ATG2A

autophagy related 2A, the group of bridge-like lipid transfer protein family|Autophagy related|MicroRNA protein coding host genes

Basic information

Region (hg38): 11:64894546-64917209

Links

ENSG00000110046 ∙ NCBI:23130 ∙ OMIM:616225 ∙ HGNC:29028 ∙ Uniprot:Q2TAZ0 ∙ 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 ATG2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG2A 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	4
missense			125	12	3	140
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	125	14	5

Variants in ATG2A

This is a list of pathogenic ClinVar variants found in the ATG2A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64895033-A-C		not specified	Uncertain significance (Nov 08, 2022)
11-64895043-C-T		not specified	Uncertain significance (Jun 27, 2022)
11-64895061-C-T		not specified	Likely benign (Jun 29, 2022)
11-64895076-G-A		not specified	Uncertain significance (Oct 25, 2022)
11-64895080-C-T		not specified	Uncertain significance (Mar 28, 2024)
11-64895103-G-A		not specified	Uncertain significance (Nov 03, 2022)
11-64895118-C-T		not specified	Uncertain significance (Sep 13, 2023)
11-64895134-C-T		not specified	Uncertain significance (Apr 20, 2024)
11-64895142-G-C		not specified	Uncertain significance (Apr 13, 2022)
11-64895176-C-T		not specified	Uncertain significance (Mar 15, 2024)
11-64895355-G-A		not specified	Uncertain significance (Sep 18, 2024)
11-64895363-C-T		not specified	Uncertain significance (Aug 12, 2021)
11-64895364-G-A		not specified	Uncertain significance (Aug 28, 2023)
11-64895378-T-A		not specified	Uncertain significance (Jun 21, 2021)
11-64895391-G-A		not specified	Uncertain significance (Apr 18, 2023)
11-64895397-C-T			Benign (May 18, 2018)
11-64896482-G-A		not specified	Uncertain significance (Mar 11, 2022)
11-64896541-T-C		not specified	Uncertain significance (Apr 07, 2022)
11-64896554-T-G		not specified	Uncertain significance (Nov 09, 2023)
11-64896605-G-A		not specified	Uncertain significance (Jul 05, 2024)
11-64896767-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-64896807-T-C		not specified	Uncertain significance (Nov 27, 2024)
11-64897446-C-G		not specified	Uncertain significance (Jun 06, 2023)
11-64897688-C-T		not specified	Uncertain significance (Jan 11, 2023)
11-64897727-A-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG2A	protein_coding	protein_coding	ENST00000377264	41	22716

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0535	0.946	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	1027	1.20e+3	0.853	0.0000808	12254
Missense in Polyphen		223	346.41	0.64374		3616
Synonymous	0.407	522	534	0.978	0.0000371	4165
Loss of Function	6.70	22	90.9	0.242	0.00000473	995

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.000121	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000236	0.000231
European (Non-Finnish)	0.000178	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for both autophagosome formation and regulation of lipid droplet morphology and dispersion. {ECO:0000269|PubMed:22219374}.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.327
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.58

Haploinsufficiency Scores

• pHI: 0.196
• hipred: Y
• hipred_score: 0.520
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.896

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atg2a

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion
• Cellular component: phagophore assembly site;nucleus;lipid droplet;cytosol;extrinsic component of membrane;phagophore assembly site membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding