MYBBP1A
protein-codingMYB binding protein 1a, the group of B-WICH chromatin-remodelling complex subunits|Armadillo like helical domain containing
Gene summary
This gene encodes a nucleolar transcriptional regulator that was first identified by its ability to bind specifically to the Myb proto-oncogene protein. The encoded protein is thought to play a role in many cellular processes including response to nucleolar stress, tumor suppression and synthesis of ribosomal DNA. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0015193
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MYBBP1A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014520.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | 9 | 6 | 23 | ||
| missense | 325 | 32 | 8 | 365 | ||
| nonsense | 3 | 1 | 4 | |||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 344 | 41 | 15 | 400 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055335.2 | 26 | MANE Select | |
| Ensembl | ENSP00000254718.4 | 26 | MANE Select | |
| RefSeq | NP_001099008.1 | 27 | Standard | |
| Ensembl | ENSP00000370968.2 | 27 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| mybbp1a | Danio rerio | Structure: trunk Quality: necrotic abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Energy Metabolism
- B-WICH complex positively regulates rRNA expression
- Positive epigenetic regulation of rRNA expression
- Epigenetic regulation of gene expression
- Gene expression (Transcription)
Biological Process
- osteoblast differentiation
- regulation of transcription, DNA-templated
- respiratory electron transport chain
- circadian regulation of gene expression
- cellular response to glucose starvation
Molecular Function
- transcription corepressor activity
- RNA binding
- transcription factor binding
- sequence-specific DNA binding
- E-box binding
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
- cytoplasm
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381556
- Coding exons
- 27
- Length
- 16735
- Individuals with no LoFs
- 125298
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 447
- Defined
- 125748
- p
- 0.00179
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.75 | 1022 | 803 | 1.27 | 0.0000512 | 8550 |
| Missense (PolyPhen) | 300 | 243.15 | 1.2338 | 2778 | ||
| Synonymous | -5.57 | 479 | 347 | 1.38 | 0.0000221 | 2696 |
| Loss of Function | 0.154 | 64 | 65.3 | 0.979 | 0.00000321 | 732 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0093 | 0.0092 | notable |
| Latino/Admixed American | 0.0015 | 0.0015 | notable |
| Ashkenazi Jewish | 0.00079 | 0.00079 | rare |
| East Asian | 0.00087 | 0.00087 | rare |
| Finnish | 0.00034 | 0.00032 | rare |
| European (Non-Finnish) | 0.00095 | 0.00089 | rare |
| South Asian | 0.0035 | 0.0035 | notable |
| Other | 0.0022 | 0.0020 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May activate or repress transcription via interactions with sequence specific DNA-binding proteins (By similarity). Repression may be mediated at least in part by histone deacetylase activity (HDAC activity) (By similarity). Acts as a corepressor and in concert with CRY1, represses the transcription of the core circadian clock component PER2 (By similarity). Preferentially binds to dimethylated histone H3 'Lys-9' (H3K9me2) on the PER2 promoter (By similarity). Has a role in rRNA biogenesis together with PWP1 (PubMed:29065309). {ECO:0000250|UniProtKB:Q7TPV4, ECO:0000269|PubMed:29065309}.;
Recessive Scores
- pRec
- 0.230
Intolerance Scores
- LoFtool
- 0.961
- RVIS EVS
- 2.3
- RVIS percentile EVS
- 98.33
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.765
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |