ATAD2B

Summary

ATAD2B (ATPase family AAA domain containing 2B, HGNC:29230) is a protein-coding gene on chromosome 2p24.1-p23.3, encoding ATPase family AAA domain-containing protein 2B (Q9ULI0).

The protein encoded by this gene belongs to the AAA ATPase family. This family member includes an N-terminal bromodomain. It has been found to be localized to the nucleus, partly to replication sites, consistent with a chromatin-related function. Alternative splicing of this gene results in multiple transcript variants.

Source: NCBI Gene 54454 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder (Moderate, GenCC)
• GWAS associations: 32
• Clinical variants (ClinVar): 242 total
• Druggable target: yes
• MANE Select transcript: NM_017552

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29230
Approved symbol	ATAD2B
Name	ATPase family AAA domain containing 2B
Location	2p24.1-p23.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1240
Ensembl gene	ENSG00000119778
Ensembl biotype	protein_coding
OMIM	615347
Entrez	54454

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000238789, ENST00000366438, ENST00000381024, ENST00000439915, ENST00000458510, ENST00000474583, ENST00000478885, ENST00000486610, ENST00000498006, ENST00000925211, ENST00000925212, ENST00000925213, ENST00000925214

RefSeq mRNA: 3 — MANE Select: NM_017552 NM_001242338, NM_001354107, NM_017552

CCDS: CCDS46227

Canonical transcript exons

ENST00000238789 — 28 exons

Exon	Start	End
ENSE00000721122	23748664	23752087
ENSE00001558735	23926555	23927123
ENSE00001602331	23867835	23867946
ENSE00001607011	23895819	23895970
ENSE00001654093	23869663	23869761
ENSE00001654691	23885727	23885829
ENSE00001681974	23887832	23887985
ENSE00001686370	23880639	23880755
ENSE00001705994	23875829	23875904
ENSE00001707339	23888350	23888399
ENSE00001741373	23884765	23884873
ENSE00001785541	23833919	23834078
ENSE00003465608	23786027	23786223
ENSE00003472515	23782869	23783028
ENSE00003502365	23819747	23819882
ENSE00003515649	23757418	23758101
ENSE00003525095	23810316	23810502
ENSE00003549200	23798138	23798323
ENSE00003556965	23762209	23762346
ENSE00003590614	23788512	23788647
ENSE00003593984	23823258	23823569
ENSE00003636955	23754179	23754307
ENSE00003641317	23828849	23828939
ENSE00003657531	23765506	23765628
ENSE00003684040	23754647	23754774
ENSE00003732425	23857415	23857503
ENSE00003741124	23863381	23863555
ENSE00003749605	23864809	23864924

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 95.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3869 / max 310.7868, expressed in 1673 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
27296	4.4060	1419
27297	2.2349	1079
27295	1.1166	460
27298	0.6294	307

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	95.76	gold quality
calcaneal tendon	UBERON:0003701	91.14	gold quality
sural nerve	UBERON:0015488	91.06	gold quality
oocyte	CL:0000023	87.17	gold quality
colonic epithelium	UBERON:0000397	87.14	gold quality
adrenal tissue	UBERON:0018303	86.24	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.85	gold quality
secondary oocyte	CL:0000655	85.56	gold quality
tendon	UBERON:0000043	85.55	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.21	gold quality
monocyte	CL:0000576	84.50	gold quality
mononuclear cell	CL:0000842	84.18	gold quality
bone marrow cell	CL:0002092	83.97	gold quality
leukocyte	CL:0000738	83.88	gold quality
tonsil	UBERON:0002372	83.66	gold quality
epithelium of nasopharynx	UBERON:0001951	83.44	gold quality
ganglionic eminence	UBERON:0004023	83.41	gold quality
cortical plate	UBERON:0005343	83.14	gold quality
bone marrow	UBERON:0002371	83.05	gold quality
skin of abdomen	UBERON:0001416	82.56	gold quality
vagina	UBERON:0000996	82.25	gold quality
hair follicle	UBERON:0002073	82.10	silver quality
ventricular zone	UBERON:0003053	81.65	gold quality
oviduct epithelium	UBERON:0004804	81.64	gold quality
skin of leg	UBERON:0001511	81.52	gold quality
tibia	UBERON:0000979	81.21	gold quality
zone of skin	UBERON:0000014	81.11	gold quality
endometrium	UBERON:0001295	80.99	gold quality
choroid plexus epithelium	UBERON:0003911	80.97	gold quality
upper leg skin	UBERON:0004262	80.86	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

220 targeting ATAD2B, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3646	100.00	73.56	5283
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-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882

Literature-anchored findings (GeneRIF, showing 1)

• The ATAD2B may play a role in neuronal differentiation and tumor progression. (PMID:21158754)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	atad2b	ENSDARG00000060537
mus_musculus	Atad2b	ENSMUSG00000052812
rattus_norvegicus	Atad2b	ENSRNOG00000058973
caenorhabditis_elegans		WBGENE00008682

Paralogs (1): ATAD2 (ENSG00000156802)

Protein

Protein identifiers

ATPase family AAA domain-containing protein 2B — Q9ULI0 (reviewed: Q9ULI0)

All UniProt accessions (4): C9J1G9, C9JG15, Q9ULI0, H7BYF1

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Binds acetylated lysine residues in histone H1.4, H2A, H2B, H3 and H4 (in vitro).

