POU3F1

POU class 3 homeobox 1, the group of POU class homeoboxes and pseudogenes

Basic information

Region (hg38): 1:38043829-38046793

Previous symbols: [ "OTF6" ]

Links

ENSG00000185668 ∙ NCBI:5453 ∙ OMIM:602479 ∙ HGNC:9214 ∙ Uniprot:Q03052 ∙ 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 POU3F1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU3F1 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		1
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in POU3F1

This is a list of pathogenic ClinVar variants found in the POU3F1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-38045395-A-T		not specified	Uncertain significance (May 27, 2022)
1-38045401-C-T		not specified	Uncertain significance (Feb 23, 2025)
1-38045480-C-T		not specified	Uncertain significance (Mar 22, 2023)
1-38045633-C-A		not specified	Uncertain significance (Nov 09, 2024)
1-38046015-C-G		not specified	Uncertain significance (Apr 07, 2023)
1-38046044-C-T		not specified	Uncertain significance (Jul 29, 2022)
1-38046065-C-A		not specified	Uncertain significance (Jun 07, 2024)
1-38046087-G-T		not specified	Uncertain significance (Jun 06, 2023)
1-38046107-G-C		not specified	Uncertain significance (Jun 05, 2024)
1-38046137-A-C		not specified	Uncertain significance (Nov 16, 2021)
1-38046143-C-T		not specified	Uncertain significance (Dec 20, 2021)
1-38046158-G-A		not specified	Uncertain significance (Dec 23, 2024)
1-38046227-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-38046260-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-38046266-C-G		not specified	Uncertain significance (May 09, 2024)
1-38046331-C-T		not specified	Uncertain significance (Mar 10, 2025)
1-38046350-T-C		not specified	Likely benign (Apr 07, 2023)
1-38046414-T-G			Likely benign (Jul 01, 2022)
1-38046428-C-T		not specified	Uncertain significance (Dec 19, 2023)
1-38046439-C-T		not specified	Uncertain significance (May 09, 2023)
1-38046452-C-G		not specified	Uncertain significance (Nov 09, 2023)
1-38046454-C-T		not specified	Uncertain significance (Mar 07, 2025)
1-38046461-C-T		not specified	Uncertain significance (Aug 06, 2024)
1-38046467-C-G		not specified	Uncertain significance (Sep 02, 2024)
1-38046499-C-A		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU3F1	protein_coding	protein_coding	ENST00000373012	1	2928

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.565	0.424	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.54	64	152	0.420	0.00000697	2802
Missense in Polyphen		14	43.191	0.32414		585
Synonymous	-0.226	76	73.5	1.03	0.00000362	1007
Loss of Function	2.05	1	6.72	0.149	2.90e-7	105

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 binds to the octamer motif (5'-ATTTGCAT-3'). Thought to be involved in early embryogenesis and neurogenesis.

Haploinsufficiency Scores

• pHI: 0.734
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.777

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou3f1
• 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); normal phenotype; growth/size/body region phenotype; 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;axon ensheathment;positive regulation of gene expression;myelination in peripheral nervous system;keratinocyte differentiation;forebrain development;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coactivator activity;sequence-specific DNA binding