Free for academic non-profit institutions. Other users need a Commercial license

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 Neuropathy, Hereditary Sensory, Type Ie. 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.

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

Regulatory Elements for ATL3 Gene

Enhancers for ATL3 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
GH11G063760 1.6 Ensembl ENCODE dbSUPER 34.9 -93.5 -93487 9.8 PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF143 FOS ATL3 RTN3 C11orf95 GC11M063761
GH11G063718 1 dbSUPER 24.7 -49.2 -49247 6.1 ATF1 FOXA2 TCF12 ZNF766 GATA2 SP5 NFIL3 SMARCA4 HMBOX1 NBN ATL3 RTN3 PLA2G16 ENSG00000256789 ENSG00000203520 C11orf84 ENSG00000271100 GC11M063761
GH11G063665 1.3 ENCODE dbSUPER 17 +2.9 2876 6.6 HDGF CREB3L1 SIN3A YY1 ZNF766 CBX5 ZNF207 ZNF143 FOS KLF13 ATL3 C11orf84 TRMT112 TAF6L TTC9C PLA2G16 PIR31666 GC11P063651
GH11G063621 0.8 ENCODE 27.2 +49.5 49508 1.3 PKNOX1 FOXA2 SIN3A RAD21 RARA FOS ZHX2 USF2 ZNF217 SREBF1 ATL3 PLA2G16 GC11P063622 PIR57141 PIR34098 GC11P063626
GH11G063530 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11.4 +137.0 136956 8.4 PKNOX1 ATF1 ARNT YY1 ETS1 ZNF766 GATA2 ELK1 FOS KLF13 HRASLS2 ATL3 PLA2G16 ENSG00000203520 ENSG00000256789 AHNAK OTUB1 RARRES3 MARK2 PIR35897
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ATL3 on UCSC Golden Path with GeneCards custom track

Promoters for ATL3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000040551 974 1601 HDGF CREB3L1 SIN3A YY1 ZNF766 CBX5 ZNF207 ZNF143 KLF13 DEK

Genomic Location for ATL3 Gene

Chromosome:
11
Start:
63,624,082 bp from pter
End:
63,671,974 bp from pter
Size:
47,893 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};

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

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

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

No data available for Gene Families for ATL3 Gene

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.

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

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for ATL3

Flow Cytometry Products

No data available for 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}.

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
golgi apparatus 2
mitochondrion 1

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,IDA 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
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

Transcripts for ATL3 Gene

Unigene Clusters for ATL3 Gene

Atlastin GTPase 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for ATL3

Flow Cytometry Products

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
ECgene alternative splicing isoforms for
ATL3

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, PaxDb, 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:

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

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
Organs:
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

Primer Products

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 34 35
  • 99.74 (n)
dog
(Canis familiaris)
Mammalia ATL3 34 35
  • 91.5 (n)
cow
(Bos Taurus)
Mammalia ATL3 34 35
  • 90.7 (n)
mouse
(Mus musculus)
Mammalia Atl3 34 16 35
  • 90.02 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 90 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Atl3 34
  • 89.4 (n)
oppossum
(Monodelphis domestica)
Mammalia ATL3 35
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ATL3 35
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia atl3 34
  • 70.57 (n)
zebrafish
(Danio rerio)
Actinopterygii atl3 34 35
  • 67.14 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8856 34
fruit fly
(Drosophila melanogaster)
Insecta atl 35
  • 50 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea atln-1 35
  • 50 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 42 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1135 34
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

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

Paralogs for ATL3 Gene

Paralogs for ATL3 Gene

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

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 Sequence Context AA Info Type
rs587777108 Pathogenic, Neuropathy, hereditary sensory, 1F (HSN1F) [MIM:615632] 63,646,550(+) GACCG(C/T)ATTCT intron-variant, reference, missense
rs776571949 Likely benign 63,636,230(+) TCCCC(A/G)ACAGG intron-variant, reference, missense
rs864622016 Uncertain significance 63,631,379(-) AAGAA(G/T)ACCAA intron-variant, reference, missense
rs1000002768 -- 63,649,697(+) CAGCT(A/C)ATTTT intron-variant
rs1000054864 -- 63,650,131(+) TTGTT(C/T)AGTGG intron-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)

Relevant External Links for ATL3 Gene

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

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: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
neuropathy, hereditary sensory, type if
  • hereditary sensory neuropathy type if
neuropathy, hereditary sensory, type ie
  • hereditary sensory neuropathy type 1
spastic paraplegia 3a
  • spastic paraplegia 3, autosomal dominant
hereditary spastic paraplegia 3a
  • spastic paraplegia 3, autosomal dominant
hereditary sensory neuropathy
  • congenital insensitivity to pain
- 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.

Relevant External Links for ATL3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (Hum. Mol. Genet. 2008) 2 3 4 64
  2. Sensory neuropathy with bone destruction due to a mutation in the membrane-shaping atlastin GTPase 3. (PMID: 24459106) Kornak U. … Kurth I. (Brain 2014) 3 4 64
  3. Protrudin binds atlastins and endoplasmic reticulum-shaping proteins and regulates network formation. (PMID: 23969831) Chang J. … Blackstone C. (Proc. Natl. Acad. Sci. U.S.A. 2013) 3 4 64
  4. 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 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for ATL3 Gene

Sources for ATL3 Gene

Content
Loading form....