POU6F2

POU class 6 homeobox 2, the group of POU class homeoboxes and pseudogenes

Basic information

Region (hg38): 7:38977909-39493095

Links

ENSG00000106536 ∙ NCBI:11281 ∙ OMIM:609062 ∙ HGNC:21694 ∙ Uniprot:P78424 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Wilms tumor 5 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Wilms tumor 5	AD	Oncologic	Individuals may be at high risk for Wilms tumor, and surveillance may allow early diagnosis and treatment	Oncologic	11284034
Germline variants can predispose to disease due to loss of heterozygosity

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POU6F2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU6F2 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				14	3	17
missense			45	6	5	56
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	45	20	9

Variants in POU6F2

This is a list of pathogenic ClinVar variants found in the POU6F2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-38978015-C-G		Wilms tumor 5	Pathogenic (Nov 01, 2004)
7-39085873-C-A		not specified	Uncertain significance (Aug 12, 2021)
7-39085895-G-A			Likely benign (Nov 03, 2018)
7-39085902-G-C		not specified	Uncertain significance (Mar 30, 2024)
7-39085951-C-T		not specified	Uncertain significance (Jun 18, 2021)
7-39085960-G-A		not specified	Uncertain significance (Mar 30, 2024)
7-39086030-C-T			Likely benign (Dec 31, 2019)
7-39204240-A-G		not specified	Uncertain significance (Jan 20, 2023)
7-39204265-C-T		Hypogonadotropic hypogonadism	Uncertain significance (-)
7-39204282-C-A		not specified	Uncertain significance (Feb 06, 2024)
7-39204305-C-G			Likely benign (Dec 31, 2019)
7-39204319-G-A		Hypogonadotropic hypogonadism • not specified	Uncertain significance (Jun 29, 2023)
7-39207416-G-T		not specified	Uncertain significance (Feb 13, 2024)
7-39207426-T-C		not specified	Uncertain significance (Dec 06, 2021)
7-39207431-G-A		not specified	Uncertain significance (Dec 11, 2023)
7-39207456-C-T		not specified	Uncertain significance (Sep 01, 2021)
7-39207462-A-G		Hypogonadotropic hypogonadism	Uncertain significance (-)
7-39207475-C-T			Likely benign (Mar 29, 2018)
7-39207519-T-C		not specified	Uncertain significance (May 01, 2024)
7-39339681-T-A		POU6F2-related disorder	Likely benign (May 04, 2023)
7-39339681-T-G		POU6F2-related disorder	Likely benign (Oct 17, 2018)
7-39339682-C-G		POU6F2-related disorder	Likely benign (May 04, 2023)
7-39339687-T-A			Likely benign (Oct 17, 2018)
7-39339688-C-G			Likely benign (Oct 17, 2018)
7-39339688-CCAG-C		POU6F2-related disorder	Benign (May 02, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU6F2	protein_coding	protein_coding	ENST00000403058	10	515097

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00152	0.998	125361	1	247	125609	0.000988

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.455	361	386	0.935	0.0000218	4427
Missense in Polyphen		52	53.591	0.97031		578
Synonymous	-0.220	174	170	1.02	0.0000107	1470
Loss of Function	3.52	11	32.7	0.336	0.00000165	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000735	0.000735
Ashkenazi Jewish	0.00135	0.000695
East Asian	0.000111	0.000109
Finnish	0.00301	0.00111
European (Non-Finnish)	0.000837	0.000520
Middle Eastern	0.000111	0.000109
South Asian	0.00826	0.00445
Other	0.00203	0.000979

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcription factor likely to be involved in early steps in the differentiation of amacrine and ganglion cells. Recognizes and binds to the DNA sequence 5'-ATGCAAAT-3'. Isoform 1 does not bind DNA.

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.110
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.93

Haploinsufficiency Scores

• pHI: 0.818
• hipred: N
• hipred_score: 0.492
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.207

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou6f2
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;ganglion mother cell fate determination;central nervous system development;visual perception
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity