BAZ2A

bromodomain adjacent to zinc finger domain 2A, the group of Bromodomain containing|Methyl-CpG binding domain containing|PHD finger proteins

Basic information

Region (hg38): 12:56595596-56636816

Links

ENSG00000076108 ∙ NCBI:11176 ∙ OMIM:605682 ∙ HGNC:962 ∙ Uniprot:Q9UIF9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BAZ2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAZ2A gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			124	5		129
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	125	9	0

Variants in BAZ2A

This is a list of pathogenic ClinVar variants found in the BAZ2A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-56598625-T-C		not specified	Uncertain significance (May 31, 2023)
12-56598628-G-C		not specified	Uncertain significance (Dec 07, 2024)
12-56598659-G-A		not specified	Uncertain significance (Nov 17, 2023)
12-56598676-C-T		not specified	Uncertain significance (Aug 13, 2021)
12-56598717-G-A			Likely benign (Nov 01, 2022)
12-56598920-T-G		not specified	Uncertain significance (Nov 10, 2022)
12-56598923-T-C		not specified	Uncertain significance (Oct 29, 2021)
12-56598935-C-G		not specified	Uncertain significance (Feb 21, 2025)
12-56598962-C-G		not specified	Uncertain significance (May 30, 2023)
12-56599165-G-A		not specified	Uncertain significance (Aug 28, 2023)
12-56599171-C-T		not specified	Uncertain significance (Aug 12, 2024)
12-56599178-G-A		not specified	Uncertain significance (Jun 26, 2024)
12-56599199-C-T		not specified	Uncertain significance (Mar 17, 2023)
12-56599204-G-A		not specified	Uncertain significance (Nov 03, 2023)
12-56599211-G-A		not specified	Uncertain significance (Sep 11, 2024)
12-56599256-G-A		not specified	Uncertain significance (Nov 13, 2023)
12-56599261-C-T		not specified	Uncertain significance (Oct 03, 2024)
12-56599262-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-56599321-G-C		not specified	Uncertain significance (Oct 05, 2022)
12-56599832-C-CG			Uncertain significance (Sep 03, 2021)
12-56599970-G-C		not specified	Uncertain significance (Jan 07, 2022)
12-56600014-G-C		not specified	Uncertain significance (Jul 06, 2021)
12-56600050-C-T		not specified	Uncertain significance (Dec 07, 2021)
12-56600074-T-C		not specified	Likely benign (Feb 15, 2023)
12-56600091-T-C		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BAZ2A	protein_coding	protein_coding	ENST00000551812	29	41221

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.59e-10	124634	0	8	124642	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	874	1.07e+3	0.820	0.0000631	12308
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000601	0.0000601
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000356	0.0000354
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription) (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: -1.39
• rvis_percentile_EVS: 4.32

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.736
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Baz2a

Gene ontology

• Biological process: chromatin silencing at rDNA;RNA polymerase I preinitiation complex assembly;DNA methylation;chromatin remodeling;transcription, DNA-templated;regulation of transcription, DNA-templated;histone deacetylation
• Cellular component: chromatin silencing complex;nucleolus;cytosol;nuclear speck;rDNA heterochromatin
• Molecular function: RNA polymerase I CORE element sequence-specific DNA binding;RNA binding;protein binding;nuclear receptor binding;histone binding;metal ion binding;lysine-acetylated histone binding