FOXN4
forkhead box N4, the group of Forkhead boxes
Basic information
Region (hg38): 12:109277977-109309284
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 FOXN4 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 | 39 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 39 | 0 | 0 |
Variants in FOXN4
This is a list of pathogenic ClinVar variants found in the FOXN4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-109279753-G-A | not specified | Uncertain significance (Jul 05, 2023) | ||
| 12-109279819-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 12-109279834-C-A | not specified | Uncertain significance (Sep 29, 2022) | ||
| 12-109279835-C-T | not specified | Uncertain significance (Aug 08, 2022) | ||
| 12-109279877-C-T | not specified | Uncertain significance (Nov 17, 2023) | ||
| 12-109281416-C-T | not specified | Uncertain significance (Jun 22, 2021) | ||
| 12-109281437-C-T | not specified | Uncertain significance (Jul 12, 2022) | ||
| 12-109281464-C-T | not specified | Uncertain significance (Jun 09, 2022) | ||
| 12-109281509-G-T | not specified | Uncertain significance (Feb 12, 2024) | ||
| 12-109281538-G-A | not specified | Uncertain significance (Aug 10, 2021) | ||
| 12-109281590-G-C | not specified | Uncertain significance (Mar 30, 2022) | ||
| 12-109281595-G-A | not specified | Uncertain significance (May 06, 2024) | ||
| 12-109281617-G-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 12-109281638-A-G | not specified | Uncertain significance (Jan 23, 2024) | ||
| 12-109281685-C-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 12-109281718-A-G | not specified | Uncertain significance (Jun 05, 2023) | ||
| 12-109281725-G-A | not specified | Uncertain significance (Feb 07, 2023) | ||
| 12-109281736-T-C | not specified | Uncertain significance (Jan 16, 2024) | ||
| 12-109281749-C-T | not specified | Uncertain significance (Dec 18, 2023) | ||
| 12-109281755-G-A | not specified | Uncertain significance (Nov 08, 2022) | ||
| 12-109281774-G-C | not specified | Uncertain significance (Mar 30, 2022) | ||
| 12-109285333-G-T | not specified | Uncertain significance (Oct 25, 2023) | ||
| 12-109285334-C-T | not specified | Uncertain significance (Jun 18, 2021) | ||
| 12-109285418-G-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 12-109285436-T-G | not specified | Uncertain significance (Dec 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FOXN4 | protein_coding | protein_coding | ENST00000299162 | 9 | 31242 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.861 | 0.139 | 125681 | 0 | 9 | 125690 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.23 | 242 | 302 | 0.801 | 0.0000182 | 3312 |
| Missense in Polyphen | 82 | 100.66 | 0.81461 | 1053 | ||
| Synonymous | 1.05 | 120 | 136 | 0.885 | 0.00000945 | 1082 |
| Loss of Function | 3.48 | 3 | 19.6 | 0.153 | 0.00000106 | 220 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000155 | 0.000153 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000358 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000657 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor essential for neural and some non- neural tissues development, such as retina and lung respectively. Binds to an 11-bp consensus sequence containing the invariant tetranucleotide 5'-ACGC-3'. During development of the central nervous system, is required to specify the amacrine and horizontal cell fates from multipotent retinal progenitors while suppressing the alternative photoreceptor cell fates through activating DLL4- NOTCH signaling. Also acts synergistically with ASCL1/MASH1 to activate DLL4-NOTCH signaling and drive commitment of p2 progenitors to the V2b interneuron fates during spinal cord neurogenesis. In development of non-neural tissues, plays an essential role in the specification of the atrioventricular canal and is indirectly required for patterning the distal airway during lung development (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.152
Intolerance Scores
- loftool
- 0.255
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.77
Haploinsufficiency Scores
- pHI
- 0.167
- hipred
- N
- hipred_score
- 0.411
- ghis
- 0.462
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.204
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Foxn4
- Phenotype
- cellular 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); vision/eye 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
- foxn4
- Affected structure
- heart valve
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- heart looping;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;regulation of heart contraction;retina layer formation;amacrine cell differentiation;atrioventricular canal development;positive regulation of transcription, DNA-templated;ventral spinal cord interneuron fate commitment
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;enhancer sequence-specific DNA binding;chromatin binding;DNA-binding transcription factor activity;protein binding