POU2AF2

protein-coding

POU class 2 homeobox associating factor 2

Gene summary

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

Previous symbols:

C11orf53

MANE transcript

NM_198498.3

Inheritance

—

ClinVar variants

U:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr11:111,245,725-111,286,401

External References & Databases

Ensembl (ENSG00000150750)

Transcript & Mutation Effects

hg38 • Region Span ~40.7 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 POU2AF2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198498.3. 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						0
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	2	0	0	2

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198498.3	RefSeq	NP_940900.2	5	MANE Select
ENST00000280325.7	Ensembl	ENSP00000280325.6	5	MANE Select
ENST00000635886.1	Ensembl	ENSP00000489980.1	3	Standard
ENST00000637637.1	Ensembl	ENSP00000489630.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000280325
Coding exons: 3
Length: 30420
Individuals with no LoFs: 125643
Homozygous LoFs: 0
Heterozygous LoFs: 105
Defined: 125748
p: 0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.230	143	151	0.947	0.00000953	1499
Missense (PolyPhen)		42	46.909	0.89535		494
Synonymous	0.0607	78	78.7	0.991	0.00000617	512
Loss of Function	0.890	5	7.66	0.653	3.25e-7	88

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00018	rare
Latino/Admixed American	0.00083	0.00081	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00053	0.00052	rare
South Asian	0.00020	0.00020	rare
Other	0.00083	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0988

Intolerance Scores

RVIS EVS: -0.18
RVIS percentile EVS: 40.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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