RBBP4
RB binding protein 4, chromatin remodeling factor, the group of NuRD complex subunits|EMSY complex|WD repeat domain containing|SIN3 histone deacetylase complex subunits|Polycomb repressive complex 2|NURF complex
Basic information
Region (hg38): 1:32651142-32686211
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 RBBP4 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 | 1 | |||||
| missense | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 4 | |||||
| Total | 0 | 0 | 5 | 0 | 2 |
Variants in RBBP4
This is a list of pathogenic ClinVar variants found in the RBBP4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-32651310-G-T | not specified | Uncertain significance (May 30, 2024) | ||
| 1-32668257-A-T | not specified | Uncertain significance (Nov 09, 2023) | ||
| 1-32668367-T-C | Benign (Apr 25, 2019) | |||
| 1-32672915-A-C | Benign (Mar 30, 2020) | |||
| 1-32679679-G-A | not specified | Uncertain significance (Jun 07, 2023) | ||
| 1-32684061-G-C | not specified | Uncertain significance (Jan 26, 2022) | ||
| 1-32684280-C-T | not specified | Uncertain significance (Aug 11, 2022) | ||
| 1-32684324-T-C | not specified | Uncertain significance (Feb 23, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBBP4 | protein_coding | protein_coding | ENST00000373493 | 12 | 35070 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00435 | 125744 | 0 | 3 | 125747 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.63 | 35 | 234 | 0.149 | 0.0000117 | 2834 |
| Missense in Polyphen | 0 | 49.143 | 0 | 666 | ||
| Synonymous | -0.190 | 82 | 79.8 | 1.03 | 0.00000423 | 762 |
| Loss of Function | 4.25 | 2 | 24.9 | 0.0803 | 0.00000113 | 294 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000882 | 0.00000879 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex. {ECO:0000269|PubMed:10866654}.;
- Pathway
- Cellular senescence - Homo sapiens (human);Retinoblastoma (RB) in Cancer;Interactome of polycomb repressive complex 2 (PRC2);Tumor suppressor activity of SMARCB1;EMT transition in Colorectal Cancer;ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);the prc2 complex sets long-term gene silencing through modification of histone tails;Transcriptional Regulation by E2F6;Generic Transcription Pathway;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;HDACs deacetylate histones;RNA Polymerase I Promoter Clearance;PKMTs methylate histone lysines;RNA Polymerase II Transcription;Chromatin modifying enzymes;Polo-like kinase mediated events;Transcription of E2F targets under negative control by DREAM complex;G0 and Early G1;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;Mitotic G1-G1/S phases;Nucleosome assembly;Cellular responses to external stimuli;Chromosome Maintenance;Regulation of PTEN gene transcription;G2/M Transition;Mitotic G2-G2/M phases;PTEN Regulation;PIP3 activates AKT signaling;Deposition of new CENPA-containing nucleosomes at the centromere;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle;Cell Cycle, Mitotic;Intracellular signaling by second messengers;Regulation of Telomerase;Regulation of retinoblastoma protein;Signaling events mediated by HDAC Class I;Hedgehog signaling events mediated by Gli proteins;Regulation of nuclear SMAD2/3 signaling;E2F transcription factor network;PRC2 methylates histones and DNA
(Consensus)
Recessive Scores
- pRec
- 0.350
Intolerance Scores
- loftool
- 0.412
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.622
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.726
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.969
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbbp4
- Phenotype
Gene ontology
- Biological process
- DNA replication;DNA replication-dependent nucleosome assembly;DNA replication-independent nucleosome assembly;chromatin remodeling;cell cycle;negative regulation of cell population proliferation;histone deacetylation;chromatin assembly;CENP-A containing nucleosome assembly;ATP-dependent chromatin remodeling;negative regulation of gene expression, epigenetic;regulation of cell cycle;negative regulation of G0 to G1 transition
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;cytosol;Sin3 complex;NuRD complex;NURF complex;protein-containing complex;CAF-1 complex;ESC/E(Z) complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;histone deacetylase activity;protein binding;DNA-dependent ATPase activity;nucleosomal DNA binding;histone binding;histone deacetylase binding