BAZ1A

Summary

BAZ1A (bromodomain adjacent to zinc finger domain 1A, HGNC:960) is a protein-coding gene on chromosome 14q13.1-q13.2, encoding Bromodomain adjacent to zinc finger domain protein 1A (Q9NRL2). Regulatory subunit of the ATP-dependent ACF-1 and ACF-5 ISWI chromatin remodeling complexes, which form ordered nucleosome arrays on chromatin and slide edge- and center-positioned histone octamers away from their original location on the DNA template to facilitate access to DNA….

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]).

Source: NCBI Gene 11177 — RefSeq curated summary.

At a glance

• Gene–disease (curated): multiple congenital anomalies/dysmorphic syndrome (Limited, GenCC)
• GWAS associations: 26
• Clinical variants (ClinVar): 201 total — 3 pathogenic
• Druggable target: yes
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 1 cancer types
• MANE Select transcript: NM_013448

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:960
Approved symbol	BAZ1A
Name	bromodomain adjacent to zinc finger domain 1A
Location	14q13.1-q13.2
Locus type	gene with protein product
Status	Approved
Aliases	hACF1, ACF1, WALp1, WCRF180
Ensembl gene	ENSG00000198604
Ensembl biotype	protein_coding
OMIM	605680
Entrez	11177

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 10 protein_coding, 4 retained_intron, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000358716, ENST00000360310, ENST00000382422, ENST00000553385, ENST00000553573, ENST00000553853, ENST00000554391, ENST00000554865, ENST00000555273, ENST00000555331, ENST00000556314, ENST00000557739, ENST00000934221, ENST00000934222, ENST00000934223, ENST00000934224, ENST00000934225, ENST00000934226

RefSeq mRNA: 2 — MANE Select: NM_013448 NM_013448, NM_182648

CCDS: CCDS41943, CCDS9651

Canonical transcript exons

ENST00000360310 — 27 exons

Exon	Start	End
ENSE00003468445	34785777	34786001
ENSE00003505204	34783762	34783927
ENSE00003511617	34765021	34765268
ENSE00003524817	34773572	34773726
ENSE00003545007	34783119	34783232
ENSE00003843546	34875138	34875360
ENSE00003889201	34801094	34801193
ENSE00003889736	34826013	34826156
ENSE00003889793	34775919	34776515
ENSE00003889893	34862044	34862322
ENSE00003890347	34792775	34792921
ENSE00003890359	34761757	34762223
ENSE00003890733	34780186	34780310
ENSE00003890802	34874492	34874662
ENSE00003891069	34758704	34758846
ENSE00003891426	34752731	34753704
ENSE00003891733	34754827	34754914
ENSE00003892673	34802854	34802988
ENSE00003892983	34800224	34800390
ENSE00003893470	34807451	34807538
ENSE00003894222	34786126	34786221
ENSE00003894275	34794749	34794887
ENSE00003895157	34795670	34795765
ENSE00003895392	34764707	34764933
ENSE00003895527	34771511	34771659
ENSE00003895900	34774327	34774490
ENSE00003896053	34810935	34811036

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 99.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.3372 / max 1695.7283, expressed in 1803 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
142827	15.9472	1747
142828	12.2653	1585
142813	1.1374	540
142829	1.0903	446
142825	0.9485	496
142824	0.3808	203
142826	0.3591	140
142823	0.1366	57
142822	0.0721	26

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.34	gold quality
oocyte	CL:0000023	99.10	gold quality
secondary oocyte	CL:0000655	98.11	gold quality
male germ cell	CL:0000015	97.00	gold quality
monocyte	CL:0000576	96.43	gold quality
mononuclear cell	CL:0000842	95.93	gold quality
superior surface of tongue	UBERON:0007371	95.74	gold quality
leukocyte	CL:0000738	95.65	gold quality
bone marrow	UBERON:0002371	95.51	gold quality
blood	UBERON:0000178	95.25	gold quality
trabecular bone tissue	UBERON:0002483	94.98	gold quality
pericardium	UBERON:0002407	94.78	gold quality
pharyngeal mucosa	UBERON:0000355	94.75	gold quality
pylorus	UBERON:0001166	94.22	gold quality
bone marrow cell	CL:0002092	93.89	gold quality
ventricular zone	UBERON:0003053	93.51	gold quality
penis	UBERON:0000989	93.06	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.85	gold quality
right testis	UBERON:0004534	92.79	gold quality
skin of abdomen	UBERON:0001416	92.61	gold quality
spleen	UBERON:0002106	92.60	gold quality
left testis	UBERON:0004533	92.56	gold quality
vena cava	UBERON:0004087	92.28	gold quality
ganglionic eminence	UBERON:0004023	92.23	gold quality
oral cavity	UBERON:0000167	92.15	gold quality
testis	UBERON:0000473	92.11	gold quality
granulocyte	CL:0000094	91.94	gold quality
bronchial epithelial cell	CL:0002328	91.85	gold quality
tongue	UBERON:0001723	91.82	gold quality
lower lobe of lung	UBERON:0008949	91.36	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-5	yes	22.87
E-GEOD-93593	yes	6.56
E-MTAB-7303	no	222.95
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HNF4A

miRNA regulators (miRDB)

110 targeting BAZ1A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-3686	99.90	70.53	2432
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-137-3P	99.87	74.74	2401
HSA-LET-7G-3P	99.85	70.43	1929

Literature-anchored findings (GeneRIF, showing 13)

• ACF1 alters the remodeling strategy of SNF2h (PMID:16877760)
• Has a critical role in the transcriptional repression of specific nuclear hormone receptor-regulated genes. (PMID:17519354)
• The data support a model in which the human ACF anf yeast RSC remodeling enzymes move nucleosomes to new locations by a general sequence-independent mechanism. (PMID:19450608)
• The ACF1 and its complexes play important roles in DNA double-strand breaks (DSBs) repair. (PMID:21172662)
• ISWI proteins Snf2H, Snf2L as well as Acf1 accumulate at UV-induced DNA damage sites within tens of seconds and reach a plateau after a few minutes. (PMID:21738833)
• hACF1-containing factors are more generally involved in the DNA damage response. (PMID:21745822)
• CHD3.1 and ACF1-SNF2H display counteractive activities but similar histone affinities. (PMID:25533843)
• Results from the study on gene variability in early stage embryos identifies BAZ1A as a putative variability marker of the 8-cell embryo stage. (PMID:26288249)
• Study reports de novo mutation in BAZ1A, in a patient with a syndromic form of intellectual disability (ID). This mutation affects the expression of genes involved in several biological pathways such as vitamin D regulation, Wnt signaling, and postsynaptic signaling. Data point to an important role for BAZ1A in neurodevelopment, and highlight a possible link for BAZ1A to ID. (PMID:27328812)
• Results from the study suggest that acute cocaine exposure increased Baz1a expression in nucleus accumbens while repeated cocaine exposure produced the opposite effect. Findings implicate BAZ1A in molecular and behavioral plasticity to cocaine and offer new insight into the pathophysiology of cocaine addiction. (PMID:28412501)
• promotes recovery after DNA damage, in part by recruiting SMARCA5 to damaged chromatin (PMID:29021563)
• results revealed chromatin remodeling modulator BAZ1A acting as a novel regulator of cellular senescence in both normal and cancer cells, indicating a new target for potential cancer treatment (PMID:31085244)
• African American Prostate Cancer Displays Quantitatively Distinct Vitamin D Receptor Cistrome-transcriptome Relationships Regulated by BAZ1A. (PMID:37082578)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	baz1a	ENSDARG00000063233
mus_musculus	Baz1a	ENSMUSG00000035021
rattus_norvegicus	Baz1a	ENSRNOG00000006828
drosophila_melanogaster	Acf	FBGN0027620
caenorhabditis_elegans		WBGENE00001470

Paralogs (11): BAZ1B (ENSG00000009954), BAZ2A (ENSG00000076108), CECR2 (ENSG00000099954), KAT2A (ENSG00000108773), KAT2B (ENSG00000114166), BAZ2B (ENSG00000123636), BRDT (ENSG00000137948), BRD4 (ENSG00000141867), BRD3 (ENSG00000169925), BPTF (ENSG00000171634), BRD2 (ENSG00000204256)

Protein

Protein identifiers

Bromodomain adjacent to zinc finger domain protein 1A — Q9NRL2 (reviewed: Q9NRL2)

Alternative names: ATP-dependent chromatin-remodeling protein, ATP-utilizing chromatin assembly and remodeling factor 1, CHRAC subunit ACF1, Williams syndrome transcription factor-related chromatin-remodeling factor 180, hWALp1

