POU2AF1

POU class 2 homeobox associating factor 1

Basic information

Region (hg38): 11:111352254-111455630

Links

ENSG00000110777 ∙ NCBI:5450 ∙ OMIM:601206 ∙ HGNC:9211 ∙ Uniprot:Q16633 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• agammaglobulinemia (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POU2AF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU2AF1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			11		1	12
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					9	9
Total	0	0	12	1	12

Variants in POU2AF1

This is a list of pathogenic ClinVar variants found in the POU2AF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-111354293-G-A		not specified	Uncertain significance (Apr 01, 2024)
11-111354295-G-A		not specified	Uncertain significance (Apr 15, 2024)
11-111354309-A-C		not specified	Uncertain significance (Dec 21, 2022)
11-111354385-A-G		not specified	Uncertain significance (Jan 31, 2024)
11-111354445-G-A		not specified	Uncertain significance (Oct 12, 2021)
11-111354470-T-C		not specified	Uncertain significance (Mar 30, 2024)
11-111354485-G-C		not specified	Uncertain significance (Apr 20, 2023)
11-111354512-G-T		not specified	Uncertain significance (Jan 26, 2023)
11-111356445-T-C		not specified	Benign (Jan 24, 2024)
11-111357617-G-T		not specified	Uncertain significance (Feb 07, 2023)
11-111357618-T-G		not specified	Uncertain significance (Jul 28, 2021)
11-111357645-C-T		not specified	Uncertain significance (Jan 03, 2022)
11-111357647-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-111357667-TG-T			Uncertain significance (Jul 01, 2019)
11-111357676-A-G			Likely benign (May 08, 2018)
11-111357713-G-A			Benign (Mar 01, 2018)
11-111357804-T-C			Benign (Jul 11, 2017)
11-111357841-G-A			Likely benign (Feb 23, 2018)
11-111358695-T-TAC		not specified	Benign (Jan 24, 2024)
11-111358696-A-ACT		not specified	Benign (Jan 24, 2024)
11-111358698-T-TCC		not specified	Benign (Jan 24, 2024)
11-111358745-T-C		not specified	Benign (Jan 24, 2024)
11-111358806-T-C			Benign (Jan 24, 2018)
11-111358821-G-A			Benign (May 08, 2017)
11-111358898-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU2AF1	protein_coding	protein_coding	ENST00000393067	5	103379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.566	0.432	125691	0	4	125695	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.949	120	153	0.784	0.00000898	1595
Missense in Polyphen		32	55.318	0.57847		628
Synonymous	-1.14	84	71.7	1.17	0.00000480	564
Loss of Function	2.53	2	11.1	0.180	5.45e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional coactivator that specifically associates with either OCT1 or OCT2. It boosts the OCT1 mediated promoter activity and to a lesser extent, that of OCT2. It has no intrinsic DNA-binding activity. It recognizes the POU domains of OCT1 and OCT2. It is essential for the response of B-cells to antigens and required for the formation of germinal centers.
• Disease: DISEASE: Note=A chromosomal aberration involving POU2AF1/OBF1 may be a cause of a form of B-cell leukemia. Translocation t(3;11)(q27;q23) with BCL6. {ECO:0000269|PubMed:8574789}.

Recessive Scores

• pRec: 0.276

Intolerance Scores

• loftool: 0.0796
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.423
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.263

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou2af1
• Phenotype: hematopoietic system phenotype; immune system phenotype; renal/urinary system phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: transcription by RNA polymerase II;humoral immune response;positive regulation of transcription by RNA polymerase II
• Cellular component: RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;transcription coregulator activity;transcription coactivator activity;protein binding