The protein encoded by this gene is an autophagy factor and a target of the TOR kinase signaling pathway. The encoded protein is essential for autophagosome formation and mitophagy. [provided by RefSeq, Oct 2016] See more...

Aliases for ATG13 Gene

Aliases for ATG13 Gene

  • Autophagy Related 13 2 3 5
  • KIAA0652 2 3 4
  • Autophagy-Related Protein 13 3 4
  • ATG13 Autophagy Related 13 Homolog (S. Cerevisiae) 2
  • ATG13 Autophagy Related 13 Homolog 3
  • PARATARG8 3
  • ATG13 5

External Ids for ATG13 Gene

Previous HGNC Symbols for ATG13 Gene

  • KIAA0652

Previous GeneCards Identifiers for ATG13 Gene

  • GC11P046638
  • GC11P046345
  • GC11P046619
  • GC11P046621
  • GC11P046623
  • GC11P046625

Summaries for ATG13 Gene

Entrez Gene Summary for ATG13 Gene

  • The protein encoded by this gene is an autophagy factor and a target of the TOR kinase signaling pathway. The encoded protein is essential for autophagosome formation and mitophagy. [provided by RefSeq, Oct 2016]

GeneCards Summary for ATG13 Gene

ATG13 (Autophagy Related 13) is a Protein Coding gene. Diseases associated with ATG13 include Charcot-Marie-Tooth Disease, Axonal, Type 2E and Huntington Disease. Among its related pathways are Pathways of neurodegeneration - multiple diseases and Macroautophagy. Gene Ontology (GO) annotations related to this gene include protein kinase binding.

UniProtKB/Swiss-Prot Summary for ATG13 Gene

  • Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.

Gene Wiki entry for ATG13 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATG13 Gene

Genomics for ATG13 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ATG13 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATG13 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATG13

Genomic Locations for ATG13 Gene

Latest Assembly
chr11:46,617,527-46,674,818
(GRCh38/hg38)
Size:
57,292 bases
Orientation:
Plus strand

Previous Assembly
chr11:46,639,103-46,696,068
(GRCh37/hg19 by Entrez Gene)
Size:
56,966 bases
Orientation:
Plus strand

chr11:46,638,826-46,696,368
(GRCh37/hg19 by Ensembl)
Size:
57,543 bases
Orientation:
Plus strand

Genomic View for ATG13 Gene

Genes around ATG13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATG13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATG13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ATG13 Gene

Proteins for ATG13 Gene

  • Protein details for ATG13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75143-ATG13_HUMAN
    Recommended name:
    Autophagy-related protein 13
    Protein Accession:
    O75143
    Secondary Accessions:
    • B4DFI4
    • D3DQQ1
    • D3DQQ2
    • E9PQZ8
    • Q53EN6
    • Q9BRL3
    • Q9H8B0

    Protein attributes for ATG13 Gene

    Size:
    517 amino acids
    Molecular mass:
    56572 Da
    Quaternary structure:
    • Part of a complex consisting of ATG13, ULK1 and RB1CC1 (PubMed:19597335, PubMed:19211835, PubMed:19225151, PubMed:24290141). Interacts with ATG101 (PubMed:19597335, PubMed:19287211, PubMed:26299944). Interacts with ULK1 (via C-terminus); this interaction is increased in the absence of TMEM39A (PubMed:19287211, PubMed:21855797, PubMed:18936157, PubMed:31806350). Interacts with ULK2 (via C-terminus) (PubMed:19225151, PubMed:18936157). Interacts (via the LIR motif) with GABARAP, GABARAPL, GABARAPL2 (PubMed:23043107). Interacts (via the LIR motif) with MAP1LC3A, MAP1LC3B and MAP1LC3C (PubMed:24290141). Interacts with TAB2 and TAB3 (PubMed:21976705). Interacts with C9orf72 (PubMed:27334615). Interacts with RB1CC1; this interaction is increased in the absence of TMEM39A (PubMed:31806350).
    SequenceCaution:
    • Sequence=BAA31627.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAD97323.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ATG13 Gene

    Alternative splice isoforms for ATG13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATG13 Gene

Post-translational modifications for ATG13 Gene

  • Phosphorylated by ULK1, ULK2 and mTOR. Phosphorylation status depends on nutrient-rich conditions; dephosphorylated during starvation or following treatment with rapamycin. ULK1-mediated phosphorylation of ATG13 at Ser-355 is required for efficient clearance of depolarized mitochondria.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ATG13 Gene

