ATG4C Gene (Protein Coding)

Autophagy Related 4C Cysteine Peptidase

GC01P062784
GIFtS:
41
Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling t... See more...

Aliases for ATG4C Gene

Aliases for ATG4C Gene

  • Autophagy Related 4C Cysteine Peptidase 2 3 5
  • Autophagy-Related Cysteine Endopeptidase 3 3 4
  • Autophagy-Related Protein 4 Homolog C 3 4
  • AUT-Like 3 Cysteine Endopeptidase 3 4
  • Cysteine Protease ATG4C 3 4
  • Autophagin-3 3 4
  • APG4C 3 4
  • AUTL1 3 4
  • AUTL3 3 4
  • AUT (S. Cerevisiae)-Like 1, Cysteine Endopeptidase; AUT-Like 1, Cysteine Endopeptidase (S. Cerevisiae) 2
  • ATG4 Autophagy Related 4 Homolog C (S. Cerevisiae) 2
  • Epididymis Secretory Sperm Binding Protein 3
  • APG4 Autophagy 4 Homolog C (S. Cerevisiae) 2
  • Autophagy Related 4C, Cysteine Peptidase 2
  • ATG4 Autophagy Related 4 Homolog C 3
  • AUT-Like 1, Cysteine Endopeptidase 3
  • APG4 Autophagy 4 Homolog C 3
  • EC 3.4.22.- 4
  • EC 3.4.22 52
  • APG4-C 3

External Ids for ATG4C Gene

Previous HGNC Symbols for ATG4C Gene

  • AUTL1
  • APG4C

Previous GeneCards Identifiers for ATG4C Gene

  • GC01P062962
  • GC01P063249
  • GC01P061361

Summaries for ATG4C Gene

Entrez Gene Summary for ATG4C Gene

  • Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. Alternate transcriptional splice variants, encoding the same protein, have been characterized. [provided by RefSeq, Jul 2008]

GeneCards Summary for ATG4C Gene

ATG4C (Autophagy Related 4C Cysteine Peptidase) is a Protein Coding gene. Diseases associated with ATG4C include Rem Sleep Behavior Disorder and Childhood Disintegrative Disease. Among its related pathways are Autophagy - animal and Autophagy Pathway. Gene Ontology (GO) annotations related to this gene include peptidase activity and cysteine-type peptidase activity. An important paralog of this gene is ATG4D.

UniProtKB/Swiss-Prot Summary for ATG4C Gene

  • Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Is not essential for autophagy development under normal conditions but is required for a proper autophagic response under stressful conditions such as prolonged starvation (By similarity). Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3 and GABARAPL2, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms.

Additional gene information for ATG4C Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATG4C Gene

Genomics for ATG4C Gene

GeneHancer (GH) Regulatory Elements for ATG4C Gene

Promoters and enhancers for ATG4C 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
GH01J062686 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 510.5 -95.1 -95052 6.1 FOXK2 EP300 ZSCAN5C TCF12 POLR2G NCOR1 GTF2E2 PHF8 PHB2 FOS DOCK7 ATG4C ENSG00000235545 ITGB3BP USP1 piR-59769-017
GH01J062782 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 528.5 +0.2 195 3 ZBTB40 ZNF217 EP300 SIN3A NRF1 USF1 POLR2G SP1 PHF8 SIX5 ATG4C lnc-DOCK7-2
GH01J062754 Promoter 0.4 EPDnew 500.3 -29.7 -29719 0.1 NFATC3 MG828444 piR-36921-001 piR-53063-007 ATG4C
GH01J062811 Enhancer 0.9 Ensembl ENCODE 39.1 +27.0 26994 1.8 EP300 RCOR1 TRIM22 BCL11A ARNT MEF2B BATF IRF4 EBF1 TBP ATG4C lnc-ANGPTL3-5 piR-35674-025
GH01J062761 Enhancer 0.7 Ensembl ENCODE 41.2 -23.8 -23812 2.6 ZNF217 CTBP1 MCM5 DPF2 GATA3 SMARCE1 ZNF24 MCM2 piR-39891-002 piR-54040-002 ATG4C ALG6 L1TD1 DOCK7 piR-33730-002 MG828444
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATG4C on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATG4C

Genomic Locations for ATG4C Gene

Genomic Locations for ATG4C Gene
chr1:62,784,106-62,865,516
(GRCh38/hg38)
Size:
81,411 bases
Orientation:
Plus strand
chr1:63,249,777-63,331,184
(GRCh37/hg19)
Size:
81,408 bases
Orientation:
Plus strand