All UniProt accessions (5): A0A087WWN7, Q9NRL2, H0YJ68, H0YJ74, H0YJP5

UniProt curated annotations — full annotation on UniProt →

Function. Regulatory subunit of the ATP-dependent ACF-1 and ACF-5 ISWI chromatin remodeling complexes, which form ordered nucleosome arrays on chromatin and slide edge- and center-positioned histone octamers away from their original location on the DNA template to facilitate access to DNA during DNA-templated processes such as DNA replication, transcription, and repair. Both complexes regulate the spacing of nucleosomes along the chromatin and have the ability to slide mononucleosomes to the center of a DNA template in an ATP-dependent manner. The ACF-1 ISWI chromatin remodeling complex has a lower ATP hydrolysis rate than the ACF-5 ISWI chromatin remodeling complex. Has a role in sensing the length of DNA which flank nucleosomes, which modulates the nucleosome spacing activity of the ACF-5 ISWI chromatin remodeling complex. Involved in DNA replication and together with SMARCA5/SNF2H is required for replication of pericentric heterochromatin in S-phase. May have a role in nuclear receptor-mediated transcription repression.

Subunit / interactions. Component of the ACF-1 ISWI chromatin remodeling complex at least composed of SMARCA1 and BAZ1A, which regulates the spacing of histone octamers on the DNA template to facilitate access to DNA. Within the ACF-1 ISWI chromatin remodeling complex interacts with SMARCA1; the interaction is direct. Component of the ACF-5 ISWI chromatin remodeling complex (also called the ACF complex) at least composed of BAZ1A and SMARCA5/SNF2H, which regulates the spacing of histone octamers on the DNA template to facilitate access to DNA. Within the ACF-5 ISWI chromatin remodeling complex interacts with SMARCA5/SNF2H; the interaction is direct. Component of the CHRAC ISWI chromatin remodeling complex at least composed of SMARCA5/SNF2H, BAZ1A/ACF1, CHRAC1 and POLE3; the complex preferentially binds DNA through the CHRAC1-POLE3 heterodimer and possesses ATP-dependent nucleosome-remodeling activity. Within the complex interacts (via N-terminus) with POLE3-CHRAC1 heterodimer; the interaction is direct and is required for the complex to preferentially bind to DNA. Within the complex interacts with SMARCA5/SNF2H; the interaction is direct and promotes the interaction with the POLE3-CHRAC1 heterodimer. Interacts with NCOR1 (via its RD1 domain); the interaction corepresses a number of NCOR1-regulated genes.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in testis and at low or undetectable levels in other tissues analyzed.

Miscellaneous. Stimulated by double-stranded DNA and nucleosomal DNA.

Similarity. Belongs to the WAL family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NRL2-1	1	yes
Q9NRL2-2	2

RefSeq proteins (2): NP_038476, NP_872589 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001487	Bromodomain	Domain
IPR001965	Znf_PHD	Domain
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR013136	WSTF_Acf1_Cbp146	Domain
IPR018359	Bromodomain_CS	Conserved_site
IPR018501	DDT_dom	Domain
IPR019786	Zinc_finger_PHD-type_CS	Conserved_site
IPR019787	Znf_PHD-finger	Domain
IPR028941	WHIM2_dom	Domain
IPR028942	WHIM1_dom	Domain
IPR036427	Bromodomain-like_sf	Homologous_superfamily
IPR037325	Acf1_Bromo	Domain
IPR047171	BAZ1A	Family

Pfam: PF00439, PF00628, PF02791, PF10537, PF15612, PF15613

UniProt features (65 total): modified residue 15, sequence conflict 12, compositionally biased region 10, region of interest 8, helix 6, domain 3, coiled-coil region 2, sequence variant 2, mutagenesis site 2, chain 1, zinc finger region 1, cross-link 1, splice variant 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
5UIY	X-RAY DIFFRACTION	1.69

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NRL2-F1	68.97	0.32

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (16): 270, 702, 731, 960, 961, 1281, 1320, 1339, 1353, 1363, 1371, 1402, 1413, 1417, 1547, 952

Mutagenesis-validated functional residues (2):

Position	Phenotype
1–128	abolishes interaction with the chrac1-pole3 heterodimer.
667–933	abolishes interaction with smarca5/snf2h, and abolishes the formation of the chrac iswi chromatin remodeling complex.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 266 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GOBP_POSITIVE_REGULATION_OF_DNA_REPLICATION, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, LHX3_01, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, BROWNE_HCMV_INFECTION_24HR_UP, CDP_01, ONKEN_UVEAL_MELANOMA_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, BRN2_01, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, OCT1_06

GO Biological Process (8): DNA-templated DNA replication (GO:0006261), regulation of DNA replication (GO:0006275), nucleosome assembly (GO:0006334), chromatin remodeling (GO:0006338), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), regulation of heterochromatin formation (GO:0031445), positive regulation of DNA replication (GO:0045740)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): nuclear chromosome (GO:0000228), nucleus (GO:0005634), pericentric heterochromatin (GO:0005721), CHRAC (GO:0008623), ACF complex (GO:0016590)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA replication	3
chromatin organization	2
regulation of gene expression	2
ISWI-type complex	2
regulation of DNA metabolic process	1
nucleosome organization	1
protein-DNA complex assembly	1
DNA-templated transcription	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
heterochromatin formation	1
regulation of heterochromatin organization	1
regulation of DNA replication	1
positive regulation of DNA metabolic process	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
nucleus	1
chromosome	1
nuclear lumen	1
intracellular membrane-bounded organelle	1
chromosome, centromeric region	1
heterochromatin	1

Protein interactions and networks

STRING

1432 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BAZ1A	SMARCA5	O60264	999
BAZ1A	SMARCA1	P28370	999
BAZ1A	CHRAC1	Q9NRG0	991
BAZ1A	POLE3	Q9NRF9	986
BAZ1A	SMARCA2	P51531	797
BAZ1A	SMARCA4	P51532	752
BAZ1A	XRCC6	P12956	701
BAZ1A	ZNF214	Q9UL59	677
BAZ1A	RSF1	Q96T23	673
BAZ1A	ZNF215	Q9UL58	651
BAZ1A	BAZ1B	Q9UIG0	635
BAZ1A	H2AC20	Q16777	634
BAZ1A	H2AC19	P20670	634
BAZ1A	H2BC21	Q16778	614
BAZ1A	POLE4	Q9NR33	596

IntAct

220 interactions, top by confidence:

A	B	Type	Score
SMARCA5	BAZ1A	psi-mi:“MI:0915”(physical association)	0.720
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
POLR1E	POLR1C	psi-mi:“MI:0914”(association)	0.670
KPNA1	TCERG1	psi-mi:“MI:0914”(association)	0.640
CAPN6	UBA6	psi-mi:“MI:0914”(association)	0.530
MECP2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
YWHAQ	IGLC7	psi-mi:“MI:0914”(association)	0.530
SMARCA5	RBBP4	psi-mi:“MI:0914”(association)	0.530
POLE3	SMARCA5	psi-mi:“MI:0914”(association)	0.530
ZBTB7A	BAZ1A	psi-mi:“MI:0915”(physical association)	0.510
BAZ1A	E2	psi-mi:“MI:0915”(physical association)	0.490
DDX21	MED19	psi-mi:“MI:2364”(proximity)	0.480
ESR2	FBLL1	psi-mi:“MI:0914”(association)	0.460
BAZ1A	PDZD7	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	GRID2IP	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	PATJ	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	WHRN	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	GOPC	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	PTPN3	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	ARHGEF11	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	APBA3	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	MPP2	psi-mi:“MI:0407”(direct interaction)	0.440
BAZ1A	PALS2	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (217): BAZ1A (Affinity Capture-MS), BAZ1A (Reconstituted Complex), BAZ1A (Biochemical Activity), BAZ1A (Affinity Capture-MS), BAZ1A (Affinity Capture-MS), BAZ1A (Affinity Capture-MS), BAZ1A (Affinity Capture-MS), BAZ1A (Affinity Capture-MS), BAZ1A (Affinity Capture-MS), BAZ1A (Affinity Capture-MS), BAZ1A (Affinity Capture-MS), SMARCA5 (Affinity Capture-Western), BAZ1A (Affinity Capture-Western), HIST1H4A (Affinity Capture-Western), H2AFX (Affinity Capture-Western)

