POU2F1

POU class 2 homeobox 1, the group of POU class homeoboxes and pseudogenes

Basic information

Region (hg38): 1:167220875-167427345

Previous symbols: [ "OTF1" ]

Links

ENSG00000143190 ∙ NCBI:5451 ∙ OMIM:164175 ∙ HGNC:9212 ∙ Uniprot:P14859 ∙ 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 POU2F1 gene.

• Inborn genetic diseases (16 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU2F1 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			16	1	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	16	1	3

Variants in POU2F1

This is a list of pathogenic ClinVar variants found in the POU2F1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-167220916-G-C		not specified	Uncertain significance (Oct 12, 2021)
1-167332470-A-G		not specified	Uncertain significance (Oct 20, 2021)
1-167332523-G-A		not specified	Uncertain significance (Oct 12, 2022)
1-167370211-A-G			Benign (Dec 31, 2019)
1-167370224-G-A			Benign (Jun 23, 2018)
1-167371945-C-T		not specified	Uncertain significance (Aug 22, 2023)
1-167374234-T-A		not specified	Uncertain significance (Jan 18, 2022)
1-167374282-A-C		not specified	Uncertain significance (Aug 08, 2023)
1-167376113-C-T		not specified	Uncertain significance (Nov 17, 2023)
1-167383859-C-G		not specified	Uncertain significance (Oct 26, 2022)
1-167383884-C-T		not specified	Uncertain significance (Mar 16, 2022)
1-167389588-C-G		not specified	Uncertain significance (Nov 17, 2023)
1-167389600-A-G			Benign (Aug 29, 2018)
1-167389661-G-A		not specified	Uncertain significance (Oct 27, 2023)
1-167389672-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-167397994-A-G		not specified	Uncertain significance (Feb 22, 2023)
1-167398050-A-G		not specified	Uncertain significance (Dec 13, 2021)
1-167398081-G-T		not specified	Uncertain significance (Oct 17, 2023)
1-167411994-G-A		not specified	Uncertain significance (Dec 07, 2023)
1-167412073-C-T		not specified	Uncertain significance (Oct 26, 2021)
1-167412139-C-T		not specified	Uncertain significance (Sep 22, 2023)
1-167415539-A-G		not specified	Uncertain significance (Jun 07, 2023)
1-167415577-G-A		not specified	Uncertain significance (Dec 05, 2022)
1-167415742-T-C			Likely benign (Dec 27, 2017)
1-167415772-G-C		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU2F1	protein_coding	protein_coding	ENST00000367866	16	206517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.902	0.0977	125721	0	24	125745	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	292	421	0.694	0.0000224	4914
Missense in Polyphen		31	48.107	0.6444		586
Synonymous	-0.134	176	174	1.01	0.0000104	1651
Loss of Function	4.69	7	38.4	0.182	0.00000190	398

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000657	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.000657	0.000653
South Asian	0.0000662	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds to the octamer motif (5'-ATTTGCAT-3') and activates the promoters of the genes for some small nuclear RNAs (snRNA) and of genes such as those for histone H2B and immunoglobulins. Modulates transcription transactivation by NR3C1, AR and PGR (By similarity). In case of human herpes simplex virus (HSV) infection, POU2F1 forms a multiprotein-DNA complex with the viral transactivator protein VP16 and HCFC1 thereby enabling the transcription of the viral immediate early genes. {ECO:0000250, ECO:0000269|PubMed:1684878}.
• Pathway: Integrated Cancer Pathway;Interleukin-4 and 13 signaling;Signal Transduction;Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;ATF-2 transcription factor network;Glucocorticoid receptor regulatory network;FOXA1 transcription factor network;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;RNA Polymerase III Abortive And Retractive Initiation;ESR-mediated signaling;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;Regulation of Androgen receptor activity;Calcium signaling in the CD4+ TCR pathway (Consensus)

Recessive Scores

• pRec: 0.416

Intolerance Scores

• loftool: 0.181
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.978
• hipred: Y
• hipred_score: 0.745
• ghis: 0.563

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.857

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou2f1
• Phenotype: endocrine/exocrine gland phenotype; taste/olfaction 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); growth/size/body region phenotype; craniofacial 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); 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; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; vision/eye phenotype

Gene ontology

• Biological process: cytokine-mediated signaling pathway;snRNA transcription by RNA polymerase II;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;endoplasmic reticulum;intracellular membrane-bounded organelle;RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;RNA polymerase II general transcription initiation factor activity;sequence-specific DNA binding