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    ATG4C autophagy related 4C cysteine peptidase [ Homo sapiens (human) ]

    Gene ID: 84938, updated on 17-Jun-2024

    Summary

    Official Symbol
    ATG4Cprovided by HGNC
    Official Full Name
    autophagy related 4C cysteine peptidaseprovided by HGNC
    Primary source
    HGNC:HGNC:16040
    See related
    Ensembl:ENSG00000125703 MIM:611339; AllianceGenome:HGNC:16040
    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
    APG4C; AUTL1; AUTL3; APG4-C; HsAPG4C
    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. Alternate transcriptional splice variants, encoding the same protein, have been characterized. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 4.0), placenta (RPKM 3.4) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See ATG4C in Genome Data Viewer
    Location:
    1p31.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (62784132..62865516)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (62662283..62743647)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (63249803..63331187)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 946 Neighboring gene Sharpr-MPRA regulatory region 4934 Neighboring gene DOCK7 divergent transcript Neighboring gene uncharacterized LOC124904194 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:63220743-63221288 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:63221289-63221835 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:63221836-63222381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1121 Neighboring gene Sharpr-MPRA regulatory region 3967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1123 Neighboring gene NANOG hESC enhancer GRCh37_chr1:63347799-63348356 Neighboring gene VISTA enhancer hs311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:63432364-63432864 Neighboring gene VISTA enhancer hs168 Neighboring gene VISTA enhancer hs169 Neighboring gene long intergenic non-protein coding RNA 1739 Neighboring gene MPRA-validated peak269 silencer Neighboring gene uncharacterized LOC105378770 Neighboring gene long intergenic non-protein coding RNA 466 Neighboring gene RNA, 5S ribosomal pseudogene 49

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
    EBI GWAS Catalog
    Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women.
    EBI GWAS Catalog
    Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
    EBI GWAS Catalog

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ14867

    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 endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    Process Evidence Code Pubs
    involved_in C-terminal protein lipidation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 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 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 cellular_component ND
    No biological Data available
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    cysteine protease ATG4C
    Names
    APG4 autophagy 4 homolog C
    ATG4 autophagy related 4 homolog C
    AUT-like 1, cysteine endopeptidase
    AUT-like 3 cysteine endopeptidase
    autophagin-3
    autophagy-related cysteine endopeptidase 3
    autophagy-related protein 4 homolog C
    epididymis secretory sperm binding protein
    NP_116241.2
    NP_835739.1

    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_032852.4NP_116241.2  cysteine protease ATG4C

      See identical proteins and their annotated locations for NP_116241.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the predominant transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC099794, BC033024, BI518482, BM146035, BQ777265
      Consensus CDS
      CCDS623.1
      UniProtKB/Swiss-Prot
      A6NLR8, D3DQ58, Q96DT6, Q96K04
      UniProtKB/TrEMBL
      A0A384MTY5, Q05D29
      Related
      ENSP00000322159.4, ENST00000317868.9
      Conserved Domains (1) summary
      pfam03416
      Location:77394
      Peptidase_C54; Peptidase family C54
    2. NM_178221.3NP_835739.1  cysteine protease ATG4C

      See identical proteins and their annotated locations for NP_835739.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses a different splice site in the 5' UTR as compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC099794, BC008395, BC033024, BM146035, BM720875, BQ777265, DB183325
      Consensus CDS
      CCDS623.1
      UniProtKB/Swiss-Prot
      A6NLR8, D3DQ58, Q96DT6, Q96K04
      UniProtKB/TrEMBL
      A0A384MTY5, Q05D29
      Related
      ENSP00000360161.3, ENST00000371120.7
      Conserved Domains (1) summary
      pfam03416
      Location:77394
      Peptidase_C54; Peptidase family C54

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      62784132..62865516
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      62662283..62743647
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)