BAZ2A
protein-codingbromodomain adjacent to zinc finger domain 2A, the group of Bromodomain containing|Methyl-CpG binding domain containing|PHD finger proteins
Gene summary
Enables histone binding activity. Contributes to RNA polymerase I core promoter sequence-specific DNA binding activity. Predicted to be involved in DNA methylation-dependent constitutive heterochromatin formation; negative regulation of transcription by RNA polymerase I; and rDNA heterochromatin formation. Predicted to act upstream of or within heterochromatin formation. Located in nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BAZ2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001300905.2. 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 | 3 | 4 | 7 | |||
| missense | 261 | 8 | 269 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 275 | 12 | 0 | 287 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001287834.1 | 28 | MANE Select | |
| Ensembl | ENSP00000447941.1 | 28 | MANE Select | |
| RefSeq | NP_001338085.1 | 29 | Standard | |
| RefSeq | NP_038477.2 | 29 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- NoRC negatively regulates rRNA expression
- Negative epigenetic regulation of rRNA expression
- Epigenetic regulation of gene expression
- Gene expression (Transcription)
Biological Process
- chromatin silencing at rDNA
- RNA polymerase I preinitiation complex assembly
- DNA methylation
- chromatin remodeling
- transcription, DNA-templated
Molecular Function
- RNA polymerase I CORE element sequence-specific DNA binding
- RNA binding
- protein binding
- nuclear receptor binding
- histone binding
Cellular Component
- chromatin silencing complex
- nucleolus
- cytosol
- nuclear speck
- rDNA heterochromatin
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000551812
- Coding exons
- 29
- Length
- 41221
- Individuals with no LoFs
- 124634
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 124642
- p
- 0.0000321
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.08 | 874 | 1.07e+3 | 0.820 | 0.0000631 | 12308 |
| Missense (PolyPhen) | 369 | 520.73 | 0.70861 | 5973 | ||
| Synonymous | 1.24 | 360 | 391 | 0.920 | 0.0000202 | 3882 |
| Loss of Function | 8.10 | 7 | 89.9 | 0.0779 | 0.00000508 | 1011 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000060 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential component of the NoRC (nucleolar remodeling complex) complex, a complex that mediates silencing of a fraction of rDNA by recruiting histone-modifying enzymes and DNA methyltransferases, leading to heterochromatin formation and transcriptional silencing. In the complex, it plays a central role by being recruited to rDNA and by targeting chromatin modifying enzymes such as HDAC1, leading to repress RNA polymerase I transcription. Recruited to rDNA via its interaction with TTF1 and its ability to recognize and bind histone H4 acetylated on 'Lys- 16' (H4K16ac), leading to deacetylation of H4K5ac, H4K8ac, H4K12ac but not H4K16ac. Specifically binds pRNAs, 150-250 nucleotide RNAs that are complementary in sequence to the rDNA promoter; pRNA- binding is required for heterochromatin formation and rDNA silencing (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- RVIS EVS
- -1.39
- RVIS percentile EVS
- 4.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.969
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |