FOXJ1

forkhead box J1, the group of Forkhead boxes

Basic information

Region (hg38): 17:76136332-76141245

Previous symbols: [ "FKHL13" ]

Links

ENSG00000129654 ∙ NCBI:2302 ∙ OMIM:602291 ∙ HGNC:3816 ∙ Uniprot:Q92949 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliary dyskinesia, primary, 43 (Strong), mode of inheritance: AD
• ciliary dyskinesia, primary, 43 (Moderate), mode of inheritance: AD
• ciliary dyskinesia, primary, 43 (Strong), mode of inheritance: AD
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• ciliary dyskinesia, primary, 43 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 43	AD	Allergy/Immunology/Infectious; Cardiovascular; Pulmonary	Pulmonary surveillance may be beneficial to assess respiratory function and institute early management measures; In order to facilitate mucus clearance, aggressive interventions (eg, chest percussion and oscillatory vest), as well as vaccinations and early and aggressive treatment of respiratory infections may be beneficial; Individuals have been described requiring shunting due to obstructive hydrocephalus, and awareness may allow early interventions; The condition can involve congenital cardiac anomalies, and awareness may allow early management	Allergy/Immunology/Infectious; Cardiovascular; Genitourinary; Neurologic; Pulmonary	31630787

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FOXJ1 gene.

• Ciliary dyskinesia, primary, 43 (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXJ1 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				4	1	5
missense			30	5		35
nonsense	1					1
start loss						0
frameshift		2	1			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	1	2	31	9	4

Variants in FOXJ1

This is a list of pathogenic ClinVar variants found in the FOXJ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-76137164-C-T			Benign (May 21, 2021)
17-76137356-C-A		FOXJ1-related disorder	Likely benign (Dec 14, 2023)
17-76137370-C-T		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
17-76137380-G-C		Inborn genetic diseases	Uncertain significance (Jan 02, 2024)
17-76137399-A-C		Inborn genetic diseases	Uncertain significance (May 04, 2022)
17-76137409-C-T		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
17-76137471-T-G		Inborn genetic diseases	Uncertain significance (Jan 31, 2024)
17-76137489-AG-A		Ciliary dyskinesia, primary, 43	not provided (-)
17-76137490-G-C		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
17-76137503-G-C		FOXJ1-related disorder	Uncertain significance (Jul 12, 2023)
17-76137508-C-T		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
17-76137533-C-T		FOXJ1-related disorder	Likely benign (May 21, 2021)
17-76137568-G-A		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
17-76137571-C-T		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
17-76137578-G-GGTGAGGTCCACGTCCACGT			Uncertain significance (Sep 28, 2023)
17-76137583-G-C		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
17-76137595-C-T		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
17-76137604-C-T		Ciliary dyskinesia, primary, 43 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 14, 2023)
17-76137646-C-G		Inborn genetic diseases	Uncertain significance (Jun 10, 2022)
17-76137651-TC-T		Ciliary dyskinesia, primary, 43	Pathogenic (Dec 13, 2019)
17-76137661-G-C			Uncertain significance (Apr 23, 2021)
17-76137670-C-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
17-76137705-A-AG		Ciliary dyskinesia, primary, 43	Likely pathogenic (Sep 25, 2023)
17-76137718-C-A		Ciliary dyskinesia, primary, 43	Pathogenic (Dec 13, 2019)
17-76137732-G-A		Inborn genetic diseases	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXJ1	protein_coding	protein_coding	ENST00000322957	2	4967

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0310	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.699	202	232	0.871	0.0000136	2645
Missense in Polyphen		51	75.328	0.67704		893
Synonymous	1.07	96	110	0.870	0.00000713	897
Loss of Function	3.04	0	10.8	0.00	4.62e-7	128

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

• Function: FUNCTION: Transcription factor specifically required for the formation of motile cilia. Acts by activating transcription of genes that mediate assembly of motile cilia, such as CFAP157. Binds the DNA consensus sequences 5'-HWDTGTTTGTTTA-3' or 5'- KTTTGTTGTTKTW-3' (where H is not G, W is A or T, D is not C, and K is G or T). Activates the transcription of a variety of ciliary proteins in the developing brain and lung. {ECO:0000250|UniProtKB:Q61660}.
• Disease: DISEASE: Allergic rhinitis (ALRH) [MIM:607154]: A common disease with complex inheritance characterized by mucosal inflammation caused by allergen exposure. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.257

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.540
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxj1
• Phenotype: growth/size/body region phenotype; cellular 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; 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); embryo phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Zebrafish Information Network

• Gene name: foxj1a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: circling

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;central tolerance induction;negative regulation of germinal center formation;positive regulation of central B cell tolerance induction;negative regulation of humoral immune response mediated by circulating immunoglobulin;humoral immune response;spermatogenesis;determination of left/right symmetry;pattern specification process;brain development;heart development;actin cytoskeleton organization;negative regulation of NF-kappaB transcription factor activity;negative regulation of T cell differentiation in thymus;establishment of apical/basal cell polarity;metanephric part of ureteric bud development;negative regulation of T cell proliferation;motile cilium assembly;negative regulation of interleukin-6 biosynthetic process;positive regulation of transcription by RNA polymerase II;negative regulation of B cell activation;leukocyte migration;cilium assembly;lung epithelium development;epithelium development;left/right pattern formation;glomerular parietal epithelial cell development;activation of GTPase activity;positive regulation of lung ciliated cell differentiation
• Cellular component: nucleus
• Molecular function: transcription regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding