Seroatlas · Human Serome Atlas

ATG4D

Cysteine protease ATG4D

Also known as: APG4-D, APG4D, ATG4D_HUMAN, AUTL4

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q86TL0
Gene: ATG4D
Ensembl: ENSG00000130734
Chromosome: 19
Canonical length: 474 aa
Protein class: Enzymes, Predicted intracellular proteins, Transporters
Subcellular location: Nucleoplasm,Mitochondria

OverviewNCBI 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 belongs to the autophagy-related protein 4 (Atg4) family of C54 endopeptidases. Members of this family encode proteins that play a role in the biogenesis of autophagosomes, which sequester the cytosol and organelles for degradation by lysosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

Canonical amino-acid sequenceUniProt

474 residues, UniProt reviewed canonical sequence.

>Q86TL0|ATG4D
     1  MNSVSPAAAQ YRSSSPEDAR RRPEARRPRG PRGPDPNGLG PSGASGPALG SPGAGPSEPD
    61  EVDKFKAKFL TAWNNVKYGW VVKSRTSFSK ISSIHLCGRR YRFEGEGDIQ RFQRDFVSRL
   121  WLTYRRDFPP LPGGCLTSDC GWGCMLRSGQ MMLAQGLLLH FLPRDWTWAE GMGLGPPELS
   181  GSASPSRYHG PARWMPPRWA QGAPELEQER RHRQIVSWFA DHPRAPFGLH RLVELGQSSG
   241  KKAGDWYGPS LVAHILRKAV ESCSDVTRLV VYVSQDCTVY KADVARLVAR PDPTAEWKSV
   301  VILVPVRLGG ETLNPVYVPC VKELLRCELC LGIMGGKPRH SLYFIGYQDD FLLYLDPHYC
   361  QPTVDVSQAD FPLESFHCTS PRKMAFAKMD PSCTVGFYAG DRKEFETLCS ELTRVLSSSS
   421  ATERYPMFTL AEGHAQDHSL DDLCSQLAQP TLRLPRTGRL LRAKRPSSED FVFL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against ATG4D can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.36
Highest tissue expression: 36 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 36 nTPM
bone marrow: 31 nTPM
esophagus: 26 nTPM
skin: 24 nTPM
testis: 24 nTPM
small intestine: 22 nTPM

Single-cell type

late primary spermatocytes: 211 nCPM
megakaryocytes: 136 nCPM
enterocytes: 113 nCPM
colonocytes: 103 nCPM
esophageal apical cells: 90 nCPM
esophageal suprabasal cells: 72 nCPM

Immune cell

plasmacytoid DC: 4.2 nTPM
eosinophil: 3.7 nTPM
T-reg: 2.2 nTPM
naive CD8 T-cell: 1.7 nTPM
basophil: 1.6 nTPM
MAIT T-cell: 1.5 nTPM

Brain region

cerebellum: 22 nTPM
choroid plexus: 22 nTPM
cerebral cortex: 18 nTPM
white matter: 17 nTPM
thalamus: 16 nTPM
pons: 16 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about ATG4D.

Disease | GeneticClinVar

7 pathogenic / likely-pathogenic of 111 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Spermatogenic failure 101
ASHER
See cases

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.72
gnomAD pLI: 0
gnomAD missense Z: 0.8
DepMap mean gene effect: -0.01
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads ATG4D as an antibody target. Whether an autoantibody or antibody against ATG4D could matter depends on whether native ATG4D is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

ATG4D is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label ATG4D as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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