ATG13

autophagy related 13, the group of Autophagy related

Basic information

Region (hg38): 11:46617527-46674818

Previous symbols: [ "KIAA0652" ]

Links

ENSG00000175224 ∙ NCBI:9776 ∙ OMIM:615088 ∙ HGNC:29091 ∙ Uniprot:O75143 ∙ 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 ATG13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG13 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					2	2
missense			40			40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	0	2

Variants in ATG13

This is a list of pathogenic ClinVar variants found in the ATG13 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-46644332-A-G		not specified	Uncertain significance (Apr 12, 2022)
11-46644355-C-G		not specified	Uncertain significance (Nov 07, 2022)
11-46645381-T-G		not specified	Uncertain significance (Jun 03, 2024)
11-46645398-T-A			Benign (Jul 16, 2018)
11-46645400-C-T		not specified	Uncertain significance (Aug 13, 2021)
11-46645886-A-G		not specified	Uncertain significance (Apr 04, 2024)
11-46645966-G-A		not specified	Uncertain significance (Sep 01, 2024)
11-46649165-G-T		not specified	Uncertain significance (May 30, 2024)
11-46650206-C-T		not specified	Uncertain significance (Oct 20, 2024)
11-46656260-T-A		not specified	Uncertain significance (May 05, 2023)
11-46657119-C-T		not specified	Uncertain significance (Feb 22, 2023)
11-46657146-C-G		not specified	Uncertain significance (Oct 05, 2021)
11-46657562-T-C		not specified	Uncertain significance (Dec 14, 2024)
11-46657579-C-T		not specified	Uncertain significance (May 15, 2024)
11-46657580-G-A		not specified	Uncertain significance (Mar 03, 2025)
11-46657616-A-G		not specified	Uncertain significance (Mar 11, 2022)
11-46659419-A-G		not specified	Uncertain significance (Apr 22, 2024)
11-46659462-T-C		not specified	Uncertain significance (Jan 03, 2024)
11-46659465-T-C		not specified	Uncertain significance (Oct 02, 2023)
11-46664072-G-A		not specified	Uncertain significance (Jan 02, 2024)
11-46664858-T-G		not specified	Uncertain significance (Aug 08, 2022)
11-46664891-G-A		not specified	Uncertain significance (Jun 07, 2024)
11-46664891-G-T		not specified	Uncertain significance (Dec 13, 2023)
11-46664909-G-A		not specified	Uncertain significance (Jan 08, 2025)
11-46664940-A-G		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG13	protein_coding	protein_coding	ENST00000528494	17	57543

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.964	0.0364	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	232	307	0.756	0.0000155	3591
Missense in Polyphen		102	157.45	0.64784		1891
Synonymous	0.0733	113	114	0.991	0.00000601	1106
Loss of Function	4.20	4	27.9	0.143	0.00000119	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000725	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1- RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation. {ECO:0000269|PubMed:18936157, ECO:0000269|PubMed:19211835, ECO:0000269|PubMed:19225151, ECO:0000269|PubMed:19287211, ECO:0000269|PubMed:21795849, ECO:0000269|PubMed:21855797}.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);PI3K-AKT-mTOR signaling pathway and therapeutic opportunities;Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli;mTOR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.342
• hipred: Y
• hipred_score: 0.591
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atg13

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion;mitophagy;macroautophagy;regulation of macroautophagy;activation of protein kinase activity;protein localization to phagophore assembly site;piecemeal microautophagy of the nucleus;response to mitochondrial depolarisation;positive regulation of protein targeting to mitochondrion
• Cellular component: phagophore assembly site;mitochondrion;endoplasmic reticulum membrane;cytosol;extrinsic component of membrane;Atg1/ULK1 kinase complex
• Molecular function: protein binding;protein kinase regulator activity;protein kinase binding