FOXB1
forkhead box B1, the group of Forkhead boxes
Basic information
Region (hg38): 15:60004233-60061730
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXB1 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 | 0 | |||||
| missense | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 0 |
Variants in FOXB1
This is a list of pathogenic ClinVar variants found in the FOXB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-60004976-G-A | not specified | Uncertain significance (Dec 19, 2023) | ||
| 15-60005001-A-G | not specified | Uncertain significance (Nov 10, 2022) | ||
| 15-60005046-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 15-60005100-G-A | not specified | Uncertain significance (Jun 13, 2024) | ||
| 15-60005115-G-A | not specified | Uncertain significance (Apr 24, 2023) | ||
| 15-60005292-A-G | not specified | Uncertain significance (Jan 08, 2024) | ||
| 15-60005308-C-G | not specified | Uncertain significance (Mar 30, 2024) | ||
| 15-60005441-G-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 15-60005580-C-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 15-60005603-G-A | not specified | Uncertain significance (Dec 06, 2021) | ||
| 15-60005627-G-C | not specified | Uncertain significance (Jul 16, 2021) | ||
| 15-60005687-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 15-60005771-G-A | not specified | Uncertain significance (Feb 01, 2023) | ||
| 15-60005862-C-A | not specified | Uncertain significance (Jun 07, 2023) | ||
| 15-60005871-G-A | not specified | Uncertain significance (Jan 22, 2024) | ||
| 15-60005895-C-G | not specified | Uncertain significance (Dec 06, 2022) | ||
| 15-60005919-T-C | not specified | Uncertain significance (Jun 17, 2024) | ||
| 15-60005927-G-C | not specified | Uncertain significance (Jun 07, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FOXB1 | protein_coding | protein_coding | ENST00000396057 | 1 | 57509 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.906 | 0.0930 | 125732 | 0 | 2 | 125734 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.48 | 138 | 197 | 0.702 | 0.00000894 | 2081 |
| Missense in Polyphen | 45 | 66.356 | 0.67816 | 714 | ||
| Synonymous | -0.0438 | 91 | 90.5 | 1.01 | 0.00000451 | 698 |
| Loss of Function | 2.56 | 0 | 7.64 | 0.00 | 3.27e-7 | 83 |
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) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000337 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.103
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.769
- hipred
- Y
- hipred_score
- 0.736
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.283
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Foxb1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo 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); 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); 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;
Gene ontology
- Biological process
- urogenital system development;somitogenesis;regulation of transcription by RNA polymerase II;axon target recognition;lactation;visual learning;anatomical structure morphogenesis;spinal cord development;mammillary body development;thalamus development;hypothalamus cell migration;telencephalon cell migration;cell differentiation;midbrain development;floor plate development;negative regulation of neuron apoptotic process;epithelial cell differentiation involved in mammary gland alveolus development;mammillothalamic axonal tract development;mammary gland lobule development;inferior colliculus development;cell migration in diencephalon
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding