POU5F2

POU domain class 5, transcription factor 2, the group of POU class homeoboxes and pseudogenes

Basic information

Region (hg38): 5:93733219-93741600

Links

ENSG00000248483 ∙ NCBI:134187 ∙ ∙ HGNC:26367 ∙ Uniprot:Q8N7G0 ∙ 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 POU5F2 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU5F2 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			7			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	7	0	0

Variants in POU5F2

This is a list of pathogenic ClinVar variants found in the POU5F2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-93740605-G-A		not specified	Uncertain significance (May 27, 2022)
5-93740656-G-C		not specified	Uncertain significance (Apr 25, 2023)
5-93740905-C-G		not specified	Uncertain significance (Apr 27, 2023)
5-93740905-C-T		not specified	Uncertain significance (Oct 17, 2023)
5-93740908-C-T		not specified	Uncertain significance (Aug 26, 2022)
5-93740986-G-A		not specified	Uncertain significance (Dec 06, 2023)
5-93741107-C-T		not specified	Uncertain significance (Sep 06, 2022)
5-93741139-T-C		not specified	Uncertain significance (Jun 24, 2022)
5-93741241-C-G		not specified	Uncertain significance (Dec 28, 2023)
5-93741269-C-A		not specified	Uncertain significance (Nov 19, 2022)
5-93741284-G-A		not specified	Uncertain significance (Nov 05, 2021)
5-93741530-G-T		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU5F2	protein_coding	protein_coding	ENST00000510627	1	6836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000403	0.419	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.409	185	201	0.919	0.0000127	2081
Missense in Polyphen		25	22.508	1.1107		210
Synonymous	-0.0496	89	88.4	1.01	0.00000573	729
Loss of Function	0.0110	5	5.03	0.995	2.17e-7	53

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 preferentially to the octamer motif (5'-ATGTTAAT-3'). May exert a regulatory function in meiotic events that are required for terminal differentiation of male germ cell (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou5f2
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding