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATL1 Gene

Disorders for ATL1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for ATL1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
spastic paraplegia 3a, autosomal dominant
  • spastic paraplegia 3, autosomal dominant
neuropathy, hereditary sensory, type id
  • hereditary sensory neuropathy type id
spastic paraplegia 3a
  • spastic paraplegia 3, autosomal dominant
spastic paraplegia 3
  • spastic paraplegia 3, autosomal dominant
neuropathy, hereditary sensory, type ie
  • hereditary sensory neuropathy type 1
- elite association - COSMIC cancer census association via MalaCards
Search ATL1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

ATLA1_HUMAN
  • Neuropathy, hereditary sensory, 1D (HSN1D) [MIM:613708]: A disease characterized by adult-onset distal axonal sensory neuropathy leading to mutilating ulcerations as well as hyporeflexia. Some patients may show features suggesting upper neuron involvement. {ECO:0000269 PubMed:21194679}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Spastic paraplegia 3, autosomal dominant (SPG3) [MIM:182600]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269 PubMed:11685207, ECO:0000269 PubMed:12112092, ECO:0000269 PubMed:12939451, ECO:0000269 PubMed:14695538, ECO:0000269 PubMed:15184642, ECO:0000269 PubMed:16533974, ECO:0000269 PubMed:17427918, ECO:0000269 PubMed:20718791, ECO:0000269 PubMed:20932283, ECO:0000269 PubMed:21336785, ECO:0000269 PubMed:23483706, ECO:0000269 PubMed:24473461}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for ATL1

Genetic Association Database (GAD)
ATL1
Human Genome Epidemiology (HuGE) Navigator
ATL1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ATL1
genes like me logo Genes that share disorders with ATL1: view

No data available for Genatlas for ATL1 Gene

Publications for ATL1 Gene

  1. Mutations in the SPG3A gene encoding the GTPase atlastin interfere with vesicle trafficking in the ER/Golgi interface and Golgi morphogenesis. (PMID: 17321752) Namekawa M. … Ruberg M. (Mol. Cell. Neurosci. 2007) 3 4 22 64
  2. Characterization of a novel SPG3A deletion in a French-Canadian family. (PMID: 17427918) Meijer I.A. … Rouleau G.A. (Ann. Neurol. 2007) 3 4 22 64
  3. De novo occurrence of novel SPG3A/atlastin mutation presenting as cerebral palsy. (PMID: 16533974) Rainier S. … Fink J.K. (Arch. Neurol. 2006) 3 4 22 64
  4. Interaction of two hereditary spastic paraplegia gene products, spastin and atlastin, suggests a common pathway for axonal maintenance. (PMID: 16815977) Evans K.J. … Lauring B.P. (Proc. Natl. Acad. Sci. U.S.A. 2006) 3 4 22 64
  5. Novel mutations in the Atlastin gene (SPG3A) in families with autosomal dominant hereditary spastic paraplegia and evidence for late onset forms of HSP linked to the SPG3A locus. (PMID: 14695538) Sauter S.M. … Neesen J. (Hum. Mutat. 2004) 3 4 22 64

Products for ATL1 Gene

Sources for ATL1 Gene

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