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    ATG4A autophagy related 4A cysteine peptidase [ Homo sapiens (human) ]

    Gene ID: 115201, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ATG4Aprovided by HGNC
    Official Full Name
    autophagy related 4A cysteine peptidaseprovided by HGNC
    Primary source
    HGNC:HGNC:16489
    See related
    Ensembl:ENSG00000101844 MIM:300663; AllianceGenome:HGNC:16489
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    APG4A; AUTL2; HsAPG4A
    Summary
    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. [provided by RefSeq, Mar 2016]
    Expression
    Ubiquitous expression in thyroid (RPKM 5.4), colon (RPKM 5.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATG4A in Genome Data Viewer
    Location:
    Xq22.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (108088829..108154671)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (106526530..106592262)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (107335008..107397901)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NACHT, LRR and PYD domains-containing protein 10-like Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:107234349-107235548 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107239283-107239988 Neighboring gene NLR family pyrin domain containing 3 pseudogene 1 Neighboring gene testis expressed 13B Neighboring gene V-set and immunoglobulin domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29839 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:107370111-107370674 Neighboring gene proteasome 26S subunit, non-ATPase 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:107399852-107400352 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107419738-107420424 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107420425-107421109 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107421110-107421795 Neighboring gene collagen type IV alpha 6 chain Neighboring gene uncharacterized LOC124905205 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:107513459-107514658 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:107596629-107597181 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:107609798-107610337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:107634248-107634889 Neighboring gene collagen type IV alpha 5 chain Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:107843610-107844540 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:107884720-107885919

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Association of ATG4A single nucleotide polymorphism rs807185 on risk of microscopic polyangiitis in Chinese population. Li Y, et al. Int Immunopharmacol, 2023 Oct. PMID 37494842
    2. ATG4A promotes tumor metastasis by inducing the epithelial-mesenchymal transition and stem-like properties in gastric cells. Yang SW, et al. Oncotarget, 2016 Jun 28. PMID 27276686, Free PMC Article
    3. An intron SNP rs807185 in ATG4A decreases the risk of lung cancer in a southwest Chinese population. He Q, et al. Eur J Cancer Prev, 2016 Jul. PMID 26061994
    4. A mammosphere formation RNAi screen reveals that ATG4A promotes a breast cancer stem-like phenotype. Wolf J, et al. Breast Cancer Res, 2013 Nov 14. PMID 24229464, Free PMC Article
    5. A systematic bioinformatics approach for selection of target and screening of ligand for malignant tumours suppressing APG4A gene on Xq22.1. Niranjan V, et al. Int J Comput Biol Drug Des, 2010. PMID 21297227

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Loss of ATG4B and ATG4A results in two-stage cell cycle defects in pancreatic ductal adenocarcinoma cells.
      Title: Loss of ATG4B and ATG4A results in two-stage cell cycle defects in pancreatic ductal adenocarcinoma cells.
    2. Association of ATG4A single nucleotide polymorphism rs807185 on risk of microscopic polyangiitis in Chinese population.
      Title: Association of ATG4A single nucleotide polymorphism rs807185 on risk of microscopic polyangiitis in Chinese population.
    3. Alterations of ATG4A and LC3B in neurons derived from Alzheimer's disease patients.
      Title: Alterations of ATG4A and LC3B in neurons derived from Alzheimer's disease patients.
    4. ATG4A regulates human erythroid maturation and mitochondrial clearance.
      Title: ATG4A regulates human erythroid maturation and mitochondrial clearance.
    5. Knockdown of ATG4A inhibits breast cancer progression and promotes tamoxifen chemosensitivity by suppressing autophagy.
      Title: Knockdown of ATG4A inhibits breast cancer progression and promotes tamoxifen chemosensitivity by suppressing autophagy.
    6. Defects in LC3B2 and ATG4A underlie HSV2 meningitis and reveal a critical role for autophagy in antiviral defense in humans.
      Title: Defects in LC3B2 and ATG4A underlie HSV2 meningitis and reveal a critical role for autophagy in antiviral defense in humans.
    7. ATG4 family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system.
      Title: ATG4 family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system.
    8. Overexpression of ATG4a promotes autophagy and proliferation, and inhibits apoptosis in lens epithelial cells via the AMPK and Akt pathways.
      Title: Overexpression of ATG4a promotes autophagy and proliferation, and inhibits apoptosis in lens epithelial cells via the AMPK and Akt pathways.
    9. Long-noncoding RNA MALAT1 sponges microRNA-92a-3p to inhibit doxorubicin-induced cardiac senescence by targeting ATG4a.
      Title: Long-noncoding RNA MALAT1 sponges microRNA-92a-3p to inhibit doxorubicin-induced cardiac senescence by targeting ATG4a.
    10. The insufficiency of ATG4A in macroautophagy.
      Title: The insufficiency of ATG4A in macroautophagy.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif binds more strongly to autophagy-related protein 4 (ATG4)-cleaved form I (LC3-I) than to ATG4-cleaved form II (LC3-II) in an A3G-independent manner PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type peptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-phosphatidylethanolamide deconjugating activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein-phosphatidylethanolamide deconjugating activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in aggrephagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagosome assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in autophagy IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein delipidation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteolysis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    cysteine protease ATG4A
    Names
    APG4 autophagy 4 homolog A
    ATG4 autophagy related 4 homolog A
    AUT-like 2, cysteine endopeptidase
    autophagin 2
    autophagy-related cysteine endopeptidase 2
    autophagy-related protein 4 homolog A
    hAPG4A
    NP_001308216.1
    NP_001308217.1
    NP_001308218.1
    NP_001308219.1
    NP_443168.2
    NP_840054.1
    NP_840055.1
    XP_011529144.1
    XP_047297757.1
    XP_047297758.1
    XP_047297759.1
    XP_054182398.1
    XP_054182399.1
    XP_054182400.1
    XP_054182401.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001321287.2 → NP_001308216.1  cysteine protease ATG4A isoform c

