FOXJ3

protein-coding

forkhead box J3, the group of Forkhead boxes

Gene summary

Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014947.5

Inheritance

—

ClinVar variants

U:94B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr1:42,176,539-42,335,877

External References & Databases

Ensembl (ENSG00000198815)

Transcript & Mutation Effects

hg38 • Region Span ~159.3 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 FOXJ3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 87

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014947.5. 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
missense			89 clinvar	1 clinvar		90
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	94	1	0	95

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014947.5	RefSeq	NP_055762.3	12	MANE Select
ENST00000361346.6	Ensembl	ENSP00000354620.1	12	MANE Select
NM_001198850.2	RefSeq	NP_001185779.1	12	Standard
NM_001198851.2	RefSeq	NP_001185780.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
sequence-specific DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372572
Coding exons: 12
Length: 159339
Individuals with no LoFs: 125689
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125695
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.31	271	339	0.799	0.0000171	4118
Missense (PolyPhen)		64	113.66	0.56308		1442
Synonymous	-1.02	134	120	1.12	0.00000617	1154
Loss of Function	4.76	4	33.9	0.118	0.00000178	365

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	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)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional activator of MEF2C involved in the regulation pf adult muscle fiber type identity and skeletal muscle regeneration. {ECO:0000250|UniProtKB:Q8BUR3}.;

Recessive Scores

pRec: 0.144

Intolerance Scores

LoFtool: 0.102
RVIS EVS: 0.29
RVIS percentile EVS: 71.5

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.946

Gene Damage Prediction

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