ESM2 similar proteins: A0A1B0GVH7, A6PVS8, A8DZJ1, A9Q751, D3ZSP7, D4AEC2, Q08AD1, Q08CX2, Q14DL3, Q2T9P0, Q2TA00, Q32KQ1, Q3UZ57, Q3V0J4, Q4G0U5, Q4R7B1, Q4R7Z7, Q5S003, Q5SUV2, Q5T1B0, Q5ZLS8, Q63164, Q66HC0, Q69CM7, Q6AXP3, Q6AYL8, Q6IRN6, Q6NXP0, Q6Q759, Q80X60, Q86WZ0, Q8C1B1, Q8C4J0, Q8C636, Q8CDN1, Q8CDU5, Q8IWF9, Q8N7B9, Q8N7U6, Q8ND61

Diamond homologs: A0A0R4IXF6, A0A7U2QYM2, A2AHJ4, A2AUY4, A2BIL7, B2RRD7, B7ZS37, D4A7T3, E9Q2Z1, F1QW93, F1R5H6, F7DRV9, G5E8P1, O15164, O60885, O74350, O88379, O88665, O95696, P13709, P21675, P25440, P35817, P51123, P53236, P54816, P55201, P87152, Q02206, Q03330, Q07442, Q08D75, Q09948, Q12830, Q15059, Q1LUC3, Q23590, Q32S26, Q338B9, Q4R8Y1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 178 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Ras activation upon Ca2+ influx through NMDA receptor	5	24.4×	2e-04
Unblocking of NMDA receptors, glutamate binding and activation	5	23.2×	2e-04
Negative regulation of NMDA receptor-mediated neuronal transmission	5	23.2×	2e-04
Long-term potentiation	5	20.3×	4e-04
Assembly and cell surface presentation of NMDA receptors	8	17.4×	1e-05
Positive epigenetic regulation of rRNA expression	5	14.8×	2e-03
Neurexins and neuroligins	8	13.5×	4e-05
B-WICH complex positively regulates rRNA expression	7	7.3×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	9	32.3×	5e-09
receptor clustering	7	27.0×	3e-06
protein localization to synapse	5	23.6×	3e-04
regulation of postsynaptic membrane neurotransmitter receptor levels	6	18.4×	2e-04
heterochromatin formation	7	11.0×	5e-04
nucleosome assembly	8	6.9×	2e-03
cell-cell adhesion	9	5.6×	3e-03
protein-containing complex assembly	8	5.6×	7e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 1 cancer types — SCLC.

Clinical variants and AI predictions

ClinVar

201 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	156
Likely benign	10
Benign	2

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
1047865	GRCh37/hg19 14q13.1-21.2(chr14:33608925-44570367)	Pathogenic
154047	GRCh38/hg38 14q13.1-21.1(chr14:33880412-42359485)x1	Pathogenic
264644	NM_013448.3(BAZ1A):c.3278G>A (p.Arg1093Gln)	Pathogenic

SpliceAI

4135 predictions. Top by Δscore:

Variant	Effect	Δscore
14:34753700:CTCAG:C	acceptor_gain	1.0000
14:34753701:TCAG:T	acceptor_gain	1.0000
14:34753702:CAG:C	acceptor_gain	1.0000
14:34753702:CAGC:C	acceptor_gain	1.0000
14:34753703:AG:A	acceptor_gain	1.0000
14:34753703:AGCTA:A	acceptor_loss	1.0000
14:34753704:GC:G	acceptor_loss	1.0000
14:34753705:C:CC	acceptor_gain	1.0000
14:34753705:CTAGA:C	acceptor_loss	1.0000
14:34753706:T:A	acceptor_loss	1.0000
14:34754820:TAC:T	donor_loss	1.0000
14:34754821:A:AC	donor_gain	1.0000
14:34754821:ACT:A	donor_loss	1.0000
14:34754822:C:CC	donor_gain	1.0000
14:34754823:TTACA:T	donor_loss	1.0000
14:34754825:A:AC	donor_gain	1.0000
14:34754825:A:C	donor_loss	1.0000
14:34754825:ACATG:A	donor_gain	1.0000
14:34754826:C:CT	donor_gain	1.0000
14:34754826:CA:C	donor_gain	1.0000
14:34754826:CAT:C	donor_gain	1.0000
14:34754826:CATG:C	donor_gain	1.0000
14:34754826:CATGC:C	donor_gain	1.0000
14:34754915:C:G	acceptor_loss	1.0000
14:34754916:T:C	acceptor_loss	1.0000
14:34764703:TTA:T	donor_loss	1.0000
14:34764704:TACCT:T	donor_loss	1.0000
14:34764705:A:AC	donor_gain	1.0000
14:34764706:C:CT	donor_gain	1.0000
14:34764706:CCTGA:C	donor_gain	1.0000

