FBXO11
Basic information
Region (hg38): 2:47789316-47906498
Links
Phenotypes
GenCC
Source:
- intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (Definitive), mode of inheritance: AD
- intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (Strong), mode of inheritance: AD
- intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic | 27620904; 29796876; 30057029 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (925 variants)
- Intellectual_developmental_disorder_with_dysmorphic_facies_and_behavioral_abnormalities (150 variants)
- Inborn_genetic_diseases (61 variants)
- FBXO11-related_disorder (23 variants)
- Neurodevelopmental_disorder (21 variants)
- not_specified (21 variants)
- Intellectual_disability (8 variants)
- See_cases (6 variants)
- Developmental_disorder (2 variants)
- Obesity (1 variants)
- Lynch_syndrome_5 (1 variants)
- Delayed_speech_and_language_development (1 variants)
- Marfanoid_habitus_and_intellectual_disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001190274.2. 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 | 191 | 12 | 210 | |||
missense | 62 | 306 | 69 | 13 | 452 | |
nonsense | 13 | |||||
start loss | 0 | |||||
frameshift | 19 | 14 | 35 | |||
splice donor/acceptor (+/-2bp) | 14 | 24 | ||||
Total | 35 | 98 | 316 | 260 | 25 |
Highest pathogenic variant AF is 0.000030796313
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FBXO11 | protein_coding | protein_coding | ENST00000403359 | 23 | 116478 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 1.07e-7 | 125632 | 0 | 5 | 125637 | 0.0000199 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 4.38 | 208 | 477 | 0.436 | 0.0000235 | 6136 |
Missense in Polyphen | 33 | 191.33 | 0.17247 | 2342 | ||
Synonymous | -2.44 | 188 | 150 | 1.25 | 0.00000705 | 1682 |
Loss of Function | 6.35 | 1 | 48.9 | 0.0205 | 0.00000255 | 622 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000145 | 0.000145 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
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, such as DTL/CDT2, BCL6 and PRDM1/BLIMP1. The SCF(FBXO11) complex mediates ubiquitination and degradation of BCL6, thereby playing a role in the germinal center B-cells terminal differentiation toward memory B-cells and plasma cells. The SCF(FBXO11) complex also mediates ubiquitination and degradation of DTL, an important step for the regulation of TGF- beta signaling, cell migration and the timing of the cell-cycle progression and exit. Binds to and neddylates phosphorylated p53/TP53, inhibiting its transcriptional activity. SCF(FBXO11) does not seem to direct ubiquitination of p53/TP53. {ECO:0000269|PubMed:17098746, ECO:0000269|PubMed:22113614, ECO:0000269|PubMed:23478441, ECO:0000269|PubMed:23478445, ECO:0000269|PubMed:23892434, ECO:0000269|PubMed:24613396}.;
- Disease
- DISEASE: Note=Defects in FBXO11 may be a cause of diffuse large B- cell lymphoma by allowing the accumulation of BCL6, an oncoprotein that has a critical role in lymphomas. {ECO:0000269|PubMed:22113614}.;
- 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;p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- loftool
- 0.112
- rvis_EVS
- -0.69
- rvis_percentile_EVS
- 15.12
Haploinsufficiency Scores
- pHI
- 0.567
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.680
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fbxo11
- Phenotype
- growth/size/body region 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); craniofacial phenotype; homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); digestive/alimentary phenotype; hearing/vestibular/ear phenotype; vision/eye phenotype; immune system phenotype;
Gene ontology
- Biological process
- protein polyubiquitination;cellular protein modification process;ubiquitin-dependent protein catabolic process;sensory perception of sound;protein ubiquitination;peptidyl-arginine N-methylation;post-translational protein modification
- Cellular component
- ubiquitin ligase complex;nucleus;chromosome;nucleolus;cytoplasm;cytosol
- Molecular function
- ubiquitin-protein transferase activity;protein binding;zinc ion binding;protein-arginine N-methyltransferase activity