BAZ1A

protein-coding

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

Gene summary

The BAZ1A gene encodes the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), a member of the ISWI ('imitation switch') family of chromatin remodeling complexes (summarized by Racki et al., 2009 [PubMed 20033039]).[supplied by OMIM, Apr 2010]

MANE transcript

NM_013448.3

Inheritance

ClinVar variants

P:1U:169B:12

Top phenotype

BAZ1A-related disorder

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr14:34,752,731-34,875,647

External References & Databases

Ensembl (ENSG00000198604)

Transcript & Mutation Effects

hg38 • Region Span ~122.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

multiple congenital anomalies/dysmorphic syndromeLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0019042

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BAZ1A variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 149

BAZ1A-related disorderTotal: 14

not providedTotal: 8

VATER/VACTERL association with CNS malformationsTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013448.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	4 clinvar	1 clinvar	7
missense	1 clinvar		159 clinvar	6 clinvar	1 clinvar	167
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	1	0	169	10	2	182

Highest pathogenic variant AF is 0.0000031081577

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013448.3	RefSeq	NP_038476.2	26	MANE Select
ENST00000360310.6	Ensembl	ENSP00000353458.1	26	MANE Select
NM_182648.2	RefSeq	NP_872589.1	25	Standard
ENST00000358716.8	Ensembl	ENSP00000351555.4	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation

Biological Process

DNA-dependent DNA replication
chromatin remodeling
regulation of transcription by RNA polymerase II
histone acetylation

Molecular Function

histone acetyltransferase activity
protein binding
metal ion binding

Cellular Component

CHRAC
ACF complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360310
Coding exons: 26
Length: 122917
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125748
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.94	568	803	0.708	0.0000422	10245
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.192
RVIS EVS: -0.66
RVIS percentile EVS: 16.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.689

Gene Damage Prediction

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