Genomic View for ATG4C Gene

Genes around ATG4C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATG4C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATG4C Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ATG4C Gene

Proteins for ATG4C Gene

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  • Protein details for ATG4C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DT6-ATG4C_HUMAN
    Recommended name:
    Cysteine protease ATG4C
    Protein Accession:
    Q96DT6
    Secondary Accessions:
    • A6NLR8
    • D3DQ58
    • Q96K04

    Protein attributes for ATG4C Gene

    Size:
    458 amino acids
    Molecular mass:
    52497 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB55356.1; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for ATG4C Gene

Protein Expression for ATG4C Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for ATG4C Gene

Q96DT6:
  • ILVPVRLGGE
  • SLIYMDPH
  • AGDWYGP
  • GQMLLAQGL
  • IGGKPKQS
  • KMDPSCT
  • GIIGGKPK

Post-translational modifications for ATG4C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ATG4C Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for ATG4C Gene

Gene Families for ATG4C Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for ATG4C Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ATG4C Gene

GenScript: Design optimal peptide antigens:
  • Autophagy-related protein 4 homolog C (ATG4C_HUMAN)
  • ATG4C protein (Q05D29_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96DT6

UniProtKB/Swiss-Prot:

ATG4C_HUMAN :
  • Belongs to the peptidase C54 family.
Family:
  • Belongs to the peptidase C54 family.
genes like me logo Genes that share domains with ATG4C: view

Function for ATG4C Gene

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  2. CRISPR
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  6. Cell Line

Molecular function for ATG4C Gene

UniProtKB/Swiss-Prot Function:
Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Is not essential for autophagy development under normal conditions but is required for a proper autophagic response under stressful conditions such as prolonged starvation (By similarity). Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3 and GABARAPL2, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by N-ethylmaleimide.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=47.5 uM for MAP1LC3B {ECO:0000269 PubMed:21177865}; KM=12.4 uM for GABARAPL2 {ECO:0000269 PubMed:21177865};

Enzyme Numbers (IUBMB) for ATG4C Gene

Phenotypes From GWAS Catalog for ATG4C Gene

Gene Ontology (GO) - Molecular Function for ATG4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IEA --
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with ATG4C: view
genes like me logo Genes that share phenotypes with ATG4C: view

Animal Models for ATG4C Gene

MGI Knock Outs for ATG4C:

Animal Model Products

  • Taconic Biosciences Mouse Models for ATG4C

CRISPR Products

miRNA for ATG4C Gene

miRTarBase miRNAs that target ATG4C

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ATG4C Gene

Localization for ATG4C Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATG4C Gene

Cytoplasm.

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 ATG4C gene
Compartment Confidence
cytosol 4
nucleus 3
mitochondrion 2
endoplasmic reticulum 2
lysosome 2
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
endosome 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for ATG4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with ATG4C: view

Pathways & Interactions for ATG4C Gene

genes like me logo Genes that share pathways with ATG4C: view

Pathways by source for ATG4C Gene

2 Reactome pathways for ATG4C Gene
2 KEGG pathways for ATG4C Gene
1 GeneTex pathway for ATG4C Gene

Gene Ontology (GO) - Biological Process for ATG4C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006914 autophagy IEA --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with ATG4C: view

No data available for SIGNOR curated interactions for ATG4C Gene

Drugs & Compounds for ATG4C Gene

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(7) Drugs for ATG4C Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Nimodipine Approved, Investigational Pharma Potentiation, Activator Ca2+ channel blocker (L-type) 36
Omeprazole Approved, Investigational, Vet_approved Pharma Activator H+,K+-ATPase inhibitor 427
Chloroquine diphosphate Pharma Antimalarial drug 164
Dexamethasone (DHAP) Pharma Glucocorticoidan;ti-inflammatory 0
Sulfacetamide Sodium Pharma Sulfonamide antibiotic 0

(7) ApexBio Compounds for ATG4C Gene

Compound Action Cas Number
Chloroquine diphosphate Antimalarial drug 50-63-5
Dexamethasone (DHAP) Glucocorticoidan;ti-inflammatory 1950-02-2
Divalproex Sodium Epilepsy/migraines/bipolar disorder medicine 76584-70-8
Nimodipine 66085-59-4
Omeprazole H+,K+-ATPase inhibitor 73590-58-6
Sulfacetamide Sodium Sulfonamide antibiotic 127-56-0
Trifluoperazine 2HCl 440-17-5
genes like me logo Genes that share compounds with ATG4C: view

