RBX1
ring-box 1, the group of SCF complex core subunits|Ring finger proteins
Basic information
Region (hg38): 22:40951347-40973309
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 RBX1 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 |
Variants in RBX1
This is a list of pathogenic ClinVar variants found in the RBX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-40964118-G-T | not specified | Uncertain significance (Oct 20, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBX1 | protein_coding | protein_coding | ENST00000216225 | 5 | 21963 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.947 | 0.0530 | 125688 | 0 | 1 | 125689 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.38 | 11 | 65.1 | 0.169 | 0.00000326 | 727 |
| Missense in Polyphen | 3 | 26.155 | 0.1147 | 257 | ||
| Synonymous | -0.266 | 25 | 23.4 | 1.07 | 0.00000128 | 183 |
| Loss of Function | 2.82 | 0 | 9.26 | 0.00 | 5.93e-7 | 83 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin ligase component of multiple cullin-RING- based E3 ubiquitin-protein ligase (CRLs) complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins, including proteins involved in cell cycle progression, signal transduction, transcription and transcription- coupled nucleotide excision repair (PubMed:10230407, PubMed:10579999, PubMed:15983046, PubMed:16678110, PubMed:19112177, PubMed:19679664, PubMed:23455478, PubMed:27565346, PubMed:29769719, PubMed:11961546, PubMed:22748924). CRLs complexes and ARIH1 collaborate in tandem to mediate ubiquitination of target proteins, ARIH1 mediating addition of the first ubiquitin on CRLs targets (PubMed:27565346). The functional specificity of the E3 ubiquitin-protein ligase complexes depends on the variable substrate recognition components. As a component of the CSA complex promotes the ubiquitination of ERCC6 resulting in proteasomal degradation. Recruits the E2 ubiquitin-conjugating enzyme CDC34 to the complex and brings it into close proximity to the substrate. Probably also stimulates CDC34 autoubiquitination. May be required for histone H3 and histone H4 ubiquitination in response to ultraviolet and for subsequent DNA repair. Promotes the neddylation of CUL1, CUL2, CUL4 and CUL4 via its interaction with UBE2M. Involved in the ubiquitination of KEAP1, ENC1 and KLHL41. In concert with ATF2 and CUL3, promotes degradation of KAT5 thereby attenuating its ability to acetylate and activate ATM. {ECO:0000269|PubMed:10230407, ECO:0000269|PubMed:10579999, ECO:0000269|PubMed:11027288, ECO:0000269|PubMed:11961546, ECO:0000269|PubMed:15983046, ECO:0000269|PubMed:16678110, ECO:0000269|PubMed:16751180, ECO:0000269|PubMed:18397884, ECO:0000269|PubMed:19112177, ECO:0000269|PubMed:19679664, ECO:0000269|PubMed:22748924, ECO:0000269|PubMed:23455478, ECO:0000269|PubMed:27565346, ECO:0000269|PubMed:29769719}.;
- Pathway
- Nucleotide excision repair - Homo sapiens (human);Circadian rhythm - Homo sapiens (human);TGF-beta signaling pathway - Homo sapiens (human);Renal cell carcinoma - Homo sapiens (human);Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Ubiquitin mediated proteolysis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);HH-Ncore;Dual hijack model of Vif in HIV infection;regulation of p27 phosphorylation during cell cycle progression;TGF-beta Signaling Pathway;Type 2 papillary renal cell carcinoma;Degradation of beta-catenin by the destruction complex;Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha;Regulation of Hypoxia-inducible Factor (HIF) by oxygen;Cellular response to hypoxia;Transcriptional regulation by RUNX2;Notch;DNA Repair;Disease;Signaling by WNT;Signal Transduction;Gene expression (Transcription);Signaling by Interleukins;GLI3 is processed to GLI3R by the proteasome;er associated degradation (erad) pathway;Prolactin receptor signaling;Generic Transcription Pathway;Cytokine Signaling in Immune system;Host Interactions of HIV factors;HIV Infection;Cellular responses to stress;Post-translational protein modification;Metabolism of proteins;Interleukin-1 signaling;RNA Polymerase II Transcription;Infectious disease;Immune System;Regulation of RAS by GAPs;Adaptive Immune System;Hypoxic and oxygen homeostasis regulation of HIF-1-alpha;Signaling by NOTCH1;Antigen processing: Ubiquitination & Proteasome degradation;Orc1 removal from chromatin;DNA Replication;Switching of origins to a post-replicative state;Class I MHC mediated antigen processing & presentation;Signaling by NOTCH;Synthesis of DNA;S Phase;Degradation of GLI2 by the proteasome;Degradation of GLI1 by the proteasome;Hedgehog ,off, state;Cellular responses to external stimuli;Hedgehog ,on, state;Signaling by Hedgehog;TGF_beta_Receptor;Neddylation;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;FBXL7 down-regulates AURKA during mitotic entry and in early mitosis;G2/M Transition;Mitotic G2-G2/M phases;Recognition of DNA damage by PCNA-containing replication complex;Degradation of DVL;Vif-mediated degradation of APOBEC3G;DNA Damage Bypass;Cell Cycle;DNA Damage Recognition in GG-NER;Formation of Incision Complex in GG-NER;Dual Incision in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Cell Cycle, Mitotic;Formation of TC-NER Pre-Incision Complex;TCF dependent signaling in response to WNT;NOTCH1 Intracellular Domain Regulates Transcription;Interleukin-1 family signaling;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair;Regulation of RUNX2 expression and activity
(Consensus)
Recessive Scores
- pRec
- 0.174
Intolerance Scores
- loftool
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.43
Haploinsufficiency Scores
- pHI
- 0.810
- hipred
- Y
- hipred_score
- 0.711
- ghis
- 0.645
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Mouse Genome Informatics
- Gene name
- Rbx1
- Phenotype
- embryo 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); cellular phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- MAPK cascade;protein polyubiquitination;nucleotide-excision repair, DNA damage recognition;transcription-coupled nucleotide-excision repair;nucleotide-excision repair, preincision complex stabilization;nucleotide-excision repair, preincision complex assembly;nucleotide-excision repair, DNA incision, 5'-to lesion;ubiquitin-dependent protein catabolic process;protein monoubiquitination;SCF complex assembly;negative regulation of G2/M transition of mitotic cell cycle;viral process;Wnt signaling pathway;protein ubiquitination;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;nucleotide-excision repair, DNA incision;DNA damage response, detection of DNA damage;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification;protein neddylation;regulation of transcription from RNA polymerase II promoter in response to hypoxia;interleukin-1-mediated signaling pathway;global genome nucleotide-excision repair;negative regulation of canonical Wnt signaling pathway
- Cellular component
- nucleus;nucleoplasm;cytosol;SCF ubiquitin ligase complex;VCB complex;cullin-RING ubiquitin ligase complex;Cul2-RING ubiquitin ligase complex;Cul3-RING ubiquitin ligase complex;Cul4A-RING E3 ubiquitin ligase complex;Cul4B-RING E3 ubiquitin ligase complex;Cul5-RING ubiquitin ligase complex;Cul7-RING ubiquitin ligase complex;nuclear SCF ubiquitin ligase complex;Cul4-RING E3 ubiquitin ligase complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;transcription factor binding;zinc ion binding;NEDD8 transferase activity;ubiquitin protein ligase binding;ubiquitin-ubiquitin ligase activity;protein-containing complex binding;ubiquitin protein ligase activity;cullin family protein binding