RBBP7
RB binding protein 7, chromatin remodeling factor, the group of EMSY complex|NuRD complex subunits|WD repeat domain containing|SIN3 histone deacetylase complex subunits|Polycomb repressive complex 2|NURF complex
Basic information
Region (hg38): X:16839282-16870362
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 RBBP7 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 5 | 2 | 1 |
Variants in RBBP7
This is a list of pathogenic ClinVar variants found in the RBBP7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-16841437-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| X-16841458-C-G | not specified | Uncertain significance (Jun 06, 2022) | ||
| X-16841525-A-G | not specified | Uncertain significance (Jan 16, 2024) | ||
| X-16841526-T-C | Likely benign (Feb 01, 2023) | |||
| X-16841675-C-T | not specified | Likely benign (Mar 31, 2024) | ||
| X-16841706-A-C | Benign (Nov 15, 2018) | |||
| X-16841738-C-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| X-16841740-G-C | not specified | Uncertain significance (Jun 06, 2023) | ||
| X-16841757-G-T | Likely benign (Feb 01, 2023) | |||
| X-16845050-C-G | not specified | Uncertain significance (Aug 26, 2022) | ||
| X-16845071-A-T | not specified | Uncertain significance (Feb 14, 2024) | ||
| X-16852820-T-C | not specified | Uncertain significance (Apr 13, 2022) | ||
| X-16852835-A-C | not specified | Uncertain significance (Apr 17, 2024) | ||
| X-16863002-T-C | not specified | Uncertain significance (Sep 30, 2021) | ||
| X-16869171-G-T | Benign (May 18, 2018) | |||
| X-16869191-T-C | Uncertain significance (Jan 01, 2023) | |||
| X-16869561-T-G | Likely benign (Jun 01, 2022) | |||
| X-16869594-C-A | Likely benign (Nov 01, 2022) | |||
| X-16869637-G-A | not specified | Uncertain significance (May 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBBP7 | protein_coding | protein_coding | ENST00000380084 | 12 | 31132 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.984 | 0.0161 | 112025 | 0 | 1 | 112026 | 0.00000446 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.79 | 72 | 176 | 0.409 | 0.0000132 | 3090 |
| Missense in Polyphen | 18 | 82.883 | 0.21717 | 1392 | ||
| Synonymous | -0.805 | 75 | 66.6 | 1.13 | 0.00000531 | 887 |
| Loss of Function | 3.59 | 1 | 17.0 | 0.0590 | 0.00000113 | 301 |
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) | 0.0000130 | 0.00000944 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Core histone-binding subunit that may target chromatin remodeling factors, histone acetyltransferases 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 type B histone acetyltransferase (HAT) complex, which is required for chromatin assembly following DNA replication; 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; and 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
- Retinoblastoma (RB) in Cancer;Interactome of polycomb repressive complex 2 (PRC2);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;Post-translational protein modification;HDACs deacetylate histones;Metabolism of proteins;RNA Polymerase I Promoter Clearance;PKMTs methylate histone lysines;RNA Polymerase II Transcription;RMTs methylate histone arginines;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;Nucleosome assembly;HATs acetylate histones;Cellular responses to external stimuli;Chromosome Maintenance;EGFR1;Regulation of PTEN gene transcription;Neddylation;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;Intracellular signaling by second messengers;Regulation of Telomerase;Signaling events mediated by HDAC Class I;Hedgehog signaling events mediated by Gli proteins;Regulation of nuclear SMAD2/3 signaling;PRC2 methylates histones and DNA
(Consensus)
Recessive Scores
- pRec
- 0.314
Intolerance Scores
- loftool
- 0.112
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.970
- hipred
- Y
- hipred_score
- 0.776
- ghis
- 0.636
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.437
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbbp7
- Phenotype
- growth/size/body region phenotype; craniofacial phenotype; embryo phenotype; skeleton phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;DNA replication;multicellular organism development;cell population proliferation;histone deacetylation;negative regulation of cell growth;CENP-A containing nucleosome assembly;post-translational protein modification;negative regulation of gene expression, epigenetic;response to steroid hormone;negative regulation of G0 to G1 transition;cellular heat acclimation
- Cellular component
- nucleus;nucleoplasm;cytosol;NuRD complex;ESC/E(Z) complex
- Molecular function
- RNA binding;histone deacetylase activity;protein binding