POU2AF3

Chr 11

POU class 2 homeobox associating factor 3

Also known as: C11orf93, CASC13, COLCA2, LOH11CR1G, OCA-T2

NCBI Gene: 120376 ENSG00000214290 UniProt: A8K830 OMIM: 615694

Enables DNA binding activity and transcription coactivator activity. Predicted to be involved in DNA-templated transcription and positive regulation of DNA-templated transcription. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

OMIM Research

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

0.65

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.65LOEUF

pLI 0.751

Z-score 1.99

OE 0.00 (0.00–0.65)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

0.55Z-score

OE missense 0.82 (0.67–1.01)

62 obs / 75.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.65)

0≤0.351.4

Missense OE?0.82 (0.67–1.01)

0≤0.61.4

Synonymous OE?0.70

0≤1.21.6

LoF obs/exp: 0 / 4.6Missense obs/exp: 62 / 75.5Syn Z: 1.38

Background carrier burden — how many people carry a rare variant somewhere in POU2AF3?

gnomAD v4 · ~700k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 140

344 rare PASS variants

Rare truncating (LoF)

1 in 3,100

33 rare PASS variants

Rare synonymous (reference)

1 in 260

140 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for POU2AF3. 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)	~540k	1 in 250	1 in 2,900
South Asian	~40k	1 in 110	≈ 1 in 9,700
Remaining (unassigned)	~29k	1 in 96	1 in 2,500
European (Finnish)	~25k	1 in 440	none seen
African / African American	~21k	1 in 120	1 in 2,000
East Asian	~18k	1 in 180	1 in 3,000
Admixed American	~18k	1 in 110	1 in 2,700
Ashkenazi Jewish	~13k	1 in 340	1 in 1,800
Middle Eastern	~2,852	1 in 170	≈ 1 in 1,400

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): 2 of 5 coding exons well covered in gnomAD exomes; exons 1, 2, 3 marginal. Genomes: all 5.? see exons ↓