      Status: REVIEWED

      Source sequence(s)
      AL031177
      UniProtKB/TrEMBL
      B4DEA4
      Conserved Domains (1) summary
      pfam03416
      Location:1 → 258
      Peptidase_C54; Peptidase family C54

    2. NM_001321288.2 → NP_001308217.1  cysteine protease ATG4A isoform c

      Status: REVIEWED

      Source sequence(s)
      AL031177
      UniProtKB/TrEMBL
      B4DEA4
      Conserved Domains (1) summary
      pfam03416
      Location:1 → 258
      Peptidase_C54; Peptidase family C54

    3. NM_001321289.2 → NP_001308218.1  cysteine protease ATG4A isoform d

      Status: REVIEWED

      Source sequence(s)
      AA648264, AK293533, AL031177, BC041862, BC061696
      UniProtKB/TrEMBL
      B4DEA4
      Conserved Domains (1) summary
      pfam03416
      Location:1 → 196
      Peptidase_C54; Peptidase family C54

    4. NM_001321290.2 → NP_001308219.1  cysteine protease ATG4A isoform e

      Status: REVIEWED

      Source sequence(s)
      AL031177
      Conserved Domains (1) summary
      pfam03416
      Location:1 → 163
      Peptidase_C54; Peptidase family C54

    5. NM_052936.5 → NP_443168.2  cysteine protease ATG4A isoform a

      See identical proteins and their annotated locations for NP_443168.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform (a).
      Source sequence(s)
      AA648264, BC041862, BC061696
      Consensus CDS
      CCDS14538.1
      UniProtKB/Swiss-Prot
      A6NCH2, B2RAZ7, D3DUY0, O95534, Q5JYY9, Q5JYZ0, Q86VE5, Q8WYN0, Q96KQ0, Q96KQ1
      Related
      ENSP00000361306.3, ENST00000372232.8
      Conserved Domains (1) summary
      pfam03416
      Location:42 → 335
      Peptidase_C54; Peptidase family C54

    6. NM_178270.4 → NP_840054.1  cysteine protease ATG4A isoform b

      See identical proteins and their annotated locations for NP_840054.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes isoform b.
      Source sequence(s)
      AA648264, AJ320509, BC041862, BC061696
      Consensus CDS
      CCDS14539.1
      UniProtKB/Swiss-Prot
      Q8WYN0
      Related
      ENSP00000298131.5, ENST00000345734.7
      Conserved Domains (1) summary
      pfam03416
      Location:43 → 273
      Peptidase_C54; Peptidase family C54

    7. NM_178271.3 → NP_840055.1  cysteine protease ATG4A isoform c

      Status: REVIEWED

      Source sequence(s)
      AA648264, BC041862, BM541631
      UniProtKB/TrEMBL
      B4DEA4
      Conserved Domains (1) summary
      pfam03416
      Location:1 → 258
      Peptidase_C54; Peptidase family C54

    RNA

    1. NR_135608.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL031177
      Related
      ENST00000343524.9

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      108088829..108154671
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441801.1 → XP_047297757.1  cysteine protease ATG4A isoform X1

    2. XM_047441802.1 → XP_047297758.1  cysteine protease ATG4A isoform X2

    3. XM_047441803.1 → XP_047297759.1  cysteine protease ATG4A isoform X3

      UniProtKB/TrEMBL
      B4DEA4

    4. XM_011530842.2 → XP_011529144.1  cysteine protease ATG4A isoform X3

      See identical proteins and their annotated locations for XP_011529144.1

      UniProtKB/TrEMBL
      B4DEA4
      Conserved Domains (1) summary
      pfam03416
      Location:1 → 258
      Peptidase_C54; Peptidase family C54

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      106526530..106592262
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326424.1 → XP_054182399.1  cysteine protease ATG4A isoform X2

    2. XM_054326423.1 → XP_054182398.1  cysteine protease ATG4A isoform X1

    3. XM_054326425.1 → XP_054182400.1  cysteine protease ATG4A isoform X3

      UniProtKB/TrEMBL
      B4DEA4

    4. XM_054326426.1 → XP_054182401.1  cysteine protease ATG4A isoform X3

      UniProtKB/TrEMBL
      B4DEA4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WYN0.1 GenPept UniProtKB/Swiss-Prot:Q8WYN0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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