POU5F1B

protein-coding

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

Gene summary

This intronless gene was thought to be a transcribed pseudogene of POU class 5 homeobox 1, however, it has been reported that this gene can encode a functional protein. The encoded protein is nearly the same length as and highly similar to the POU class 5 homeobox 1 transcription factor, has been shown to be a weak transcriptional activator and may play a role in carcinogenesis and eye development. [provided by RefSeq, Apr 2009]

Previous symbols:

OTF3P1
POU5F1P1

MANE transcript

NM_001159542.3

Inheritance

—

ClinVar variants

U:57B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.1

Max pathogenic AF

—

Genomic locus

chr8:127,322,183-127,420,066

External References & Databases

Ensembl (ENSG00000212993)

Transcript & Mutation Effects

hg38 • Region Span ~97.9 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 POU5F1B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001159542.3. 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				1 clinvar		1
missense			57 clinvar			57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	1	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001159542.3	RefSeq	NP_001153014.1	1	MANE Select
ENST00000696633.1	Ensembl	ENSP00000512769.1	1	MANE Select
NM_001395745.1	RefSeq	NP_001382674.1	1	Standard
ENST00000465342.4	Ensembl	ENSP00000419298.2	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human)

Biological Process

regulation of transcription, DNA-templated
regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription factor activity
sequence-specific DNA binding

Cellular Component

nucleoplasm
mitochondrion
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000465342
Coding exons: 1
Length: 5777
Individuals with no LoFs: 125403
Homozygous LoFs: 2
Heterozygous LoFs: 283
Defined: 125688
p: 0.00113

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.356	205	191	1.07	0.0000111	2251
Missense (PolyPhen)		48	46.717	1.0275		641
Synonymous	-0.880	97	86.6	1.12	0.00000555	747
Loss of Function	-0.190	5	4.56	1.10	1.95e-7	58

Population LoF Frequency

Population	CAF	p-value	Status
African	0.014	0.013	notable
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00052	0.00046	rare
European (Non-Finnish)	0.00035	0.00033	rare
South Asian	0.00019	0.00016	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Shows weak transcriptional activator activity. {ECO:0000269|PubMed:18949397}.;

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High