ATG16L2

protein-coding

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

Gene summary

Predicted to be involved in macroautophagy. Predicted to act upstream of or within negative stranded viral RNA replication. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_033388.2

Inheritance

—

ClinVar variants

U:92B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr11:72,814,406-72,843,674

External References & Databases

Ensembl (ENSG00000168010)

Transcript & Mutation Effects

hg38 • Region Span ~29.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATG16L2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033388.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	3 clinvar		7
missense			81 clinvar	5 clinvar	1 clinvar	87
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	92	8	1	101

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033388.2	RefSeq	NP_203746.1	18	MANE Select
ENST00000321297.10	Ensembl	ENSP00000326340.5	18	MANE Select
NM_001318766.2	RefSeq	NP_001305695.1	15	Standard
ENST00000435507.6	Ensembl	ENSP00000400705.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Autophagy - animal - Homo sapiens (human)

Biological Process

autophagosome assembly
protein transport
negative stranded viral RNA replication

Cellular Component

autophagosome membrane
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321297
Coding exons: 18
Length: 29367
Individuals with no LoFs: 125623
Homozygous LoFs: 0
Heterozygous LoFs: 125
Defined: 125748
p: 0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	283	338	0.838	0.0000187	3919
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0033	0.0033	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00013	0.00013	rare
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in autophagy. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.549
RVIS EVS: -0.67
RVIS percentile EVS: 15.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.518

Gene Damage Prediction

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