POU2AF3

POU class 2 homeobox associating factor 3

Basic information

Region (hg38): 11:111298546-111308735

Previous symbols: [ "C11orf93", "COLCA2" ]

Links

ENSG00000214290 ∙ NCBI:120376 ∙ OMIM:615694 ∙ HGNC:26978 ∙ Uniprot:A8K830 ∙ 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 POU2AF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POU2AF3 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	9	1	1

Variants in POU2AF3

This is a list of pathogenic ClinVar variants found in the POU2AF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-111299891-G-A			Benign (Jan 01, 2023)
11-111306577-T-G		not specified	Uncertain significance (Apr 28, 2022)
11-111306615-C-A		not specified	Uncertain significance (Nov 18, 2023)
11-111308120-A-G		not specified	Uncertain significance (Jan 24, 2023)
11-111308204-C-A		not specified	Uncertain significance (Oct 04, 2022)
11-111308207-C-G		not specified	Uncertain significance (Dec 14, 2023)
11-111308208-C-G		not specified	Uncertain significance (Jan 03, 2024)
11-111308229-A-G		not specified	Uncertain significance (May 20, 2024)
11-111308243-G-A		not specified	Likely benign (Jun 23, 2023)
11-111308295-C-T		not specified	Uncertain significance (May 24, 2024)
11-111308330-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-111308400-A-G		not specified	Uncertain significance (Jun 16, 2023)
11-111308430-A-G		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POU2AF3	protein_coding	protein_coding	ENST00000398035	2	9896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.751	0.240	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.554	62	75.5	0.821	0.00000366	1000
Missense in Polyphen		10	15.643	0.63928		247
Synonymous	1.38	24	34.3	0.700	0.00000208	297
Loss of Function	1.99	0	4.60	0.00	1.93e-7	66

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

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: 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: Colca2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; hearing/vestibular/ear phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Cellular component: cytoplasm