ATG4B autophagy related 4B cysteine peptidase [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATG4Bprovided by HGNC
Official Full Name: autophagy related 4B cysteine peptidaseprovided by HGNC
Primary source: HGNC:HGNC:20790
See related: Ensembl:ENSG00000168397 MIM:611338; AllianceGenome:HGNC:20790
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: APG4B; AUTL1; HsAPG4B
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 different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 14.5), duodenum (RPKM 12.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q37.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (241637693..241673857)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (242141021..242177191)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (242577108..242613272)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic splicing inhibition.
Title: TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic splicing inhibition.
FAT1 inhibits AML autophagy and proliferation via downregulating ATG4B expression.
Title: FAT1 inhibits AML autophagy and proliferation via downregulating ATG4B expression.
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.
ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1.
Title: ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1.
PFKP facilitates ATG4B phosphorylation during amino acid deprivation-induced autophagy.
Title: PFKP facilitates ATG4B phosphorylation during amino acid deprivation-induced autophagy.
The protease activity of human ATG4B is regulated by reversible oxidative modification.
Title: The protease activity of human ATG4B is regulated by reversible oxidative modification.
Distinct Mechanisms for Processing Autophagy Protein LC3-PE by RavZ and ATG4B.
Title: Distinct Mechanisms for Processing Autophagy Protein LC3-PE by RavZ and ATG4B.
Differential expression and prognostic relevance of autophagy-related markers ATG4B, GABARAP, and LC3B in breast cancer.
Title: Differential expression and prognostic relevance of autophagy-related markers ATG4B, GABARAP, and LC3B in breast cancer.
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.
Autophagy related 4B, upregulated by HIF-1alpha, attenuates the sensitivity to cisplatin in nasopharyngeal carcinoma cells.
Title: Autophagy related 4B, upregulated by HIF-1α, attenuates the sensitivity to cisplatin in nasopharyngeal carcinoma cells.

Submit: New GeneRIF Correction See all GeneRIFs (43)

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

EBI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A008U23 (e-PCR)
- UniSTS:5690

RH47370 (e-PCR)
- UniSTS:15693

WI-17974 (e-PCR)
- UniSTS:69482

D2S2042 (e-PCR)
- UniSTS:37493

SHGC-34535 (e-PCR)
- UniSTS:22144

RH35842 (e-PCR)
- UniSTS:84949

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 endopeptidase activity	TAS Traceable Author Statement more info
enables cysteine-type peptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables endopeptidase 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
enables scaffold protein binding	IPI Inferred from Physical Interaction 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 macroautophagy	TAS Traceable Author Statement more info
involved_in microautophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in mitophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in otolith mineralization completed early in development	ISS Inferred from Sequence or Structural Similarity more info
involved_in piecemeal microautophagy of the nucleus	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein delipidation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein delipidation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to phagophore assembly site	IMP Inferred from Mutant Phenotype 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 autophagosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cysteine protease ATG4B

Names: APG4 autophagy 4 homolog B; ATG4 autophagy related 4 homolog B; AUT-like 1 cysteine endopeptidase; autophagin-1; autophagy-related cysteine endopeptidase 1; autophagy-related protein 4 homolog B; hAPG4B

NP_037457.3

EC 3.4.22.-

NP_847896.1

EC 3.4.22.-

XP_005247049.2

EC 3.4.22.-

XP_047299694.1

EC 3.4.22.-

XP_047299695.1

EC 3.4.22.-

XP_047299696.1

EC 3.4.22.-

XP_047299697.1

EC 3.4.22.-

XP_047299698.1

EC 3.4.22.-

XP_054197048.1

EC 3.4.22.-

XP_054197049.1

EC 3.4.22.-

XP_054197050.1

EC 3.4.22.-

XP_054197051.1

EC 3.4.22.-

XP_054197052.1

EC 3.4.22.-

XP_054197053.1

EC 3.4.22.-

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)

NM_013325.5 → NP_037457.3 cysteine protease ATG4B isoform a

See identical proteins and their annotated locations for NP_037457.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the predominant transcript and it encodes the longer isoform (a).

Source sequence(s)

AK123425, AK125277, AL080168, BC000719

Consensus CDS

CCDS46564.1

UniProtKB/Swiss-Prot

B7WNK2, Q53NU4, Q6ZUV8, Q8WYM9, Q96K07, Q96K96, Q96SZ1, Q9Y2F2, Q9Y4P1

UniProtKB/TrEMBL

B4DL29

Related

ENSP00000384259.3, ENST00000404914.8

Conserved Domains (1) summary

pfam03416
Location:40 → 335

Peptidase_C54; Peptidase family C54
NM_178326.3 → NP_847896.1 cysteine protease ATG4B isoform b

See identical proteins and their annotated locations for NP_847896.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.

Source sequence(s)

AK027763, AK125277, AL080168, AL133638

Consensus CDS

CCDS46565.1

UniProtKB/TrEMBL

B4DNY2

Related

ENSP00000383964.3, ENST00000405546.7

Conserved Domains (1) summary

pfam03416
Location:40 → 335

Peptidase_C54; Peptidase family C54

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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

241637693..241673857

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005246992.5 → XP_005247049.2 cysteine protease ATG4B isoform X1

Conserved Domains (1) summary

pfam03416
Location:40 → 335

Peptidase_C54; Peptidase family C54
XM_047443738.1 → XP_047299694.1 cysteine protease ATG4B isoform X2
XM_047443739.1 → XP_047299695.1 cysteine protease ATG4B isoform X3
XM_047443741.1 → XP_047299697.1 cysteine protease ATG4B isoform X5

Related

ENSP00000384661.1, ENST00000402096.5
XM_047443742.1 → XP_047299698.1 cysteine protease ATG4B isoform X4
XM_047443740.1 → XP_047299696.1 cysteine protease ATG4B isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

242141021..242177191

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054341075.1 → XP_054197050.1 cysteine protease ATG4B isoform X3
XM_054341073.1 → XP_054197048.1 cysteine protease ATG4B isoform X1
XM_054341074.1 → XP_054197049.1 cysteine protease ATG4B isoform X2
XM_054341077.1 → XP_054197052.1 cysteine protease ATG4B isoform X5

UniProtKB/TrEMBL

B7ZA52
XM_054341078.1 → XP_054197053.1 cysteine protease ATG4B isoform X4
XM_054341076.1 → XP_054197051.1 cysteine protease ATG4B isoform X4