Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	84971
Gene name	Autophagy related 4D cysteine peptidase
Gene symbol	ATG4D
Synonyms (NCBI Gene)	APG4-DAPG4DAUTL4HsAPG4DSPGF101
Chromosome	19
Chromosome location	19p13.2
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, a

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miRTarBase ID	miRNA	Experiments	Reference
MIRT006151	hsa-miR-101-3p	Luciferase reporter assayMicroarrayqRT-PCRWestern blot	21915098
MIRT006151	hsa-miR-101-3p	Luciferase reporter assayMicroarrayqRT-PCRWestern blot	21915098
MIRT006151	hsa-miR-101-3p	Luciferase reporter assayMicroarrayqRT-PCRWestern blot	21915098
MIRT006151	hsa-miR-101-3p	Luciferase reporter assayMicroarrayqRT-PCRWestern blot	21915098
MIRT006151	hsa-miR-101-3p	Luciferase reporter assayMicroarrayqRT-PCRWestern blot	21915098
MIRT006151	hsa-miR-101-3p	Luciferase reporter assayMicroarrayqRT-PCRWestern blot	21915098
MIRT805544	hsa-miR-1301	CLIP-seq
MIRT805545	hsa-miR-3670	CLIP-seq
MIRT805546	hsa-miR-4463	CLIP-seq
MIRT805547	hsa-miR-4494	CLIP-seq
MIRT805548	hsa-miR-4660	CLIP-seq
MIRT805549	hsa-miR-4790-3p	CLIP-seq
MIRT805550	hsa-miR-5047	CLIP-seq
MIRT805551	hsa-miR-549	CLIP-seq
MIRT1937880	hsa-miR-328	CLIP-seq
MIRT1937881	hsa-miR-361-3p	CLIP-seq
MIRT1937882	hsa-miR-4530	CLIP-seq
MIRT1937883	hsa-miR-4691-3p	CLIP-seq
MIRT2177379	hsa-miR-101	CLIP-seq
MIRT2177380	hsa-miR-130a	CLIP-seq
MIRT2177381	hsa-miR-130b	CLIP-seq
MIRT2177382	hsa-miR-138	CLIP-seq
MIRT2177383	hsa-miR-139-5p	CLIP-seq
MIRT2177384	hsa-miR-144	CLIP-seq
MIRT2177385	hsa-miR-148a	CLIP-seq
MIRT2177386	hsa-miR-148b	CLIP-seq
MIRT2177387	hsa-miR-152	CLIP-seq
MIRT2177388	hsa-miR-1825	CLIP-seq
MIRT2177389	hsa-miR-199a-5p	CLIP-seq
MIRT2177390	hsa-miR-199b-5p	CLIP-seq
MIRT2177391	hsa-miR-19a	CLIP-seq
MIRT2177392	hsa-miR-19b	CLIP-seq
MIRT2177393	hsa-miR-301a	CLIP-seq
MIRT2177394	hsa-miR-301b	CLIP-seq
MIRT2177395	hsa-miR-3184	CLIP-seq
MIRT1937880	hsa-miR-328	CLIP-seq
MIRT1937881	hsa-miR-361-3p	CLIP-seq
MIRT2177396	hsa-miR-3666	CLIP-seq
MIRT2177397	hsa-miR-3934	CLIP-seq
MIRT2177398	hsa-miR-423-5p	CLIP-seq
MIRT2177399	hsa-miR-4295	CLIP-seq
MIRT2177400	hsa-miR-4456	CLIP-seq
MIRT1937882	hsa-miR-4530	CLIP-seq
MIRT2177401	hsa-miR-454	CLIP-seq
MIRT1937883	hsa-miR-4691-3p	CLIP-seq
MIRT2177402	hsa-miR-541	CLIP-seq
MIRT2177403	hsa-miR-552	CLIP-seq
MIRT2177404	hsa-miR-654-5p	CLIP-seq
MIRT2444171	hsa-miR-188-3p	CLIP-seq
MIRT805545	hsa-miR-3670	CLIP-seq
MIRT805551	hsa-miR-549	CLIP-seq
MIRT2444171	hsa-miR-188-3p	CLIP-seq
MIRT805545	hsa-miR-3670	CLIP-seq
MIRT805551	hsa-miR-549	CLIP-seq
MIRT2444171	hsa-miR-188-3p	CLIP-seq
MIRT805545	hsa-miR-3670	CLIP-seq
MIRT805551	hsa-miR-549	CLIP-seq

