POU2F2

POU class 2 homeobox 2, the group of POU class homeoboxes and pseudogenes|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:42086110-42196585

Previous symbols: [ "OTF2" ]

Links

ENSG00000028277 ∙ NCBI:5452 ∙ OMIM:164176 ∙ HGNC:9213 ∙ Uniprot:P09086 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POU2F2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU2F2 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						0
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in POU2F2

This is a list of pathogenic ClinVar variants found in the POU2F2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-42092105-G-A		not specified	Uncertain significance (Oct 04, 2024)
19-42092106-A-G		not specified	Uncertain significance (Dec 09, 2024)
19-42092132-G-A		not specified	Uncertain significance (Jan 04, 2024)
19-42092144-G-A		not specified	Uncertain significance (Oct 14, 2023)
19-42092171-G-A		not specified	Uncertain significance (Dec 07, 2024)
19-42092180-T-C		not specified	Uncertain significance (Dec 18, 2023)
19-42092192-G-A		not specified	Likely benign (Nov 14, 2023)
19-42092229-G-A		not specified	Uncertain significance (Apr 12, 2024)
19-42092243-G-A		not specified	Uncertain significance (Oct 26, 2021)
19-42092247-C-G		not specified	Uncertain significance (Aug 05, 2024)
19-42093864-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-42093865-G-A		not specified	Uncertain significance (Aug 01, 2024)
19-42093876-G-A		not specified	Uncertain significance (Sep 26, 2024)
19-42093895-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-42095287-A-T		not specified	Uncertain significance (Mar 03, 2025)
19-42095291-G-A		not specified	Uncertain significance (Oct 19, 2024)
19-42095347-G-A		not specified	Uncertain significance (Aug 12, 2024)
19-42095636-A-G		not specified	Uncertain significance (Jan 27, 2025)
19-42095690-G-A		not specified	Uncertain significance (Feb 27, 2025)
19-42095691-T-C		not specified	Uncertain significance (Dec 02, 2022)
19-42095794-C-T		not specified	Uncertain significance (Jan 20, 2025)
19-42096162-C-T		not specified	Uncertain significance (Feb 06, 2023)
19-42096166-G-T		not specified	Uncertain significance (Oct 25, 2022)
19-42096167-T-G		not specified	Uncertain significance (Dec 07, 2024)
19-42096210-G-A		not specified	Uncertain significance (Jan 04, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU2F2	protein_coding	protein_coding	ENST00000526816	14	110475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00116	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.60	160	283	0.565	0.0000169	3064
Missense in Polyphen		67	150.16	0.44619		1531
Synonymous	1.42	103	123	0.838	0.00000803	981
Loss of Function	4.35	1	24.0	0.0416	0.00000102	277

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. {ECO:0000269|PubMed:1739980, ECO:0000269|PubMed:2328728, ECO:0000269|PubMed:2901913, ECO:0000269|PubMed:2904654}.
• Pathway: Ectoderm Differentiation;Prion disease pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;BCR signaling pathway;Validated transcriptional targets of deltaNp63 isoforms (Consensus)

Recessive Scores

• pRec: 0.278

Intolerance Scores

• loftool: 0.185
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.492
• hipred: Y
• hipred_score: 0.775
• ghis: 0.673

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou2f2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: mature B cell differentiation;immunoglobulin secretion involved in immune response;transcription by RNA polymerase II;humoral immune response;snRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;cell maturation
• Cellular component: nucleus;nucleoplasm;cytoplasm;intracellular membrane-bounded organelle
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein domain specific binding;sequence-specific DNA binding