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): 7:73440405-73522293

Previous symbols: [ "WBSCR9", "WBSCR10" ]

Links

ENSG00000009954 ∙ NCBI:9031 ∙ OMIM:605681 ∙ HGNC:961 ∙ Uniprot:Q9UIG0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BAZ1B gene.

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.

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			1	21	6	28
missense			63	7	1	71
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4		4
non coding				1		1
Total	0	0	66	29	7

Variants in BAZ1B

This is a list of pathogenic ClinVar variants found in the BAZ1B region.

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

Position	Type	Phenotype	Significance	ClinVar
7-73442216-C-T		not specified	Uncertain significance (Mar 07, 2023)
7-73442220-G-A			Likely benign (Jun 13, 2018)
7-73442246-T-C		not specified	Uncertain significance (Mar 06, 2023)
7-73442304-T-C			Benign (Dec 31, 2019)
7-73442346-C-T			Benign (Dec 31, 2019)
7-73442355-C-T			Likely benign (Aug 30, 2017)
7-73442467-G-A		not specified	Uncertain significance (Jul 05, 2023)
7-73442504-G-A		BAZ1B-related disorder	Uncertain significance (Feb 15, 2023)
7-73442506-G-A		not specified	Uncertain significance (Apr 13, 2022)
7-73442718-C-G			Likely benign (Jun 01, 2018)
7-73442754-G-A			Likely benign (Aug 08, 2018)
7-73442782-T-C		not specified	Uncertain significance (Dec 22, 2023)
7-73442784-C-T			Likely benign (Apr 01, 2023)
7-73442800-C-T			Likely benign (Dec 31, 2019)
7-73442826-C-T			Likely benign (Jul 07, 2018)
7-73442837-A-C			Likely benign (Apr 16, 2018)
7-73444010-C-T		not specified	Uncertain significance (May 27, 2022)
7-73444016-G-A		not specified	Uncertain significance (Jun 02, 2024)
7-73444019-C-T		not specified	Uncertain significance (Feb 15, 2023)
7-73444038-G-A			Likely benign (Mar 01, 2023)
7-73444064-G-A		not specified	Uncertain significance (Jul 07, 2022)
7-73444070-C-A		not specified	Uncertain significance (May 31, 2023)
7-73444070-C-G		not specified	Uncertain significance (Mar 28, 2024)
7-73444088-G-A		not specified	Uncertain significance (Oct 04, 2022)
7-73449543-T-C		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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