FBXO7
Basic information
Region (hg38): 22:32474676-32498829
Links
Phenotypes
GenCC
Source:
- parkinsonian-pyramidal syndrome (Strong), mode of inheritance: AR
- parkinsonian-pyramidal syndrome (Strong), mode of inheritance: AR
- parkinsonian-pyramidal syndrome (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Parkinson disease 15, autosomal recessive | AR | Neurologic | Individuals have been described with levodopa response | Neurologic | 18513678; 19038853; 23318512 |
ClinVar
This is a list of variants' phenotypes submitted to
- Parkinsonian-pyramidal_syndrome (328 variants)
- not_provided (58 variants)
- Inborn_genetic_diseases (53 variants)
- FBXO7-related_disorder (6 variants)
- not_specified (5 variants)
- Parkinson_Disease,_Recessive (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012179.4. 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 | 122 | 125 | ||||
missense | 118 | 16 | 137 | |||
nonsense | 10 | 17 | ||||
start loss | 4 | 4 | ||||
frameshift | 14 | 22 | ||||
splice donor/acceptor (+/-2bp) | 6 | |||||
Total | 30 | 17 | 124 | 138 | 2 |
Highest pathogenic variant AF is 0.0000960326
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FBXO7 | protein_coding | protein_coding | ENST00000266087 | 9 | 24156 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.79e-7 | 0.969 | 125687 | 0 | 61 | 125748 | 0.000243 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.440 | 305 | 284 | 1.07 | 0.0000161 | 3359 |
Missense in Polyphen | 85 | 81.16 | 1.0473 | 960 | ||
Synonymous | 0.626 | 105 | 113 | 0.925 | 0.00000645 | 1081 |
Loss of Function | 2.03 | 14 | 25.0 | 0.561 | 0.00000150 | 286 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000420 | 0.000420 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000334 | 0.000334 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000328 | 0.000327 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Recognizes BIRC2 and DLGAP5. Plays a role downstream of PINK1 in the clearance of damaged mitochondria via selective autophagy (mitophagy) by targeting PRKN to dysfunctional depolarized mitochondria. Promotes MFN1 ubiquitination. {ECO:0000269|PubMed:15145941, ECO:0000269|PubMed:16510124, ECO:0000269|PubMed:23933751}.;
- Disease
- DISEASE: Parkinson disease 15 (PARK15) [MIM:260300]: A neurodegenerative disorder characterized by parkinsonian and pyramidal signs. Clinical manifestations include tremor, bradykinesia, rigidity, postural instability, spasticity, mainly in the lower limbs, and hyperreflexia. {ECO:0000269|PubMed:18513678, ECO:0000269|PubMed:23933751}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- 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
- 0.138
Intolerance Scores
- loftool
- 0.893
- rvis_EVS
- 0.09
- rvis_percentile_EVS
- 60.57
Haploinsufficiency Scores
- pHI
- 0.0684
- hipred
- Y
- hipred_score
- 0.614
- ghis
- 0.499
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.294
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fbxo7
- Phenotype
- homeostasis/metabolism phenotype; reproductive system phenotype; hematopoietic system phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- fbxo7
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- curled
Gene ontology
- Biological process
- protein polyubiquitination;autophagy of mitochondrion;ubiquitin-dependent protein catabolic process;protein targeting to mitochondrion;regulation of neuron projection development;protein ubiquitination;regulation of protein stability;regulation of locomotion;post-translational protein modification;negative regulation of lymphocyte differentiation;negative regulation of cyclin-dependent protein serine/threonine kinase activity;negative regulation of oxidative stress-induced neuron death;positive regulation of autophagy of mitochondrion;negative regulation of G1/S transition of mitotic cell cycle
- Cellular component
- ubiquitin ligase complex;nucleus;cytoplasm;mitochondrion;cytosol;SCF ubiquitin ligase complex;protein-containing complex;glial cytoplasmic inclusion;classical Lewy body;Lewy neurite;Lewy body core;Lewy body corona
- Molecular function
- ubiquitin-protein transferase activity;protein binding;protein kinase binding;ubiquitin protein ligase binding;ubiquitin binding;protein heterodimerization activity