Subcellular location. Nucleus.

Similarity. Belongs to the AAA ATPase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9ULI0-1	1	yes
Q9ULI0-2	2

RefSeq proteins (3): NP_001229267, NP_001341036, NP_060022* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001487	Bromodomain	Domain
IPR003593	AAA+_ATPase	Domain
IPR003959	ATPase_AAA_core	Domain
IPR003960	ATPase_AAA_CS	Conserved_site
IPR018359	Bromodomain_CS	Conserved_site
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR036427	Bromodomain-like_sf	Homologous_superfamily
IPR041569	AAA_lid_3	Domain
IPR045199	ATAD2-like	Family

Pfam: PF00004, PF00439, PF17862

UniProt features (39 total): modified residue 10, compositionally biased region 7, helix 7, region of interest 6, chain 1, domain 1, binding site 1, splice variant 1, sequence variant 1, sequence conflict 1, turn 1, strand 1, coiled-coil region 1

Structure

Experimental structures (PDB)

6 structures.

PDB	Method	Resolution (Å)
8UK5	X-RAY DIFFRACTION	1.4
8UHL	X-RAY DIFFRACTION	1.92
3LXJ	X-RAY DIFFRACTION	2.33
6VEO	X-RAY DIFFRACTION	2.4
8SDX	X-RAY DIFFRACTION	2.69
2DKW	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULI0-F1	60.47	0.17

Functional residue map

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

Ligand- & substrate-binding residues (1): 441–448

Post-translational modifications (10): 16, 79, 81, 86, 140, 221, 318, 939, 1338, 1347

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 247 (showing top): MODULE_331, WANG_LMO4_TARGETS_DN, DOANE_RESPONSE_TO_ANDROGEN_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_TRANSCRIPTION_INITIATION_AT_RNA_POLYMERASE_II_PROMOTER, SCHLOSSER_SERUM_RESPONSE_DN, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_CHROMATIN_REMODELING, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_CHROMATIN_BINDING, CHEN_HOXA5_TARGETS_9HR_UP

GO Biological Process (3): nucleosome assembly (GO:0006334), nucleosome disassembly (GO:0006337), transcription initiation-coupled chromatin remodeling (GO:0045815)

GO Molecular Function (7): chromatin binding (GO:0003682), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), histone binding (GO:0042393), histone reader activity (GO:0140566), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleosome organization	2
binding	2
chromatin organization	1
protein-DNA complex assembly	1
protein-DNA complex disassembly	1
transcription initiation at RNA polymerase II promoter	1
positive regulation of gene expression, epigenetic	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
ATP-dependent activity	1
protein binding	1
nucleosome	1
histone binding	1
chromatin-protein adaptor activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

2529 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATAD2B	BRD9	Q9H8M2	566
ATAD2B	H4C7	Q99525	557
ATAD2B	H4C16	P02304	555
ATAD2B	BRD7	Q9NPI1	487
ATAD2B	EEF2	P13639	454
ATAD2B	CECR2	Q9BXF3	432
ATAD2B	ELP3	Q9H9T3	416
ATAD2B	ARL6IP4	Q66PJ3	412
ATAD2B	BRWD3	Q6RI45	405
ATAD2B	BAZ2B	Q9UIF8	397
ATAD2B	TRIM24	O15164	393
ATAD2B	NWD2	Q9ULI1	380
ATAD2B	SP140L	Q9H930	376
ATAD2B	MCC	P23508	374
ATAD2B	SCML4	Q8N228	369
ATAD2B	OR52B4	Q8NGK2	369

IntAct

21 interactions, top by confidence:

