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

Gene ID: 84938, updated on 24-Jul-2021

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
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
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
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Genomic context

See ATG4C in Genome Data Viewer
Location:
1p31.3
Exon count:
14
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (62783765..62865516)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (63249803..63331187)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 7 Neighboring gene angiopoietin like 3 Neighboring gene ribosomal protein L13a pseudogene 9 Neighboring gene VISTA enhancer hs311 Neighboring gene VISTA enhancer hs168

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

Associated conditions

Description Tests
Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
GeneReviews: Not available
Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women.
GeneReviews: Not available
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
GeneReviews: Not available

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

Homology

Clone Names

  • FLJ14867

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cysteine-type endopeptidase activity IEA
Inferred from Electronic Annotation
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 
Process Evidence Code Pubs
involved_in autophagy IEA
Inferred from Electronic Annotation
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
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
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
XP_005271345.1
XP_011540615.1
XP_016858089.1
XP_016858090.1
XP_024306182.1

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
    Q96DT6
    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
    Q96DT6
    Related
    ENSP00000360161.3, ENST00000371120.7
    Conserved Domains (1) summary
    pfam03416
    Location:77394
    Peptidase_C54; Peptidase family C54

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    62783765..62865516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450414.1XP_024306182.1  cysteine protease ATG4C isoform X1

    Conserved Domains (1) summary
    pfam03416
    Location:77394
    Peptidase_C54; Peptidase family C54
  2. XM_017002601.2XP_016858090.1  cysteine protease ATG4C isoform X3

    Conserved Domains (1) summary
    pfam03416
    Location:77363
    Peptidase_C54; Peptidase family C54
  3. XM_017002600.1XP_016858089.1  cysteine protease ATG4C isoform X3

    Conserved Domains (1) summary
    pfam03416
    Location:77363
    Peptidase_C54; Peptidase family C54
  4. XM_011542313.2XP_011540615.1  cysteine protease ATG4C isoform X2

    Conserved Domains (1) summary
    pfam03416
    Location:77394
    Peptidase_C54; Peptidase family C54
  5. XM_005271288.2XP_005271345.1  cysteine protease ATG4C isoform X1

    See identical proteins and their annotated locations for XP_005271345.1

    UniProtKB/Swiss-Prot
    Q96DT6
    Conserved Domains (1) summary
    pfam03416
    Location:77394
    Peptidase_C54; Peptidase family C54

RNA

  1. XR_001737493.2 RNA Sequence

  2. XR_001737494.2 RNA Sequence

  3. XR_001737492.1 RNA Sequence

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