POU2F3

POU class 2 homeobox 3, the group of POU class homeoboxes and pseudogenes

Basic information

Region (hg38): 11:120236640-120319945

Links

ENSG00000137709 ∙ NCBI:25833 ∙ OMIM:607394 ∙ HGNC:19864 ∙ Uniprot:Q9UKI9 ∙ 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 POU2F3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU2F3 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in POU2F3

This is a list of pathogenic ClinVar variants found in the POU2F3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-120246503-G-T		not specified	Uncertain significance (Jul 10, 2024)
11-120298313-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-120298352-G-A		not specified	Uncertain significance (Oct 06, 2024)
11-120298386-G-A		not specified	Uncertain significance (Oct 21, 2024)
11-120299694-T-A		not specified	Uncertain significance (Jul 12, 2022)
11-120299717-G-A		not specified	Uncertain significance (Aug 30, 2021)
11-120302300-C-T		not specified	Uncertain significance (Dec 01, 2022)
11-120302327-G-A		not specified	Likely benign (May 18, 2023)
11-120302345-A-G		not specified	Uncertain significance (Jan 26, 2022)
11-120302352-C-T		not specified	Uncertain significance (Dec 04, 2024)
11-120305031-C-T		not specified	Uncertain significance (Sep 15, 2021)
11-120305034-T-C		not specified	Uncertain significance (Mar 26, 2024)
11-120305100-T-C		not specified	Uncertain significance (Jan 09, 2024)
11-120305123-G-A		not specified	Uncertain significance (Dec 21, 2023)
11-120305184-A-G		not specified	Uncertain significance (Jan 19, 2024)
11-120307506-G-A		not specified	Uncertain significance (Sep 04, 2024)
11-120307509-C-A		not specified	Uncertain significance (Jun 17, 2024)
11-120307511-C-A		not specified	Uncertain significance (Jul 06, 2022)
11-120307602-A-T		not specified	Uncertain significance (Oct 05, 2023)
11-120309427-C-A		not specified	Uncertain significance (Sep 22, 2023)
11-120309469-G-C		not specified	Uncertain significance (Dec 15, 2023)
11-120309542-C-G		not specified	Uncertain significance (Jan 16, 2024)
11-120309566-C-T		not specified	Uncertain significance (Aug 13, 2021)
11-120309579-C-G		not specified	Uncertain significance (Jun 29, 2022)
11-120315398-C-T		not specified	Uncertain significance (Nov 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU2F3	protein_coding	protein_coding	ENST00000260264	13	83305

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000103	0.986	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.317	236	250	0.944	0.0000134	2836
Missense in Polyphen		70	94.92	0.73746		1082
Synonymous	0.264	100	103	0.967	0.00000599	883
Loss of Function	2.24	14	26.5	0.529	0.00000146	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds to the octamer motif (5'-ATTTGCAT-3'). Regulated the expression of a number of genes such as SPRR2A or placental lactogen.
• Pathway: Herpes simplex infection - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.263

Intolerance Scores

• loftool: 0.195
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.659
• hipred: Y
• hipred_score: 0.527
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00408

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou2f3
• 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); taste/olfaction phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;epidermis development;negative regulation by host of viral transcription;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• 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;protein binding;sequence-specific DNA binding