FOXN3

forkhead box N3, the group of Forkhead boxes

Basic information

Region (hg38): 14:89124870-89619149

Previous symbols: [ "C14orf116", "CHES1" ]

Links

ENSG00000053254 ∙ NCBI:1112 ∙ OMIM:602628 ∙ HGNC:1928 ∙ Uniprot:O00409 ∙ 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 FOXN3 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXN3 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					1	1
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	1

Variants in FOXN3

This is a list of pathogenic ClinVar variants found in the FOXN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-89162530-T-A		not specified	Uncertain significance (Oct 03, 2022)
14-89162590-C-T		not specified	Uncertain significance (Oct 29, 2021)
14-89162650-C-T		not specified	Uncertain significance (Aug 19, 2023)
14-89162657-C-A			Benign (Jan 01, 2023)
14-89162669-C-A		not specified	Uncertain significance (Jan 08, 2024)
14-89162709-G-A		not specified	Uncertain significance (Sep 16, 2021)
14-89162841-G-A		not specified	Uncertain significance (Jul 06, 2021)
14-89162949-C-T		not specified	Uncertain significance (Apr 28, 2022)
14-89190393-G-T		not specified	Uncertain significance (Oct 26, 2022)
14-89280992-G-A		not specified	Uncertain significance (Oct 04, 2022)
14-89411949-G-T		not specified	Uncertain significance (Oct 05, 2022)
14-89412331-C-T		not specified	Uncertain significance (Mar 01, 2023)
14-89412338-C-G		not specified	Uncertain significance (Mar 06, 2023)
14-89412350-A-C		not specified	Uncertain significance (Jun 03, 2022)
14-89412353-C-T		not specified	Uncertain significance (Sep 12, 2023)
14-89412358-T-G		not specified	Uncertain significance (May 10, 2022)
14-89412412-A-C		not specified	Uncertain significance (Feb 07, 2023)
14-89412458-G-A		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXN3	protein_coding	protein_coding	ENST00000345097	6	494279

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.932	0.0683	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.28	186	296	0.628	0.0000173	3257
Missense in Polyphen		31	88.292	0.35111		1118
Synonymous	0.0784	125	126	0.991	0.00000874	941
Loss of Function	3.42	2	17.4	0.115	8.98e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints). {ECO:0000269|PubMed:16102918}.

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.0542
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.742
• hipred: Y
• hipred_score: 0.696
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.790

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxn3
• Phenotype: skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;mitotic G2 DNA damage checkpoint;negative regulation of transcription, DNA-templated;craniofacial suture morphogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;protein C-terminus binding;sequence-specific DNA binding