FOXN3

protein-coding

forkhead box N3, the group of Forkhead boxes

Gene summary

This gene is a member of the forkhead/winged helix transcription factor family. Checkpoints are eukaryotic DNA damage-inducible cell cycle arrests at G1 and G2. Checkpoint suppressor 1 suppresses multiple yeast checkpoint mutations including mec1, rad9, rad53 and dun1 by activating a MEC1-independent checkpoint pathway. Alternative splicing is observed at the locus, resulting in distinct isoforms. [provided by RefSeq, Jul 2008]

Previous symbols:

C14orf116
CHES1

MANE transcript

NM_005197.4

Inheritance

—

ClinVar variants

U:50B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr14:89,124,871-89,619,149

External References & Databases

Ensembl (ENSG00000053254)

Transcript & Mutation Effects

hg38 • Region Span ~494.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FOXN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005197.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			47 clinvar	2 clinvar		49
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	50	3	1	54

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005197.4	RefSeq	NP_005188.2	5	MANE Select
ENST00000557258.6	Ensembl	ENSP00000452005.1	5	MANE Select
NM_001085471.2	RefSeq	NP_001078940.1	6	Standard
ENST00000261302.10	Ensembl	ENSP00000261302.5	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
mitotic G2 DNA damage checkpoint
negative regulation of transcription, DNA-templated
craniofacial suture morphogenesis

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
protein binding
protein C-terminus binding
sequence-specific DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000345097
Coding exons: 6
Length: 494279
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125748
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.28	186	296	0.628	0.0000173	3257
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.790

Gene Damage Prediction

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