FBXO40
protein-codingF-box protein 40, the group of Zinc fingers TRAF-type|F-boxes other
Gene summary
Members of the F-box protein family, such as FBXO40, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to FBXO40 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016298.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 101 | 5 | 106 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 101 | 7 | 0 | 108 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057382.2 | 3 | MANE Select | |
| Ensembl | ENSP00000337510.4 | 3 | MANE Select | |
| Ensembl | ENSP00000538867.1 | 3 | Standard | |
| Ensembl | ENSP00000538867.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- Immune System
- Adaptive Immune System
- Antigen processing: Ubiquitination & Proteasome degradation
Biological Process
- protein polyubiquitination
- muscle cell differentiation
- post-translational protein modification
Molecular Function
- molecular_function
- ubiquitin-protein transferase activity
- zinc ion binding
- ubiquitin protein ligase activity
Cellular Component
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000338040
- Coding exons
- 3
- Length
- 37174
- Individuals with no LoFs
- 125458
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 288
- Defined
- 125748
- p
- 0.00115
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.217 | 376 | 388 | 0.969 | 0.0000205 | 4701 |
| Missense (PolyPhen) | 107 | 124.74 | 0.85775 | 1544 | ||
| Synonymous | -0.0717 | 152 | 151 | 1.01 | 0.00000843 | 1359 |
| Loss of Function | 1.26 | 16 | 22.5 | 0.712 | 0.00000118 | 290 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0015 | 0.0015 | notable |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00069 | 0.00069 | rare |
| East Asian | 0.0023 | 0.0023 | notable |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00063 | 0.00063 | rare |
| South Asian | 0.0044 | 0.0044 | notable |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex that may function in myogenesis. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- LoFtool
- 0.801
- RVIS EVS
- -0.79
- RVIS percentile EVS
- 12.57
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.366
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |