BAZ1B
bromodomain adjacent to zinc finger domain 1B, the group of PHD finger proteins|Bromodomain containing|B-WICH chromatin-remodelling complex subunits
Basic information
Region (hg38): 7:73440406-73522293
Previous symbols: [ "WBSCR9", "WBSCR10" ]
Links
Phenotypes
GenCC
Source:
- autism spectrum disorder (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (119 variants)
- not_provided (41 variants)
- BAZ1B-related_disorder (9 variants)
- Williams_syndrome (1 variants)
- Syndromic_intellectual_disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAZ1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032408.4. 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 | 25 | 31 | ||||
| missense | 120 | 128 | ||||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 126 | 32 | 6 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BAZ1B | protein_coding | protein_coding | ENST00000339594 | 19 | 81881 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 7.42e-10 | 125734 | 0 | 13 | 125747 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.72 | 508 | 805 | 0.631 | 0.0000446 | 9812 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000581 | 0.0000581 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000882 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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.;
- Pathway
- B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;DNA Repair;Epigenetic regulation of gene expression;Gene expression (Transcription);DNA Double-Strand Break Repair;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response
(Consensus)
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- loftool
- 0.245
- rvis_EVS
- -1.61
- rvis_percentile_EVS
- 2.95
Haploinsufficiency Scores
- pHI
- 0.446
- hipred
- Y
- hipred_score
- 0.859
- ghis
- 0.572
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.839
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Baz1b
- Phenotype
- muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; immune system phenotype; skeleton 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); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- chromatin assembly or disassembly;chromatin remodeling;regulation of transcription by RNA polymerase II;cellular response to DNA damage stimulus;histone phosphorylation;peptidyl-tyrosine phosphorylation;positive regulation of gene expression, epigenetic
- Cellular component
- condensed chromosome;nucleoplasm;pericentric heterochromatin;nuclear body;nuclear replication fork
- Molecular function
- protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding;zinc ion binding;histone kinase activity;histone binding