POU3F2

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

Basic information

Region (hg38): 6:98834574-98839458

Previous symbols: [ "OTF7" ]

Links

ENSG00000184486 ∙ NCBI:5454 ∙ OMIM:600494 ∙ HGNC:9215 ∙ Uniprot:P20265 ∙ 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 POU3F2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU3F2 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				2		2
missense		1	21			22
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	22	2	0

Variants in POU3F2

This is a list of pathogenic ClinVar variants found in the POU3F2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-98834968-G-T		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
6-98835010-G-C		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
6-98835020-G-T		Inborn genetic diseases	Uncertain significance (Sep 30, 2024)
6-98835027-G-A		Inborn genetic diseases	Uncertain significance (Mar 02, 2023)
6-98835039-A-C		Inborn genetic diseases	Uncertain significance (Dec 06, 2022)
6-98835052-A-C		Inborn genetic diseases	Uncertain significance (Mar 25, 2024)
6-98835073-A-ACGG			Likely benign (Mar 01, 2025)
6-98835104-CG-C			Uncertain significance (Jul 13, 2023)
6-98835106-G-A		Inborn genetic diseases	Uncertain significance (Aug 04, 2024)
6-98835133-G-A		Inborn genetic diseases	Uncertain significance (May 26, 2024)
6-98835141-G-A		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
6-98835147-C-T		Inborn genetic diseases	Uncertain significance (Apr 05, 2023)
6-98835241-C-T		Inborn genetic diseases	Uncertain significance (Feb 25, 2025)
6-98835244-T-TGCAGCAGCAGCATCAGCA		POU3F2-related disorder	Likely benign (Jul 22, 2023)
6-98835260-G-T		Inborn genetic diseases	Uncertain significance (Oct 25, 2024)
6-98835263-G-T		Inborn genetic diseases	Uncertain significance (Jul 07, 2022)
6-98835269-A-G			Likely benign (May 01, 2024)
6-98835273-C-A		Inborn genetic diseases	Uncertain significance (Oct 20, 2021)
6-98835308-G-A			Likely benign (May 01, 2024)
6-98835335-G-T		POU3F2-related disorder	Likely benign (Sep 19, 2019)
6-98835423-T-C		Inborn genetic diseases	Uncertain significance (Dec 13, 2022)
6-98835501-C-A		Inborn genetic diseases	Uncertain significance (Feb 13, 2024)
6-98835513-G-A		Inborn genetic diseases	Uncertain significance (Jun 02, 2023)
6-98835548-C-T		POU3F2-related disorder	Likely benign (Jun 17, 2019)
6-98835587-GCCGCCGCCC-G		POU3F2-related disorder	Likely benign (Mar 14, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU3F2	protein_coding	protein_coding	ENST00000328345	1	4081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.920	0.0798	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.72	108	222	0.486	0.0000102	2841
Missense in Polyphen		23	89.007	0.25841		1184
Synonymous	-1.11	117	103	1.14	0.00000502	907
Loss of Function	3.01	1	12.5	0.0800	5.50e-7	131

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 plays a key role in neuronal differentiation (By similarity). Binds preferentially to the recognition sequence which consists of two distinct half-sites, ('GCAT') and ('TAAT'), separated by a non-conserved spacer region of 0, 2, or 3 nucleotides (By similarity). The combination of three transcription factors, ASCL1, POU3F2/BRN2 and MYT1L, is sufficient to reprogram fibroblasts and other somatic cells into induced neuronal (iN) cells in vitro. Acts downstream of ASCL1, accessing chromatin that has been opened by ASCL1, and promotes transcription of neuronal genes (By similarity). {ECO:0000250|UniProtKB:P31360, ECO:0000250|UniProtKB:P56222}.
• Pathway: MECP2 and Associated Rett Syndrome;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways (Consensus)

Haploinsufficiency Scores

• pHI: 0.674
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou3f2
• Phenotype: endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); growth/size/body region phenotype; cellular phenotype; liver/biliary system 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: pou3f2b
• Affected structure: endothelial cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;nervous system development;positive regulation of cell population proliferation;epidermis development;negative regulation of gene expression;astrocyte development;cerebral cortex radially oriented cell migration;forebrain ventricular zone progenitor cell division;hypothalamus cell differentiation;neurohypophysis development;myelination in peripheral nervous system;neuron differentiation;positive regulation of multicellular organism growth;positive regulation of transcription by RNA polymerase II;neuron fate commitment;neuron fate specification;neuron development;regulation of axonogenesis;cellular response to organic substance
• Cellular component: nucleus;transcription factor complex
• 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;transcription coactivator activity;protein binding;identical protein binding