Show/Hide all (30)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000045	Process	Autophagosome assembly	IBA
GO:0000045	Process	Autophagosome assembly	IDA	21177865
GO:0000045	Process	Autophagosome assembly	IMP	24290141
GO:0000423	Process	Mitophagy	IBA
GO:0000423	Process	Mitophagy	IMP	33773106
GO:0004197	Function	Cysteine-type endopeptidase activity	IBA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0006508	Process	Proteolysis	IDA	21177865
GO:0006508	Process	Proteolysis	IEA
GO:0006914	Process	Autophagy	IDA	30661429
GO:0006914	Process	Autophagy	IEA
GO:0006915	Process	Apoptotic process	IEA
GO:0008233	Function	Peptidase activity	IEA
GO:0008234	Function	Cysteine-type peptidase activity	IDA	21177865, 30661429
GO:0008234	Function	Cysteine-type peptidase activity	IEA
GO:0015031	Process	Protein transport	IEA
GO:0016485	Process	Protein processing	IBA
GO:0016787	Function	Hydrolase activity	IEA
GO:0019786	Function	Protein-phosphatidylethanolamide deconjugating activity	IBA
GO:0019786	Function	Protein-phosphatidylethanolamide deconjugating activity	IEA
GO:0034497	Process	Protein localization to phagophore assembly site	IMP	33773106
GO:0034727	Process	Piecemeal microautophagy of the nucleus	IBA
GO:0035973	Process	Aggrephagy	IBA
GO:0051697	Process	Protein delipidation	IDA	29458288
GO:0070004	Function	Cysteine-type exopeptidase activity	IDA	21177865

MIM	HGNC	e!Ensembl
611340	20789	ENSG00000130734

Q86TL0

Protein name

Cysteine protease ATG4D (EC 3.4.22.-) (AUT-like 4 cysteine endopeptidase) (Autophagy-related cysteine endopeptidase 4) (Autophagin-4) (Autophagy-related protein 4 homolog D) (HsAPG4D) [Cleaved into: Cysteine protease ATG4D, mitochondrial]

Protein function

[Cysteine protease ATG4D]: Cysteine protease that plays a key role in autophagy by mediating both proteolytic activation and delipidation of ATG8 family proteins (PubMed:21177865, PubMed:29458288, PubMed:30661429). The protease activity is requi

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03416	Peptidase_C54	109 → 411	Peptidase family C54	Family

Tissue specificity

TISSUE SPECIFICITY: Widely expressed in testis. {ECO:0000269|PubMed:33988247}.

Sequence

MNSVSPAAAQYRSSSPEDARRRPEARRPRGPRGPDPNGLGPSGASGPALGSPGAGPSEPD
EVDKFKAKFLTAWNNVKYGWVVKSRTSFSKISSIHLCGRRYRFEGEGDIQRFQRDFVSRL
WLTYRRDFPPLPGGCLTSDCGWGCMLRSGQMMLAQGLLLHFLPRDWTWAEGMGLGPPELS
GSASPSRYHGPARWMPPRWAQGAPELEQERRHRQIVSWFADHPRAPFGLHRLVELGQSSG
KKAGDWYGPSLVAHILRKAVESCSDVTRLVVYVSQDCTVYKADVARLVARPDPTAEWKSV
VILVPVRLGGETLNPVYVPCVKELLRCELCLGIMGGKPRHSLYFIGYQDDFLLYLDPHYC
QPTVDVSQADFPLESFHCTSPRKMAFAKMDPSCTVGFYAGDRKEFETLCSELTRVLSSSS
ATERYPMFTLAEGHAQDHSLDDLCSQLAQPTLRLPRTGRLLRAKRPSSEDFVFL

Sequence length

474

Interactions

View interactions

	KEGG		Reactome
	Autophagy - other Autophagy - animal		Macroautophagy

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
ASHER	Pathogenic	rs1289649383	RCV001780447	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ATG4D-related neurodevelopmental condition	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	GenCC	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neurodevelopmental disorder	Conflicting classifications of pathogenicity	ClinVar GWAS catalog	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VENOUS THROMBOEMBOLISM	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (15)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
ANOPHTHALMIA AND PULMONARY HYPOPLASIA	Syndromic microphthalmia	BEFREE	30737032		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	26208877		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	26208877	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	30374741	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Coronary Disease	Coronary artery disease	Pubtator	33964876	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	28834690		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leiomyoma	Leiomyoma	Pubtator	31843092	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	29743969	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	26208877		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	26208877		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	19549685	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30374741		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	27977328, 32264916	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Sporadic Breast Carcinoma	Breast Carcinoma	BEFREE	27265029		★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of lung	Lung carcinoma	BEFREE	26208877		★★★★★ ★☆☆☆☆ Found in Text Mining only

ATG4D (autophagy related 4D cysteine peptidase)