BAZ2B

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

Basic information

Region (hg38): 2:159315312-159616569

Links

ENSG00000123636 ∙ NCBI:29994 ∙ OMIM:605683 ∙ HGNC:963 ∙ Uniprot:Q9UIF8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD
• neurodevelopmental disorder (Limited), mode of inheritance: AD
• neurodevelopmental disorder (Strong), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BAZ2B gene.

• Inborn_genetic_diseases (249 variants)
• not_provided (131 variants)
• BAZ2B-related_disorder (54 variants)
• Neurodevelopmental_disorder (9 variants)
• not_specified (7 variants)
• BAZ2B-related_Neurodevelopmental_disorder (4 variants)
• BAZ2B-associated_neurodevelopmental_disorder (2 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAZ2B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013450.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				21	5	26
missense	2	2	301	55	3	363
nonsense	2		5	1		8
start loss	1					1
frameshift	1	3	6			10
splice donor/acceptor (+/-2bp)		3	4			7
Total	6	8	316	77	8

Highest pathogenic variant AF is 0.000006580333

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BAZ2B	protein_coding	protein_coding	ENST00000392783	35	297714

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0184	124982	0	44	125026	0.000176

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	971	1.10e+3	0.887	0.0000550	14209
Missense in Polyphen		236	338.46	0.69728		4349
Synonymous	0.346	371	380	0.977	0.0000188	4061
Loss of Function	7.73	22	109	0.201	0.00000604	1381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000475	0.000345
Ashkenazi Jewish	0.000695	0.000397
East Asian	0.000171	0.000165
Finnish	0.000280	0.000278
European (Non-Finnish)	0.000162	0.000159
Middle Eastern	0.000171	0.000165
South Asian	0.0000987	0.0000980
Other	0.000691	0.000659

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in transcriptional regulation interacting with ISWI.

Recessive Scores

• pRec: 0.0949

Intolerance Scores

• loftool: 0.244
• rvis_EVS: -1.42
• rvis_percentile_EVS: 4.06

Haploinsufficiency Scores

• pHI: 0.310
• hipred: N
• hipred_score: 0.492
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.830

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Baz2b

Gene ontology

• Biological process: chromatin remodeling;regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA binding;protein binding;metal ion binding