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): 2:159318978-159616569

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

ClinVar

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

• Inborn genetic diseases (72 variants)
• not provided (22 variants)
• BAZ2B-related condition (8 variants)
• BAZ2B-related disorder (6 variants)
• BAZ2B-related Neurodevelopmental disorder (4 variants)
• Neurodevelopmental disorder (4 variants)
• not specified (1 variants)
• Autistic behavior (1 variants)
• See cases (1 variants)
• BAZ2B-associated neurodevelopmental disorder (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.

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				3	2	5
missense		2	74	15	2	93
nonsense			3			3
start loss	1					1
frameshift	1	1				2
inframe indel						0
splice donor/acceptor (+/-2bp)		2	2			4
splice region		1	1			2
non coding			1		1	2
Total	2	5	80	18	5

Highest pathogenic variant AF is 0.00000657

Variants in BAZ2B

This is a list of pathogenic ClinVar variants found in the BAZ2B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-159324847-T-C		Inborn genetic diseases	Uncertain significance (Dec 28, 2023)
2-159324866-C-T		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
2-159324887-G-A		BAZ2B-related disorder	Benign (Oct 07, 2019)
2-159324908-G-C		Inborn genetic diseases	Uncertain significance (Apr 16, 2020)
2-159324918-T-C			Likely benign (Jun 05, 2018)
2-159324957-A-G		Neurodevelopmental disorder	Uncertain significance (Oct 15, 2020)
2-159325662-G-A		Inborn genetic diseases	Uncertain significance (Feb 17, 2024)
2-159325680-T-C		Inborn genetic diseases	Uncertain significance (May 27, 2022)
2-159325687-T-C		Inborn genetic diseases	Uncertain significance (Feb 26, 2022)
2-159325728-T-G		Inborn genetic diseases	Uncertain significance (Aug 17, 2022)
2-159325791-C-T		BAZ2B-related disorder	Benign (Oct 21, 2019)
2-159325797-G-T		Inborn genetic diseases	Likely benign (Sep 06, 2022)
2-159325814-A-T		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
2-159325821-G-T		Inborn genetic diseases	Uncertain significance (May 31, 2023)
2-159325862-A-G		BAZ2B-related disorder	Likely benign (Sep 05, 2019)
2-159325866-G-C		Inborn genetic diseases	Likely benign (Oct 29, 2021)
2-159325889-T-G		Inborn genetic diseases	Uncertain significance (Nov 13, 2023)
2-159332548-T-C			Uncertain significance (Mar 30, 2022)
2-159332594-G-C		BAZ2B-related disorder	Likely benign (Feb 26, 2019)
2-159332645-A-C		BAZ2B-related disorder	Likely benign (Mar 29, 2021)
2-159332658-T-A		Inborn genetic diseases	Uncertain significance (Jul 13, 2021)
2-159332687-C-G		BAZ2B-related Neurodevelopmental disorder	Likely pathogenic (Feb 06, 2023)
2-159336964-C-T			Uncertain significance (Sep 23, 2021)
2-159336975-T-A		BAZ2B-related disorder	Uncertain significance (Feb 08, 2024)
2-159337019-G-A		Inborn genetic diseases	Likely benign (Sep 07, 2022)

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