BATF2

Chr 11

basic leucine zipper ATF-like transcription factor 2

Also known as: SARI

NCBI Gene: 116071 ENSG00000168062 UniProt: Q8N1L9 OMIM: 614983

BATF2 encodes an AP-1 family transcription factor that controls immune cell differentiation, particularly of dendritic cells, and suppresses tumor-promoting gene expression. Pathogenic variants cause autosomal recessive primary immunodeficiency with susceptibility to mycobacterial and viral infections. The gene shows intermediate constraint to loss-of-function variants.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in defense response to protozoan; myeloid dendritic cell differentiation; and regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.07

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

1.07LOEUF

pLI 0.585

Z-score 1.53

OE 0.00 (0.00–1.07)

Moderately constrained

Highly tolerant — LoF variants common in population

Missense Constraint?

0.37Z-score

OE missense 0.91 (0.80–1.05)

139 obs / 151.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–1.07)

0≤0.351.4

Missense OE?0.91 (0.80–1.05)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 0 / 2.7Missense obs/exp: 139 / 151.9Syn Z: 0.18

Background carrier burden — how many people carry a rare variant somewhere in BATF2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 120

344 rare PASS variants

Rare truncating (LoF)

1 in 540

52 rare PASS variants

Rare synonymous (reference)

1 in 140

174 rare PASS variants

Rare missense and truncating variants are carried at similar rates in BATF2; this gene does not show strong loss-of-function constraint by this measure. 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 200	1 in 1,700
South Asian	~43k	1 in 120	1 in 2,000
Remaining (unassigned)	~30k	1 in 110	1 in 4,200
European (Finnish)	~27k	1 in 1,500	1 in 1,900
Admixed American	~22k	1 in 190	≈ 1 in 6,600
African / African American	~21k	1 in 130	1 in 1,600
East Asian	~20k	1 in 120	1 in 1,800
Ashkenazi Jewish	~13k	1 in 930	none seen
Middle Eastern	~2,884	1 in 160	none seen

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): All 3 coding exons well covered in gnomAD exomes and genomes.? see exons ↓