AlphaMissense

10277 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:34753614:A:G	L1522P	1.000
14:34753623:C:T	G1519E	1.000
14:34753624:C:G	G1519R	1.000
14:34753624:C:T	G1519R	1.000
14:34753656:T:C	Y1508C	1.000
14:34753657:A:C	Y1508D	1.000
14:34753657:A:G	Y1508H	1.000
14:34753664:G:C	C1505W	1.000
14:34753666:A:G	C1505R	1.000
14:34753667:G:C	N1504K	1.000
14:34753667:G:T	N1504K	1.000
14:34754905:A:G	Y1466H	1.000
14:34758717:A:T	V1458D	1.000
14:34758734:C:A	W1452C	1.000
14:34758734:C:G	W1452C	1.000
14:34758736:A:G	W1452R	1.000
14:34758736:A:T	W1452R	1.000
14:34758768:A:G	L1441P	1.000
14:34764900:A:G	C1195R	1.000
14:34764909:A:G	C1192R	1.000
14:34764915:A:G	W1190R	1.000
14:34764915:A:T	W1190R	1.000
14:34765041:A:G	C1177R	1.000
14:34765065:A:G	C1169R	1.000
14:34765072:A:C	C1166W	1.000
14:34765073:C:G	C1166S	1.000
14:34765073:C:T	C1166Y	1.000
14:34765074:A:G	C1166R	1.000
14:34765074:A:T	C1166S	1.000
14:34765110:A:G	C1154R	1.000

dbSNP variants (sampled 300 via entrez): RS1000021049 (14:34830990 T>A,C), RS1000044137 (14:34794552 T>G), RS1000049056 (14:34845902 A>G), RS1000067614 (14:34757651 C>A), RS1000078577 (14:34757892 G>A,T), RS1000103626 (14:34839370 T>C), RS1000107715 (14:34793154 C>G), RS1000116252 (14:34773251 G>A), RS1000142444 (14:34784564 C>CTGGA), RS1000150876 (14:34848394 T>C,G), RS1000186282 (14:34790716 A>G), RS1000230576 (14:34816857 C>T), RS1000236550 (14:34766011 T>A,G), RS1000247255 (14:34873479 T>G), RS1000252434 (14:34773043 A>C,G)

Disease associations

OMIM: gene MIM:605680 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
multiple congenital anomalies/dysmorphic syndrome	Limited	Autosomal dominant

Mondo (1): multiple congenital anomalies/dysmorphic syndrome (MONDO:0019042)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

26 associations (top):

Study	Trait	p-value
GCST003800_2	Response to bupropion in depression	2.000000e-07
GCST004602_176	Mean corpuscular volume	8.000000e-09
GCST004611_196	High light scatter reticulocyte count	2.000000e-18
GCST004612_130	High light scatter reticulocyte percentage of red cells	2.000000e-21
GCST004619_123	Reticulocyte fraction of red cells	3.000000e-17
GCST004622_127	Reticulocyte count	1.000000e-12
GCST004628_56	Immature fraction of reticulocytes	5.000000e-17
GCST006288_327	Heel bone mineral density	9.000000e-08
GCST006288_432	Heel bone mineral density	2.000000e-12
GCST006979_1042	Heel bone mineral density	6.000000e-17
GCST008834_28	Non-small cell lung cancer	3.000000e-09
GCST009144_16	Disease progression in age-related macular degeneration (adjusted for baseline)	6.000000e-06
GCST010677_1	Liver fibrogenesis (alpha smooth muscle actin levels)	4.000000e-07
GCST90002385_22	High light scatter reticulocyte count	2.000000e-32
GCST90002386_165	High light scatter reticulocyte percentage of red cells	7.000000e-39
GCST90002387_140	Immature fraction of reticulocytes	8.000000e-33
GCST90002392_447	Mean corpuscular volume	6.000000e-20
GCST90002393_485	Monocyte count	5.000000e-10
GCST90002397_72	Mean spheric corpuscular volume	2.000000e-11
GCST90002403_502	Red blood cell count	6.000000e-12
GCST90002405_365	Reticulocyte count	2.000000e-19
GCST90002406_418	Reticulocyte fraction of red cells	2.000000e-26
GCST90011898_23	Alanine aminotransferase levels	9.000000e-13
GCST90011899_13	Aspartate aminotransferase levels	1.000000e-10
GCST90020026_230	Hip index	2.000000e-11
GCST90020028_1237	Hip circumference adjusted for BMI	2.000000e-09

