FOXE1
forkhead box E1, the group of Forkhead boxes
Basic information
Region (hg38): 9:97853226-97856717
Previous symbols: [ "FKHL15", "TITF2", "FOXE2" ]
Links
Phenotypes
GenCC
Source:
- Bamforth-Lazarus syndrome (Definitive), mode of inheritance: AR
- Bamforth-Lazarus syndrome (Moderate), mode of inheritance: AR
- Bamforth-Lazarus syndrome (Limited), mode of inheritance: AR
- Bamforth-Lazarus syndrome (Supportive), mode of inheritance: AR
- Bamforth-Lazarus syndrome (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Thyroid cancer, nonmedullary 4; Hypothyroidism, thyroidal, with spiky hair and cleft palate (Bamforth-Lazarus syndrome) | AD/AR | Endocrine; Oncologic | For Thyroid cancer, nonmedullary 4, individuals have been described as being susceptible to nonmedullary thyroid cancer, and awareness may allow early surveillance, diagnosis, and management; For Hypothyroidism, thyroidal, with spiky hair and cleft palate (Bamforth-Lazarus syndrome), the condition may be clinically recognizable, but recognition and prompt treatment of hypothyroidism can be beneficial | Craniofacial; Dermatologic; Endocrine; Musculoskeletal; Oncologic | 2918525; 8320710; 9697705; 12165566; 16882747; 17717707; 17318017; 19779022; 20484477; 20453517; 20094846; 21981779; 21311165; 25381600 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (45 variants)
- not_provided (17 variants)
- Bamforth-Lazarus_syndrome (15 variants)
- not_specified (11 variants)
- FOXE1-related_disorder (6 variants)
- Thyroid_cancer,_nonmedullary,_4 (5 variants)
- congenital_hypothyreodism (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXE1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004473.4. 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 | 11 | |||||
| missense | 56 | 64 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 4 | 2 | 57 | 9 | 5 |
Highest pathogenic variant AF is 0.00000658206
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FOXE1 | protein_coding | protein_coding | ENST00000375123 | 1 | 3451 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.792 | 0.203 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.315 | 149 | 160 | 0.930 | 0.00000739 | 2256 |
| Missense in Polyphen | 55 | 63.26 | 0.86943 | 738 | ||
| Synonymous | 0.328 | 70 | 73.6 | 0.951 | 0.00000363 | 840 |
| Loss of Function | 2.11 | 0 | 5.20 | 0.00 | 2.21e-7 | 84 |
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:
- Function
- FUNCTION: Transcription factor that binds consensus sites on a variety of gene promoters and activate their transcription. Involved in proper palate formation, most probably through the expression of MSX1 and TGFB3 genes which are direct targets of this transcription factor. Also implicated in thyroid gland morphogenesis. May indirectly play a role in cell growth and migration through the regulation of WNT5A expression. {ECO:0000269|PubMed:12165566, ECO:0000269|PubMed:16882747, ECO:0000269|PubMed:20094846, ECO:0000269|PubMed:20484477, ECO:0000269|PubMed:21177256, ECO:0000269|PubMed:24219130, ECO:0000269|PubMed:25381600, ECO:0000269|PubMed:9697705}.;
- Disease
- DISEASE: Bamforth-Lazarus syndrome (BLS) [MIM:241850]: A disease characterized by thyroid agenesis, cleft palate and choanal atresia. {ECO:0000269|PubMed:12165566, ECO:0000269|PubMed:21177256, ECO:0000269|PubMed:24219130, ECO:0000269|PubMed:9697705}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thyroid cancer, non-medullary, 4 (NMTC4) [MIM:616534]: A form of non-medullary thyroid cancer (NMTC), a cancer characterized by tumors originating from the thyroid follicular cells. NMTCs represent approximately 95% of all cases of thyroid cancer and are classified into papillary, follicular, Hurthle cell, and anaplastic neoplasms. {ECO:0000269|PubMed:25381600}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.106
Haploinsufficiency Scores
- pHI
- hipred
- hipred_score
- ghis
- 0.654
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.325
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Foxe1
- Phenotype
- endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism 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); digestive/alimentary phenotype;
Zebrafish Information Network
- Gene name
- foxe1
- Affected structure
- ceratobranchial cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- deformed
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;thyroid hormone generation;anatomical structure morphogenesis;cell migration;cell differentiation;thyroid gland development;hair follicle morphogenesis;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;thymus development;embryonic organ morphogenesis;hard palate development;soft palate development;pharynx development;cranial skeletal system development
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding