ATG16L2

autophagy related 16 like 2, the group of Autophagy related|WD repeat domain containing

Basic information

Region (hg38): 11:72814406-72843674

Links

ENSG00000168010 ∙ NCBI:89849 ∙ OMIM:618716 ∙ HGNC:25464 ∙ Uniprot:Q8NAA4 ∙ 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 ATG16L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG16L2 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				1		1
missense			34	3	1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			9		1	10
Total	0	0	43	4	2

Variants in ATG16L2

This is a list of pathogenic ClinVar variants found in the ATG16L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-72814467-G-A		not specified	Uncertain significance (Sep 14, 2022)
11-72814482-C-T		not specified	Uncertain significance (Mar 21, 2024)
11-72816734-A-G		not specified	Likely benign (Feb 05, 2024)
11-72816736-C-G		not specified	Uncertain significance (Jan 17, 2024)
11-72816785-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-72816815-A-G		not specified	Uncertain significance (Jan 18, 2023)
11-72817799-G-A		not specified	Likely benign (Aug 30, 2022)
11-72821717-C-T		not specified	Uncertain significance (Oct 26, 2021)
11-72822066-G-C		not specified	Uncertain significance (Jun 05, 2024)
11-72822099-G-T		not specified	Uncertain significance (Jun 11, 2024)
11-72822145-C-A		not specified	Uncertain significance (Oct 25, 2023)
11-72822214-C-G		not specified	Uncertain significance (Jul 26, 2022)
11-72822237-G-C		not specified	Uncertain significance (Oct 05, 2021)
11-72822248-G-C		not specified	Uncertain significance (Feb 28, 2024)
11-72822273-C-G		not specified	Uncertain significance (Sep 13, 2023)
11-72822489-C-T		not specified	Uncertain significance (Aug 02, 2022)
11-72822885-A-G		not specified	Uncertain significance (Jul 06, 2022)
11-72824064-G-C		not specified	Uncertain significance (Jul 06, 2022)
11-72824080-T-G		not specified	Uncertain significance (Mar 15, 2024)
11-72824083-C-T		not specified	Uncertain significance (Nov 07, 2022)
11-72824086-T-C		not specified	Uncertain significance (Apr 04, 2024)
11-72824760-T-C		not specified	Uncertain significance (Dec 26, 2023)
11-72824796-C-G		not specified	Uncertain significance (Aug 04, 2023)
11-72824802-G-C			Benign (May 09, 2018)
11-72824814-G-A		not specified	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG16L2	protein_coding	protein_coding	ENST00000321297	18	29367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.69e-16	0.160	125623	0	125	125748	0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	283	338	0.838	0.0000187	3919
Missense in Polyphen		93	124.13	0.74922		1420
Synonymous	0.269	139	143	0.971	0.00000801	1272
Loss of Function	1.17	28	35.5	0.788	0.00000177	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000570	0.000569
Ashkenazi Jewish	0.00	0.00
East Asian	0.00332	0.00332
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000347	0.000343
Middle Eastern	0.00332	0.00332
South Asian	0.000131	0.000131
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in autophagy. {ECO:0000250}.
• Pathway: Autophagy - animal - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.549
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.86

Haploinsufficiency Scores

• pHI: 0.0806
• hipred: N
• hipred_score: 0.337
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.518

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atg16l2
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: autophagosome assembly;protein transport;negative stranded viral RNA replication
• Cellular component: autophagosome membrane;nucleoplasm