ATG10

autophagy related 10, the group of Autophagy related

Basic information

Region (hg38): 5:81972023-82276857

Previous symbols: [ "APG10L" ]

Links

ENSG00000152348 ∙ NCBI:83734 ∙ OMIM:610800 ∙ HGNC:20315 ∙ Uniprot:Q9H0Y0 ∙ 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 ATG10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG10 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in ATG10

This is a list of pathogenic ClinVar variants found in the ATG10 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-81987611-G-A		not specified	Likely benign (Jun 04, 2024)
5-82058508-G-A		not specified	Uncertain significance (Mar 11, 2024)
5-82058598-T-C		not specified	Uncertain significance (Jan 11, 2023)
5-82164424-A-C		not specified	Uncertain significance (Sep 14, 2023)
5-82164426-T-C		not specified	Uncertain significance (Mar 14, 2023)
5-82164459-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-82164504-G-A		not specified	Uncertain significance (Mar 03, 2022)
5-82164510-G-A		not specified	Uncertain significance (Dec 03, 2021)
5-82178490-A-G		not specified	Uncertain significance (May 04, 2022)
5-82178571-A-G		not specified	Uncertain significance (Mar 08, 2024)
5-82253318-G-A		not specified	Uncertain significance (Sep 14, 2022)
5-82253322-A-C		not specified	Uncertain significance (Apr 30, 2024)
5-82253420-C-G		not specified	Uncertain significance (Sep 21, 2023)
5-82276112-T-C			Likely benign (Aug 24, 2018)
5-82276183-A-T		Brachycephaly, trichomegaly, and developmental delay	Pathogenic (Aug 11, 2017)
5-82276186-G-A		Brachycephaly, trichomegaly, and developmental delay	Uncertain significance (Aug 14, 2023)
5-82276365-G-C		Brachycephaly, trichomegaly, and developmental delay	Benign (Nov 07, 2021)
5-82276419-G-A			Likely benign (Nov 15, 2018)
5-82276483-C-T		Brachycephaly, trichomegaly, and developmental delay	Pathogenic (Aug 11, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG10	protein_coding	protein_coding	ENST00000282185	6	304833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.18e-8	0.267	125718	0	24	125742	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.481	104	119	0.876	0.00000580	1448
Missense in Polyphen		27	32.373	0.83402		410
Synonymous	-0.746	50	43.7	1.14	0.00000236	403
Loss of Function	0.529	13	15.2	0.854	8.28e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000265	0.000265
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.0000551	0.0000544
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E2-like enzyme involved in autophagy. Acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5. ATG12 conjugation to ATG5 is required for autophagy. Likely serves as an ATG5-recognition molecule. Not involved in ATG12 conjugation to ATG3 (By similarity). Plays a role in adenovirus-mediated cell lysis. {ECO:0000250, ECO:0000269|PubMed:21367888}.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.0878

Intolerance Scores

• loftool: 0.736
• rvis_EVS: 1.08
• rvis_percentile_EVS: 91.8

Haploinsufficiency Scores

• pHI: 0.0659
• hipred: N
• hipred_score: 0.409
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.649

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atg10

Gene ontology

• Biological process: protein lipidation;autophagy;ER overload response;protein transport;macroautophagy;positive regulation of protein modification process;protein modification by small protein conjugation
• Cellular component: cytosol
• Molecular function: Atg12 transferase activity