Domains & Families for ATG13 Gene

Gene Families for ATG13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Transporters

Protein Domains for ATG13 Gene

Suggested Antigen Peptide Sequences for ATG13 Gene

GenScript: Design optimal peptide antigens:
  • Autophagy-related protein 13 (ATG13_HUMAN)
  • cDNA FLJ59492 (B4DFI4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75143

UniProtKB/Swiss-Prot:

ATG13_HUMAN :
  • The LIR motif (LC3-interacting region) is required for the interaction with the ATG8 family proteins GABARAP, GABARAPL, GABARAPL2, and MAP1LC3A.
  • Belongs to the ATG13 family. Metazoan subfamily.
Domain:
  • The LIR motif (LC3-interacting region) is required for the interaction with the ATG8 family proteins GABARAP, GABARAPL, GABARAPL2, and MAP1LC3A.
Family:
  • Belongs to the ATG13 family. Metazoan subfamily.
genes like me logo Genes that share domains with ATG13: view

Function for ATG13 Gene

Molecular function for ATG13 Gene

UniProtKB/Swiss-Prot Function:
Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.

Phenotypes From GWAS Catalog for ATG13 Gene

Gene Ontology (GO) - Molecular Function for ATG13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19211835
GO:0019901 protein kinase binding IPI 18936157
genes like me logo Genes that share ontologies with ATG13: view
genes like me logo Genes that share phenotypes with ATG13: view

Animal Models for ATG13 Gene

MGI Knock Outs for ATG13:
  • Atg13 Atg13<tm2b(EUCOMM)Hmgu>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATG13

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ATG13 Gene

Localization for ATG13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATG13 Gene

Cytoplasm, cytosol. Preautophagosomal structure. Note=Under starvation conditions, is localized to puncate structures primarily representing the isolation membrane; the isolation membrane sequesters a portion of the cytoplasm resulting in autophagosome formation. {ECO:0000269 PubMed:19211835}.

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 ATG13 gene
Compartment Confidence
mitochondrion 5
cytosol 4
plasma membrane 3
nucleus 3
lysosome 3
extracellular 2
cytoskeleton 2
peroxisome 2
endoplasmic reticulum 2
endosome 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATG13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000407 phagophore assembly site IBA,ISS --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA 21855797
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with ATG13: view

Pathways & Interactions for ATG13 Gene

genes like me logo Genes that share pathways with ATG13: view

Pathways by source for ATG13 Gene

SIGNOR curated interactions for ATG13 Gene

Activates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for ATG13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000045 autophagosome assembly IEA,IMP 19211835
GO:0000423 mitophagy IBA 21873635
GO:0006914 autophagy IEA --
GO:0016236 macroautophagy TAS --
GO:0016241 regulation of macroautophagy TAS --
genes like me logo Genes that share ontologies with ATG13: view

Drugs & Compounds for ATG13 Gene

No Compound Related Data Available

Transcripts for ATG13 Gene

mRNA/cDNA for ATG13 Gene

51 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
30 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATG13

Alternative Splicing Database (ASD) splice patterns (SP) for ATG13 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a ·
SP1: - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - -
SP4: - - - - - - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - - - - -
SP7: - - - - - - - - - - -
SP8: - - - - - - - - - -
SP9: - - - - -
SP10: - - - - - - -
SP11: - - - - - - - - -
SP12:
SP13: - - - - - - - - - - -
SP14: - -
SP15: - - - - -
SP16: - - - - - - - -
SP17: - - - - - - - - -
SP18:
SP19:
SP20:
SP21: - - - - - - - - - - - - - - -
SP22: - - - - - - -
SP23: - - - - - - - -
SP24: - - - -
SP25: -
SP26: - -
SP27: - - - - - -
SP28: - - - -
SP29:
SP30:
SP31:

ExUns: 13b ^ 14 ^ 15a · 15b ^ 16a · 16b · 16c ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21a · 21b ^ 22 ^ 23a · 23b ^ 24 ^ 25
SP1: - -
SP2: - - - -
SP3: - - -
SP4: - - - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19: - - - -
SP20: -
SP21:
SP22:
SP23:
SP24:
SP25:
SP26:
SP27:
SP28:
SP29:
SP30: - - - - - - - - - - -
SP31:

Relevant External Links for ATG13 Gene

GeneLoc Exon Structure for
ATG13

Expression for ATG13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATG13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ATG13 Gene

This gene is overexpressed in Neutrophil (25.9), Monocytes (16.6), and Testis (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATG13 Gene



