POU5F1

POU class 5 homeobox 1, the group of POU class homeoboxes and pseudogenes

Basic information

Region (hg38): 6:31164337-31180731

Previous symbols: [ "OTF3" ]

Links

ENSG00000204531 ∙ NCBI:5460 ∙ OMIM:164177 ∙ HGNC:9221 ∙ Uniprot:Q01860 ∙ 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 POU5F1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU5F1 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in POU5F1

This is a list of pathogenic ClinVar variants found in the POU5F1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31164789-C-G		not specified	Uncertain significance (Apr 12, 2022)
6-31164798-C-G		not specified	Uncertain significance (Mar 11, 2022)
6-31164800-C-T		not specified	Uncertain significance (Oct 20, 2021)
6-31164806-G-A		not specified	Uncertain significance (Mar 28, 2023)
6-31165186-G-C		not specified	Uncertain significance (Mar 01, 2023)
6-31170218-C-T		not specified	Uncertain significance (Sep 25, 2023)
6-31170356-C-T		not specified	Likely benign (May 11, 2022)
6-31170601-G-A		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU5F1	protein_coding	protein_coding	ENST00000259915	5	16390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0463	123287	0	2	123289	0.00000811

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	136	207	0.657	0.0000118	2279
Missense in Polyphen		24	47.118	0.50936		537
Synonymous	1.59	71	90.2	0.787	0.00000556	754
Loss of Function	3.55	2	18.5	0.108	0.00000123	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000547
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000550	0.0000547
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'). Forms a trimeric complex with SOX2 on DNA and controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206. Critical for early embryogenesis and for embryonic stem cell pluripotency. {ECO:0000269|PubMed:18035408}.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Cardiac Progenitor Differentiation;Transcriptional regulation of pluripotent stem cells;Endoderm Differentiation;Mesodermal Commitment Pathway;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;let-7 inhibition of ES cell reprogramming;Preimplantation Embryo;Wnt Signaling Pathway and Pluripotency;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Developmental Biology;HIF-2-alpha transcription factor network;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Transcriptional regulation of pluripotent stem cells (Consensus)

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.895
• hipred: N
• hipred_score: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou5f1
• Phenotype: normal 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); reproductive system phenotype; embryo phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;endodermal cell fate specification;blastocyst development;regulation of transcription, DNA-templated;transcription by RNA polymerase II;response to wounding;anatomical structure morphogenesis;regulation of asymmetric cell division;regulation of gene expression;somatic stem cell population maintenance;mRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;negative regulation of gene silencing by miRNA
• Cellular component: nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol
• Molecular function: transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;RNA binding;protein binding;ubiquitin protein ligase binding;miRNA binding;sequence-specific DNA binding