ATG16L2

Chr 11

autophagy related 16 like 2

Also known as: ATG16B, WDR80

NCBI Gene: 89849 ENSG00000168010 UniProt: Q8NAA4 OMIM: 618716

The protein is predicted to be involved in autophagosome assembly as part of the Atg12-Atg5-Atg16 complex and may regulate epithelial homeostasis. This gene is not well-constrained against loss-of-function variants (LOEUF 1.08), but no established human disease associations have been reported in the provided data. The inheritance pattern and clinical phenotypes associated with ATG16L2 mutations remain to be determined.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.08

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.08LOEUF

pLI 0.000

Z-score 1.17

OE 0.79 (0.58–1.08)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.06Z-score

OE missense 0.84 (0.76–0.92)

283 obs / 337.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.79 (0.58–1.08)

0≤0.351.4

Missense OE?0.84 (0.76–0.92)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 28 / 35.5Missense obs/exp: 283 / 337.9Syn Z: 0.27

Background carrier burden — how many people carry a rare variant somewhere in ATG16L2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 60

987 rare PASS variants

Rare truncating (LoF)

1 in 650

206 rare PASS variants

Rare synonymous (reference)

1 in 200

386 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ATG16L2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 89	1 in 780
South Asian	~43k	1 in 46	1 in 410
Remaining (unassigned)	~30k	1 in 58	1 in 570
European (Finnish)	~27k	1 in 410	1 in 2,700
Admixed American	~22k	1 in 64	1 in 670
African / African American	~21k	1 in 52	1 in 290
East Asian	~20k	1 in 66	1 in 370
Ashkenazi Jewish	~13k	1 in 130	≈ 1 in 3,300
Middle Eastern	~2,884	1 in 54	1 in 240

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 16 of 18 coding exons well covered in gnomAD exomes; exons 1, 5 marginal. Genomes: all 18.? see exons ↓