FOXL1

forkhead box L1, the group of Forkhead boxes

Basic information

Region (hg38): 16:86576368-86583478

Previous symbols: [ "FKHL11" ]

Links

ENSG00000176678

∙ NCBI:2300 ∙ OMIM:603252 ∙ HGNC:3817 ∙ Uniprot:Q12952 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

congenital heart disease (Disputed Evidence), mode of inheritance: AD
otosclerosis 11 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Otosclerosis 11	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic	34633540
Stapedectomy has been reported as helpful, but cochlear implant may be necessary

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FOXL1 gene.

not_specified (61 variants)
not_provided (2 variants)
Otosclerosis_11 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005250.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			59 clinvar	2 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	59	2	0

Highest pathogenic variant AF is 0.0026638461

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXL1	protein_coding	protein_coding	ENST00000320241	1	5330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0359	0.841	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.281	199	188	1.06	0.00000887	2177
Missense in Polyphen		60	75.307	0.79674		895
Synonymous	-2.63	119	87.7	1.36	0.00000433	775
Loss of Function	1.23	3	6.34	0.473	2.75e-7	73

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 required for proper proliferation and differentiation in the gastrointestinal epithelium. Target gene of the hedgehog (Hh) signaling pathway via GLI2 AND GLI3 transcription factors (By similarity). {ECO:0000250}.;
Pathway: Ectoderm Differentiation (Consensus)

Haploinsufficiency Scores

pHI: 0.731
hipred: N
hipred_score: 0.369
ghis: 0.560

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.333

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Foxl1
Phenotype: cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; digestive/alimentary 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); neoplasm;

Zebrafish Information Network

Gene name: foxl1
Affected structure: hyosymplectic cartilage
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;visceral mesoderm-endoderm interaction involved in midgut development;heart development;anatomical structure morphogenesis;regulation of Wnt signaling pathway;cell differentiation;proteoglycan biosynthetic process;Peyer's patch morphogenesis
Cellular component: nucleus
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;DNA binding, bending;sequence-specific DNA binding