ATG4B

autophagy related 4B cysteine peptidase, the group of Autophagy related

Basic information

Region (hg38): 2:241637213-241673857

Previous symbols: [ "APG4B" ]

Links

ENSG00000168397 ∙ NCBI:23192 ∙ OMIM:611338 ∙ HGNC:20790 ∙ Uniprot:Q9Y4P1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATG4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG4B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	31	0	0

Variants in ATG4B

This is a list of pathogenic ClinVar variants found in the ATG4B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-241651034-G-A		not specified	Uncertain significance (Jul 11, 2022)
2-241651058-C-G		not specified	Uncertain significance (Nov 06, 2023)
2-241651062-G-C		not specified	Uncertain significance (Aug 13, 2021)
2-241651075-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-241651116-C-T			Benign (Jun 06, 2018)
2-241651272-G-A		not specified	Uncertain significance (Aug 20, 2023)
2-241651275-A-G		not specified	Uncertain significance (Aug 11, 2022)
2-241651275-A-T		not specified	Uncertain significance (Mar 19, 2024)
2-241653512-G-T		not specified	Uncertain significance (Feb 13, 2024)
2-241653557-G-A		not specified	Uncertain significance (May 09, 2023)
2-241653595-C-T		not specified	Uncertain significance (Oct 03, 2022)
2-241653601-C-A		not specified	Uncertain significance (Oct 03, 2023)
2-241654581-A-G		not specified	Uncertain significance (Jul 25, 2023)
2-241654592-C-G		not specified	Uncertain significance (Mar 04, 2024)
2-241654600-A-G		not specified	Uncertain significance (Sep 14, 2023)
2-241659157-A-G		not specified	Uncertain significance (Feb 03, 2022)
2-241659173-T-G		not specified	Uncertain significance (Nov 21, 2023)
2-241666637-C-T			Likely benign (Apr 01, 2022)
2-241666669-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-241666689-T-G		not specified	Uncertain significance (Oct 26, 2022)
2-241666704-G-A		not specified	Uncertain significance (Mar 16, 2022)
2-241666707-C-T		not specified	Uncertain significance (Jul 14, 2023)
2-241666713-T-A		not specified	Uncertain significance (Nov 15, 2021)
2-241666729-C-G		not specified	Uncertain significance (Feb 14, 2023)
2-241666747-A-T		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG4B	protein_coding	protein_coding	ENST00000404914	13	36645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.956	0.0435	124577	0	2	124579	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	170	230	0.738	0.0000141	2540
Missense in Polyphen		18	59.106	0.30454		642
Synonymous	0.0145	99	99.2	0.998	0.00000757	716
Loss of Function	3.87	3	23.0	0.130	0.00000107	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000102	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000890	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, to reveal a C-terminal glycine. Exposure of the glycine at the C- terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms. {ECO:0000269|PubMed:15169837, ECO:0000269|PubMed:15187094, ECO:0000269|PubMed:17347651, ECO:0000269|PubMed:19322194, ECO:0000269|PubMed:21177865, ECO:0000269|PubMed:22302004}.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.502
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.739
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Atg4b
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: autophagosome assembly;proteolysis;autophagy;protein transport;macroautophagy;positive regulation of protein catabolic process;protein delipidation
• Cellular component: cytoplasm;cytosol
• Molecular function: endopeptidase activity;cysteine-type endopeptidase activity;protein binding;cysteine-type peptidase activity