RBBP6
Basic information
Region (hg38): 16:24537693-24572863
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (196 variants)
- not_provided (12 variants)
- RBBP6-related_disorder (4 variants)
- Hereditary_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBBP6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006910.5. 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 | 11 | 14 | ||||
| missense | 182 | 191 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | |||||
| Total | 0 | 0 | 191 | 20 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBBP6 | protein_coding | protein_coding | ENST00000319715 | 18 | 35171 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 8.78e-12 | 125740 | 0 | 6 | 125746 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.49 | 809 | 937 | 0.863 | 0.0000502 | 11707 |
| Missense in Polyphen | 34 | 118.27 | 0.28747 | 1446 | ||
| Synonymous | -1.52 | 367 | 332 | 1.11 | 0.0000174 | 3433 |
| Loss of Function | 8.00 | 2 | 78.4 | 0.0255 | 0.00000490 | 1050 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000126 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000927 | 0.0000924 |
| European (Non-Finnish) | 0.0000178 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome (PubMed:18851979). May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth (By similarity). Regulates DNA-replication and the stability of chromosomal common fragile sites (CFSs) in a ZBTB38- and MCM10- dependent manner. Controls ZBTB38 protein stability and abundance via ubiquitination and proteasomal degradation, and ZBTB38 in turn negatively regulates the expression of MCM10 which plays an important role in DNA-replication (PubMed:24726359). {ECO:0000250|UniProtKB:P97868, ECO:0000269|PubMed:18851979, ECO:0000269|PubMed:24726359}.;
- Pathway
- Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- 0.281
- rvis_EVS
- -2.12
- rvis_percentile_EVS
- 1.53
Haploinsufficiency Scores
- pHI
- 0.757
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.678
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.753
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbbp6
- Phenotype
- growth/size/body region phenotype; cellular 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);
Zebrafish Information Network
- Gene name
- rbbp6
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- necrotic
Gene ontology
- Biological process
- protein polyubiquitination;in utero embryonic development;DNA replication;regulation of DNA replication;mRNA processing;ubiquitin-dependent protein catabolic process;cellular response to DNA damage stimulus;multicellular organism growth;embryonic organ development;somite development
- Cellular component
- chromosome;nucleolus;centrosome;cytosol;nuclear speck;protein-containing complex
- Molecular function
- RNA binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding;protein kinase binding;ubiquitin protein ligase activity