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count
EFO:0009270	heel bone mineral density
EFO:0008336	disease progression measurement
EFO:0010576	liver fibrosis measurement
EFO:0005091	monocyte count
EFO:0004305	erythrocyte count
EFO:0004736	aspartate aminotransferase measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105737 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: other protein — Non-enzymatic BRD containing proteins

ChEMBL bioactivities

13 potent at pChembl≥5 of 20 total, top 13 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.73	Kd	18.63	nM	CHEMBL5653589
7.73	ED50	18.63	nM	CHEMBL5653589
6.28	Kd	520	nM	CHEMBL4783401
6.27	Kd	531.8	nM	CHEMBL3752910
6.27	ED50	531.8	nM	CHEMBL3752910
5.87	Kd	1360	nM	CHEMBL1603387
5.80	Kd	1570	nM	CHEMBL4740348
5.75	Kd	1760	nM	CHEMBL4788895
5.73	Kd	1870	nM	CHEMBL4742257
5.51	Kd	3090	nM	CHEMBL4743258
5.41	Kd	3930	nM	CHEMBL4758585
5.17	Kd	6680	nM	CHEMBL4761465
5.09	Kd	8200	nM	CHEMBL4782738

PubChem BioAssay actives

11 with measured affinity, of 44 total; 11 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2147939: Binding affinity to human BAZ1A incubated for 45 mins by Kinobead based pull down assay	kd	0.0186	uM
1-(3-nitrophenyl)-3-(4-phenyl-1,3-thiazol-2-yl)urea	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	0.5200	uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2147939: Binding affinity to human BAZ1A incubated for 45 mins by Kinobead based pull down assay	kd	0.5318	uM
1-(2,3-dihydro-1,4-benzodioxin-6-yl)-3-(3-nitrophenyl)urea	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	1.3600	uM
1-(1,2,3-benzothiadiazol-6-yl)-3-(3,4-dichlorophenyl)urea	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	1.5700	uM
1-[4-(dimethylamino)phenyl]-3-(3-nitrophenyl)urea	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	1.7600	uM
2-amino-N-(1,2,3-benzothiadiazol-6-yl)-2-phenylacetamide	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	1.8700	uM
1-(3-nitrophenyl)-3-quinoxalin-6-ylurea	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	3.0900	uM
1-(1,2,3-benzothiadiazol-6-yl)-3-quinazolin-7-ylurea	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	3.9300	uM
1-(3-nitrophenyl)-3-quinolin-7-ylurea	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	6.6800	uM
1-(1,2,3-benzothiadiazol-6-yl)-3-[1-(3-fluorophenyl)ethyl]urea	1684655: Binding affinity to recombinant human N-terminal His6-tagged BAZ1A (1446 to 1516 residues) expressed in Escherichia coli BL21 (DE3) cells by MST assay	kd	8.2000	uM

CTD chemical–gene interactions

58 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, increases methylation	6
trichostatin A	affects cotreatment, increases expression	3
Vorinostat	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
Benzo(a)pyrene	increases expression	2
Estradiol	increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tretinoin	decreases expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	2
Aflatoxin B1	affects expression, increases expression	2
FR900359	affects phosphorylation	1
TAK-243	increases sumoylation	1
testosterone enanthate	affects expression	1
daidzein	affects cotreatment, increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
sodium arsenite	increases expression, increases abundance	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
glycitein	affects cotreatment, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
Fulvestrant	increases methylation	1
Air Pollutants	decreases expression, increases abundance	1

ChEMBL screening assays

10 unique, capped per target: 10 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4051545	Binding	Inhibition of BAZ1A (unknown origin) assessed as change in melting temperature at 10 uM by SYPRO Orange-dye based fluorescence thermal shift assay	Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains. — J Med Chem

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1L0	Abcam HeLa BAZ1A KO	Cancer cell line	Female
CVCL_SE70	HAP1 BAZ1A (-) 1	Cancer cell line	Male
CVCL_SE71	HAP1 BAZ1A (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.