BAZ1B
protein-codingbromodomain adjacent to zinc finger domain 1B, the group of PHD finger proteins|Bromodomain containing|B-WICH chromatin-remodelling complex subunits
Gene summary
This gene encodes a member of the bromodomain protein family. The bromodomain is a structural motif characteristic of proteins involved in chromatin-dependent regulation of transcription. This gene is deleted in Williams-Beuren syndrome, a developmental disorder caused by deletion of multiple genes at 7q11.23. [provided by RefSeq, Jul 2008]
- WBSCR9
- WBSCR10
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~81.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005258
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BAZ1B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032408.4. 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 | 2 | 29 | 3 | 34 | ||
| missense | 148 | 7 | 1 | 156 | ||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 159 | 36 | 4 | 199 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115784.1 | 19 | MANE Select | |
| Ensembl | ENSP00000342434.4 | 19 | MANE Select | |
| RefSeq | NP_001357331.1 | 19 | Standard | |
| Ensembl | ENSP00000385442.1 | 19 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- B-WICH complex positively regulates rRNA expression
- Positive epigenetic regulation of rRNA expression
- DNA Repair
- Epigenetic regulation of gene expression
- Gene expression (Transcription)
Biological Process
- chromatin assembly or disassembly
- chromatin remodeling
- regulation of transcription by RNA polymerase II
- cellular response to DNA damage stimulus
- histone phosphorylation
Molecular Function
- protein tyrosine kinase activity
- non-membrane spanning protein tyrosine kinase activity
- protein binding
- ATP binding
- zinc ion binding
Cellular Component
- condensed chromosome
- nucleoplasm
- pericentric heterochromatin
- nuclear body
- nuclear replication fork
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339594
- Coding exons
- 19
- Length
- 81881
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125747
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.72 | 508 | 805 | 0.631 | 0.0000446 | 9812 |
| Missense (PolyPhen) | 129 | 310.47 | 0.41551 | 3664 | ||
| Synonymous | -0.316 | 290 | 283 | 1.02 | 0.0000143 | 2721 |
| Loss of Function | 7.48 | 3 | 71.0 | 0.0423 | 0.00000413 | 897 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000088 | 0.000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Atypical tyrosine-protein kinase that plays a central role in chromatin remodeling and acts as a transcription regulator. Involved in DNA damage response by phosphorylating 'Tyr-142' of histone H2AX (H2AXY142ph). H2AXY142ph plays a central role in DNA repair and acts as a mark that distinguishes between apoptotic and repair responses to genotoxic stress. Essential component of the WICH complex, a chromatin remodeling complex that mobilizes nucleosomes and reconfigures irregular chromatin to a regular nucleosomal array structure. The WICH complex regulates the transcription of various genes, has a role in RNA polymerase I and RNA polymerase III transcription, mediates the histone H2AX phosphorylation at 'Tyr-142', and is involved in the maintenance of chromatin structures during DNA replication processes. In the complex, it mediates the recruitment of the WICH complex to replication foci during DNA replication. {ECO:0000269|PubMed:11980720, ECO:0000269|PubMed:15543136, ECO:0000269|PubMed:16603771, ECO:0000269|PubMed:19092802, ECO:0000269|PubMed:19234442}.;
- Disease
- DISEASE: Note=BAZ1B is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of BAZ1B may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease.;
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- LoFtool
- 0.245
- RVIS EVS
- -1.61
- RVIS percentile EVS
- 2.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.839
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |