POU6F1

POU class 6 homeobox 1, the group of POU class homeoboxes and pseudogenes

Basic information

Region (hg38): 12:51186935-51218062

Links

ENSG00000184271 ∙ NCBI:5463 ∙ OMIM:618043 ∙ HGNC:9224 ∙ Uniprot:Q14863 ∙ 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 POU6F1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU6F1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in POU6F1

This is a list of pathogenic ClinVar variants found in the POU6F1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-51190417-T-G		not specified	Uncertain significance (Oct 13, 2021)
12-51190423-G-C		not specified	Uncertain significance (Dec 12, 2023)
12-51190449-C-T		not specified	Uncertain significance (Sep 27, 2021)
12-51190566-T-C		not specified	Uncertain significance (Dec 12, 2023)
12-51191714-G-A		not specified	Uncertain significance (Aug 17, 2022)
12-51192360-C-T		not specified	Uncertain significance (Jan 19, 2024)
12-51192402-C-T		not specified	Uncertain significance (Aug 03, 2022)
12-51192404-G-C		not specified	Uncertain significance (May 24, 2023)
12-51192420-C-T		not specified	Likely benign (Apr 12, 2024)
12-51192435-G-A		not specified	Uncertain significance (Aug 14, 2023)
12-51192471-C-A		not specified	Uncertain significance (Jan 30, 2024)
12-51196007-C-T		not specified	Uncertain significance (Jun 17, 2024)
12-51196033-G-C		not specified	Uncertain significance (Mar 28, 2024)
12-51196085-G-T		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU6F1	protein_coding	protein_coding	ENST00000389243	5	30759

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.880	0.119	125737	0	3	125740	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	127	176	0.721	0.0000113	1924
Missense in Polyphen		24	41.483	0.57855		391
Synonymous	-0.454	77	72.1	1.07	0.00000443	646
Loss of Function	2.84	1	11.3	0.0885	4.88e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds preferentially to a variant of the octamer motif (5'-ATGATAAT-3'). {ECO:0000250}.
• Pathway: Developmental Biology;HIF-2-alpha transcription factor network;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Transcriptional regulation of pluripotent stem cells (Consensus)

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.159
• hipred: Y
• hipred_score: 0.550
• ghis: 0.703

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pou6f1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;brain development;heart development;muscle organ development
• Cellular component: actin cytoskeleton;nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding