RBBP5
Basic information
Region (hg38): 1:205086142-205122015
Links
Phenotypes
GenCC
Source:
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 RBBP5 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 1 |
Variants in RBBP5
This is a list of pathogenic ClinVar variants found in the RBBP5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-205096705-T-A | not specified | Uncertain significance (Jan 30, 2024) | ||
| 1-205096766-T-C | not specified | Uncertain significance (Feb 22, 2023) | ||
| 1-205096819-G-A | not specified | Uncertain significance (Dec 27, 2022) | ||
| 1-205100209-G-A | RBBP5-related syndromic neurodevelopmental condition | Pathogenic (Jul 27, 2024) | ||
| 1-205101610-G-A | not specified | Uncertain significance (Jan 26, 2023) | ||
| 1-205101640-T-C | not specified | Uncertain significance (Dec 14, 2021) | ||
| 1-205103941-C-T | Benign (Jun 06, 2018) | |||
| 1-205103979-T-C | not specified | Uncertain significance (Dec 31, 2023) | ||
| 1-205114886-C-T | not specified | Uncertain significance (Mar 16, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBBP5 | protein_coding | protein_coding | ENST00000264515 | 14 | 35874 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000192 | 125726 | 0 | 2 | 125728 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.59 | 119 | 292 | 0.408 | 0.0000151 | 3508 |
| Missense in Polyphen | 21 | 107.25 | 0.1958 | 1352 | ||
| Synonymous | 0.804 | 100 | 111 | 0.903 | 0.00000630 | 1029 |
| Loss of Function | 5.02 | 2 | 33.3 | 0.0601 | 0.00000195 | 374 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: In embryonic stem (ES) cells, plays a crucial role in the differentiation potential, particularly along the neural lineage, regulating gene induction and H3 'Lys-4' methylation at key developmental loci, including that mediated by retinoic acid (By similarity). As part of the MLL1/MLL complex, involved in mono-, di- and trimethylation at 'Lys-4' of histone H3. Histone H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. {ECO:0000250, ECO:0000269|PubMed:19556245}.;
- Pathway
- Cushing,s syndrome - Homo sapiens (human);Signaling by WNT;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;PKMTs methylate histone lysines;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Chromatin modifying enzymes;Neddylation;Chromatin organization;Transcriptional regulation by RUNX1;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT
(Consensus)
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- 0.106
- rvis_EVS
- -0.47
- rvis_percentile_EVS
- 23.04
Haploinsufficiency Scores
- pHI
- 0.426
- hipred
- Y
- hipred_score
- 0.808
- ghis
- 0.601
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.986
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbbp5
- Phenotype
Gene ontology
- Biological process
- cellular response to DNA damage stimulus;response to estrogen;post-translational protein modification;regulation of megakaryocyte differentiation;histone H3-K4 methylation;beta-catenin-TCF complex assembly
- Cellular component
- nucleus;nucleoplasm;nucleolus;histone methyltransferase complex;MLL3/4 complex;Set1C/COMPASS complex;MLL1 complex
- Molecular function
- protein binding;histone-lysine N-methyltransferase activity;methylated histone binding;histone methyltransferase activity (H3-K4 specific);transcription regulatory region DNA binding