Drug Products

Transcripts for ATG4C Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for ATG4C Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ATG4C Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
SP1: - - -
SP2: - - - -
SP3: - - - -
SP4: - - -
SP5: - - - - - - - -
SP6: - - - -
SP7: - -
SP8: -
SP9: - -

Relevant External Links for ATG4C Gene

GeneLoc Exon Structure for
ATG4C

Expression for ATG4C Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATG4C Gene

mRNA expression in normal human tissues for ATG4C Gene
mRNA expression by BioGPS for ATG4C GenemRNA expression by GTEx for ATG4C Gene

Protein differential expression in normal tissues from HIPED for ATG4C Gene

This gene is overexpressed in Frontal cortex (22.5), Heart (19.4), and Peripheral blood mononuclear cells (11.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ATG4C Gene



Protein tissue co-expression partners for ATG4C Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATG4C

SOURCE GeneReport for Unigene cluster for ATG4C Gene:

Hs.7353

mRNA Expression by UniProt/SwissProt for ATG4C Gene:

Q96DT6-ATG4C_HUMAN
Tissue specificity: Highly expressed in skeletal muscle, heart, liver and testis.

Evidence on tissue expression from TISSUES for ATG4C Gene

  • Nervous system(4.7)
  • Heart(4.4)
genes like me logo Genes that share expression patterns with ATG4C: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATG4C Gene

Orthologs for ATG4C Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ATG4C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia ATG4C 31 30
  • 100 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia ATG4C 31 30
  • 94.1 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia ATG4C 31 30
  • 93.52 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Atg4c 17 31 30
  • 87.92 (n)
rat
(Rattus norvegicus)
 Mammalia Atg4c 30
  • 85.88 (n)
oppossum
(Monodelphis domestica)
 Mammalia ATG4C 31
  • 85 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia ATG4C 31
  • 83 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves ATG4C 31 30
  • 80.35 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia ATG4C 31
  • 76 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia atg4c 30
  • 73.07 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.1688 30
zebrafish
(Danio rerio)
 Actinopterygii atg4c 31 30
  • 64.75 (n)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta CG6194 31
  • 27 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea atg-4.2 31
  • 22 (a)
 ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes ATG4 31
  • 21 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.753 31
  • 29 (a)
 OneToMany
Species where no ortholog for ATG4C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 ATG4C Gene

ENSEMBL:
Gene Tree for ATG4C (if available)
TreeFam:
Gene Tree for ATG4C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATG4C: view image

Paralogs for ATG4C Gene

Paralogs for ATG4C Gene

(1) SIMAP similar genes for ATG4C Gene using alignment to 5 proteins:

  • ATG4C_HUMAN
  • A6NGQ4_HUMAN
  • C9JC51_HUMAN
  • H7BZW5_HUMAN
  • Q05D29_HUMAN
genes like me logo Genes that share paralogs with ATG4C: view

Variants for ATG4C Gene

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Additional dbSNP identifiers (rs#s) for ATG4C Gene

Structural Variations from Database of Genomic Variants (DGV) for ATG4C Gene

Variant ID Type Subtype PubMed ID
esv3577901 CNV loss 25503493
nsv1145348 CNV deletion 24896259
nsv830015 CNV gain 17160897

Variation tolerance for ATG4C Gene

Residual Variation Intolerance Score: 76.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.74; 33.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATG4C Gene

Human Gene Mutation Database (HGMD)
ATG4C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATG4C

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATG4C Gene

Disorders for ATG4C Gene

MalaCards: The human disease database

(5) MalaCards diseases for ATG4C Gene - From: DISEASES

Disorder Aliases PubMed IDs
rem sleep behavior disorder
  • rapid eye movement sleep behavior disorder
childhood disintegrative disease
  • disintegrative psychosis
echolalia
atypical autism
  • pdd
pervasive developmental disorder
  • pervasive development disorder
- elite association - COSMIC cancer census association via MalaCards
Search ATG4C in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ATG4C

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ATG4C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATG4C Gene

Publications for ATG4C Gene

  1. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy. (PMID: 12446702) Mariño G … López-Otín C (The Journal of biological chemistry 2003) 2 4 23 54
  2. Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women. (PMID: 20966902) Croteau-Chonka DC … Mohlke KL (Obesity (Silver Spring, Md.) 2011) 3 41 54
  3. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. (PMID: 18193044) Kathiresan S … Orho-Melander M (Nature genetics 2008) 3 41 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

ExternalLinks

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