POU2F1

protein-coding

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

Gene summary

The OCT1 transcription factor was among the first identified members of the POU transcription factor family (summarized by Sturm et al., 1993 [PubMed 8314572]). Members of this family contain the POU domain, a 160-amino acid region necessary for DNA binding to the octameric sequence ATGCAAAT.[supplied by OMIM, Jul 2010]

Previous symbols:

OTF1

MANE transcript

NM_002697.4

Inheritance

—

ClinVar variants

U:75B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr1:167,220,876-167,427,345

External References & Databases

Ensembl (ENSG00000143190)

Transcript & Mutation Effects

hg38 • Region Span ~206.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to POU2F1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002697.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	1 clinvar	4
missense			67 clinvar	2 clinvar	1 clinvar	70
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	75	3	2	80

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002697.4	RefSeq	NP_002688.3	16	MANE Select
ENST00000367866.7	Ensembl	ENSP00000356840.2	16	MANE Select
NM_001198783.2	RefSeq	NP_001185712.1	16	Standard
NM_001198786.2	RefSeq	NP_001185715.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Integrated Cancer Pathway
Interleukin-4 and 13 signaling
Signal Transduction
Gene expression (Transcription)
RNA polymerase II transcribes snRNA genes

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

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

Cellular Component

nucleus
nucleoplasm
endoplasmic reticulum
intracellular membrane-bounded organelle
RNA polymerase II transcription factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367866
Coding exons: 16
Length: 206517
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125745
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.23	292	421	0.694	0.0000224	4914
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00066	0.00065	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000066	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.416

Intolerance Scores

LoFtool: 0.181
RVIS EVS: -0.33
RVIS percentile EVS: 30.7

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.857

Gene Damage Prediction

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