FBXL20
F-box and leucine rich repeat protein 20, the group of F-box and leucine rich repeat proteins
Basic information
Region (hg38): 17:39252663-39402523
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 FBXL20 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 | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in FBXL20
This is a list of pathogenic ClinVar variants found in the FBXL20 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-39264230-C-T | not specified | Uncertain significance (Nov 22, 2023) | ||
| 17-39264239-C-T | not specified | Uncertain significance (May 27, 2022) | ||
| 17-39265402-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
| 17-39275069-C-A | not specified | Uncertain significance (Jan 09, 2023) | ||
| 17-39281428-G-C | not specified | Uncertain significance (Jan 23, 2024) | ||
| 17-39281439-T-C | not specified | Uncertain significance (Jun 01, 2023) | ||
| 17-39282733-G-A | not specified | Uncertain significance (Dec 13, 2021) | ||
| 17-39282828-C-A | not specified | Uncertain significance (Feb 22, 2023) | ||
| 17-39297193-G-A | not specified | Uncertain significance (May 30, 2024) | ||
| 17-39298999-T-C | not specified | Uncertain significance (Sep 27, 2021) | ||
| 17-39299080-C-T | not specified | Uncertain significance (Feb 14, 2023) | ||
| 17-39343181-G-A | not specified | Uncertain significance (Oct 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FBXL20 | protein_coding | protein_coding | ENST00000264658 | 15 | 143393 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00309 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.12 | 101 | 236 | 0.428 | 0.0000121 | 2849 |
| Missense in Polyphen | 9 | 46.666 | 0.19286 | 643 | ||
| Synonymous | 0.243 | 82 | 84.8 | 0.966 | 0.00000402 | 839 |
| Loss of Function | 4.59 | 3 | 30.2 | 0.0993 | 0.00000181 | 326 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000913 | 0.0000913 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000546 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. Role in neural transmission (By similarity). {ECO:0000250}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation
(Consensus)
Recessive Scores
- pRec
- 0.0803
Intolerance Scores
- loftool
- 0.132
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.49
Haploinsufficiency Scores
- pHI
- 0.859
- hipred
- Y
- hipred_score
- 0.688
- ghis
- 0.503
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.427
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fbxl20
- Phenotype
- endocrine/exocrine gland 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); growth/size/body region 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);
Gene ontology
- Biological process
- protein polyubiquitination;behavioral fear response;ubiquitin-dependent protein catabolic process;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;post-translational protein modification;regulation of protein catabolic process at presynapse, modulating synaptic transmission;regulation of synaptic vesicle exocytosis
- Cellular component
- cytosol;SCF ubiquitin ligase complex;Schaffer collateral - CA1 synapse;presynapse;glutamatergic synapse
- Molecular function
- ubiquitin-protein transferase activity;protein binding