Protein tissue co-expression partners for ATG13 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATG13

SOURCE GeneReport for Unigene cluster for ATG13 Gene:

Hs.127403

Evidence on tissue expression from TISSUES for ATG13 Gene

  • Nervous system(5)
  • Lung(4.6)
  • Muscle(4.5)
  • Liver(4.5)
  • Thyroid gland(4.4)
  • Intestine(3.3)
  • Eye(3.1)
  • Skin(2.8)
  • Heart(2.5)
  • Kidney(2.5)
  • Lymph node(2.2)
  • Spleen(2.2)
  • Bone marrow(2.2)
  • Pancreas(2.2)
  • Blood(2.2)
  • Adrenal gland(2)
  • Stomach(2)
genes like me logo Genes that share expression patterns with ATG13: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATG13 Gene

Orthologs for ATG13 Gene

This gene was present in the common ancestor of animals.

Orthologs for ATG13 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ATG13 29 30
  • 97.55 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ATG13 29 30
  • 93.7 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ATG13 29 30
  • 89.86 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Atg13 29
  • 88.36 (n)
Mouse
(Mus musculus)
Mammalia Atg13 29 16 30
  • 87.09 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ATG13 30
  • 85 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia ATG13 30
  • 83 (a)
OneToOne
Chicken
(Gallus gallus)
Aves ATG13 29 30
  • 83.66 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ATG13 30
  • 89 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia atg13 29
  • 71.26 (n)
Str.15163 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.17897 29
Zebrafish
(Danio rerio)
Actinopterygii atg13 29 30
  • 69.78 (n)
OneToOne
zgc63526 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1013 29
Fruit Fly
(Drosophila melanogaster)
Insecta Atg13 30
  • 30 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea atg-13 30
  • 26 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 50 (a)
OneToOne
Species where no ortholog for ATG13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 ATG13 Gene

ENSEMBL:
Gene Tree for ATG13 (if available)
TreeFam:
Gene Tree for ATG13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATG13: view image
Alliance of Genome Resources:
Additional Orthologs for ATG13

Paralogs for ATG13 Gene

No data available for Paralogs for ATG13 Gene

Variants for ATG13 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATG13 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs143855756 Benign: not provided 46,645,398(+) T/A
NM_001205119.1(ATG13):c.129T>A (p.Ser43=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR
rs193920809 Uncertain Significance: Malignant tumor of prostate 46,672,254(+) G/C
NM_001205119.1(ATG13):c.1576-1G>C
SPLICE_ACCEPTOR
rs61736849 Benign: not provided 46,667,803(+) T/C
NM_001205119.1(ATG13):c.1167T>C (p.Ser389=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ATG13 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for ATG13 Gene

Variant ID Type Subtype PubMed ID
esv3626191 CNV gain 21293372
esv993220 OTHER inversion 20482838
nsv38662 CNV deletion 16902084

Variation tolerance for ATG13 Gene

Residual Variation Intolerance Score: 70.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.49; 43.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATG13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATG13
Leiden Open Variation Database (LOVD)
ATG13

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATG13 Gene

Disorders for ATG13 Gene

MalaCards: The human disease database

(4) MalaCards diseases for ATG13 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search ATG13 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ATG13

genes like me logo Genes that share disorders with ATG13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATG13 Gene

Publications for ATG13 Gene

  1. The ER-Localized Transmembrane Protein TMEM39A/SUSR2 Regulates Autophagy by Controlling the Trafficking of the PtdIns(4)P Phosphatase SAC1. (PMID: 31806350) Miao G … Zhang H (Molecular cell 2020) 3 4
  2. The C9orf72 protein interacts with Rab1a and the ULK1 complex to regulate initiation of autophagy. (PMID: 27334615) Webster CP … De Vos KJ (The EMBO journal 2016) 3 4
  3. Structure of the Human Atg13-Atg101 HORMA Heterodimer: an Interaction Hub within the ULK1 Complex. (PMID: 26299944) Qi S … Hurley JH (Structure (London, England : 1993) 2015) 3 4
  4. Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism. (PMID: 24290141) Suzuki H … Wakatsuki S (Structure (London, England : 1993) 2014) 3 4
  5. TGFβ-activated kinase 1 (TAK1)-binding proteins (TAB) 2 and 3 negatively regulate autophagy. (PMID: 21976705) Takaesu G … Yoshimura A (Journal of biochemistry 2012) 3 4

Products for ATG13 Gene

Sources for ATG13 Gene