BAZ1A

bromodomain adjacent to zinc finger domain 1A, the group of Bromodomain containing|Chromatin accessibility complex|PHD finger proteins

Basic information

Region (hg38): 14:34752731-34875647

Links

ENSG00000198604 ∙ NCBI:11177 ∙ OMIM:605680 ∙ HGNC:960 ∙ Uniprot:Q9NRL2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BAZ1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAZ1A 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				2	1	3
missense			78	2	1	81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	78	4	2

Variants in BAZ1A

This is a list of pathogenic ClinVar variants found in the BAZ1A region.

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

Position	Type	Phenotype	Significance	ClinVar
14-34753552-C-G		not specified	Uncertain significance (Oct 21, 2024)
14-34753639-T-C			Uncertain significance (Jan 01, 2023)
14-34753648-G-C		not specified	Uncertain significance (Feb 11, 2022)
14-34758783-G-A		BAZ1A-related disorder	Uncertain significance (May 09, 2024)
14-34758807-C-T		not specified	Uncertain significance (Feb 17, 2024)
14-34761808-A-T		not specified	Uncertain significance (Dec 06, 2022)
14-34761889-T-C		not specified	Uncertain significance (Nov 09, 2023)
14-34761900-GTAT-G		BAZ1A-related disorder	Likely benign (Dec 29, 2022)
14-34761927-C-A		not specified	Uncertain significance (Jan 20, 2025)
14-34761927-C-T		not specified	Uncertain significance (Jul 12, 2023)
14-34761936-C-T		not specified	Uncertain significance (Dec 21, 2024)
14-34761949-A-T		not specified	Uncertain significance (Oct 08, 2024)
14-34761994-T-C		not specified	Uncertain significance (Feb 23, 2023)
14-34761996-G-C		not specified	Uncertain significance (May 18, 2023)
14-34762008-A-G		not specified	Uncertain significance (Mar 25, 2024)
14-34762036-G-T		not specified	Uncertain significance (Jul 06, 2021)
14-34762146-C-T		not specified	Uncertain significance (Oct 05, 2023)
14-34762210-C-G		not specified	Uncertain significance (Nov 26, 2024)
14-34764788-T-A		not specified	Uncertain significance (Jul 09, 2021)
14-34764789-C-T		BAZ1A-related disorder	Likely benign (Aug 29, 2022)
14-34764840-C-A		not specified	Uncertain significance (Dec 14, 2021)
14-34764861-G-C		not specified	Uncertain significance (Jul 22, 2024)
14-34765046-G-T		not specified	Uncertain significance (Aug 27, 2024)
14-34765047-T-C		not specified	Uncertain significance (Jan 05, 2022)
14-34765064-C-T		not specified	Uncertain significance (Dec 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BAZ1A	protein_coding	protein_coding	ENST00000360310	26	122917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.60e-8	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.94	568	803	0.708	0.0000422	10245
Missense in Polyphen		154	287.62	0.53543		3576
Synonymous	1.15	247	271	0.911	0.0000132	2871
Loss of Function	7.57	8	82.0	0.0976	0.00000486	1012

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000625	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000983	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the ACF complex, an ATP-dependent chromatin remodeling complex, that regulates spacing of nucleosomes using ATP to generate evenly spaced nucleosomes along the chromatin. The ATPase activity of the complex is regulated by the length of flanking DNA. Also involved in facilitating the DNA replication process. BAZ1A is the accessory, non-catalytic subunit of the complex which can enhance and direct the process provided by the ATPase subunit, SMARCA5, probably through targeting pericentromeric heterochromatin in late S phase. Moves end- positioned nucleosomes to a predominantly central position. May have a role in nuclear receptor-mediated transcription repression.
• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.192
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.07

Haploinsufficiency Scores

• pHI: 0.699
• hipred: Y
• hipred_score: 0.750
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.689

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Baz1a
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: DNA-dependent DNA replication;chromatin remodeling;regulation of transcription by RNA polymerase II;histone acetylation
• Cellular component: CHRAC;ACF complex
• Molecular function: histone acetyltransferase activity;protein binding;metal ion binding