A	B	Type	Score
SCRIB	ATAD2B	psi-mi:“MI:0915”(physical association)	0.400
CSNK2B	OSBPL8	psi-mi:“MI:0914”(association)	0.350
HMGN5	SMCHD1	psi-mi:“MI:0914”(association)	0.350
NUMA1	SHANK3	psi-mi:“MI:0914”(association)	0.350
AFG2A	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC9A5	NBAS	psi-mi:“MI:0914”(association)	0.350
INSR	UBXN8	psi-mi:“MI:0914”(association)	0.350
CSNK2B	TUBAL3	psi-mi:“MI:0914”(association)	0.350
AGGF1	BLTP3B	psi-mi:“MI:2364”(proximity)	0.270
DGCR8	VWA8	psi-mi:“MI:2364”(proximity)	0.270
GPKOW	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
HNRNPC	SBNO1	psi-mi:“MI:2364”(proximity)	0.270
ILF3	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
PPIL4	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
RPS11	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
SBDS	RPSA2	psi-mi:“MI:2364”(proximity)	0.270
SF3B4	MED19	psi-mi:“MI:2364”(proximity)	0.270
SMNDC1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
ZC3H11A	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
ZC3H8	SBNO1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (23): ATAD2B (Affinity Capture-MS), ATAD2B (Affinity Capture-RNA), ATAD2B (Affinity Capture-MS), ATAD2B (Affinity Capture-MS), ATAD2B (Affinity Capture-MS), ATAD2B (Proximity Label-MS), ATAD2B (Proximity Label-MS), ATAD2B (Proximity Label-MS), ATAD2B (Proximity Label-MS), ATAD2B (Affinity Capture-MS), ATAD2B (Proximity Label-MS), ATAD2B (Proximity Label-MS), ATAD2B (Proximity Label-MS), ATAD2B (Cross-Linking-MS (XL-MS)), PRMT7 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1P8AUY4, A6ZZL8, B3LQZ6, B5VM60, C5E1C0, C7GVL2, C8ZC77, E7BQV0, F4HX15, F4I240, F4I9Q5, F4I9T0, F4IV45, F4JLK2, F4KGU4, O22243, O94248, O94536, P0C5E7, P0CE10, P34246, Q0JBY9, Q12019, Q1EHT7, Q3B8D5, Q4DCH3, Q57X81, Q5RDX4, Q5TEA3, Q6P158, Q7TT23, Q7XZU0, Q8CDM1, Q8LLD0, Q8STE5, Q8T5T1, Q8WT44, Q9C104, Q9FIN7, Q9FJ32

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 31 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
mRNA Splicing - Major Pathway	5	12.4×	8e-03
Dengue Virus-Host Interactions	5	10.4×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	193
Likely benign	11
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

7486 predictions. Top by Δscore:

Variant	Effect	Δscore
2:23752745:ATG:A	donor_gain	1.0000
2:23754174:CTTA:C	donor_loss	1.0000
2:23754175:TTA:T	donor_loss	1.0000
2:23754176:TA:T	donor_loss	1.0000
2:23754177:A:AC	donor_gain	1.0000
2:23754177:AC:A	donor_gain	1.0000
2:23754178:C:CC	donor_gain	1.0000
2:23754178:CC:C	donor_gain	1.0000
2:23754178:CCT:C	donor_gain	1.0000
2:23754178:CCTCT:C	donor_gain	1.0000
2:23754303:AATTT:A	acceptor_gain	1.0000
2:23754304:ATTT:A	acceptor_gain	1.0000
2:23754305:TTT:T	acceptor_gain	1.0000
2:23754306:TT:T	acceptor_gain	1.0000
2:23754307:TCTA:T	acceptor_loss	1.0000
2:23754308:C:CC	acceptor_gain	1.0000
2:23754308:C:T	acceptor_loss	1.0000
2:23754319:C:CT	acceptor_gain	1.0000
2:23754320:A:T	acceptor_gain	1.0000
2:23754641:GCTTA:G	donor_loss	1.0000
2:23754642:CTTA:C	donor_loss	1.0000
2:23754643:TTAC:T	donor_loss	1.0000
2:23754644:TA:T	donor_loss	1.0000
2:23762201:ATACT:A	donor_loss	1.0000
2:23762203:ACT:A	donor_loss	1.0000
2:23762204:CTC:C	donor_loss	1.0000
2:23762205:T:TA	donor_loss	1.0000
2:23762206:CACA:C	donor_loss	1.0000
2:23762207:A:AC	donor_gain	1.0000
2:23762207:ACATG:A	donor_gain	1.0000

AlphaMissense

9613 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:23758064:C:A	W1144C	1.000
2:23758064:C:G	W1144C	1.000
2:23758066:A:G	W1144R	1.000
2:23758066:A:T	W1144R	1.000
2:23765581:C:G	A1061P	1.000
2:23765587:C:G	A1059P	1.000
2:23765593:C:G	D1057H	1.000
2:23765598:A:G	L1055P	1.000
2:23765607:G:T	A1052D	1.000
2:23782888:A:C	N1038K	1.000
2:23782888:A:T	N1038K	1.000
2:23782890:T:C	N1038D	1.000
2:23782892:T:C	Y1037C	1.000
2:23782893:A:C	Y1037D	1.000
2:23782893:A:G	Y1037H	1.000
2:23782901:G:T	A1034D	1.000
2:23783018:T:C	Y995C	1.000
2:23783019:A:C	Y995D	1.000
2:23783019:A:G	Y995H	1.000
2:23786040:A:T	V987E	1.000
2:23786051:G:C	F983L	1.000
2:23786051:G:T	F983L	1.000
2:23786052:A:G	F983S	1.000
2:23786053:A:G	F983L	1.000
2:23786079:A:G	L974P	1.000
2:23786100:A:G	L967P	1.000
2:23786109:C:G	R964P	1.000
2:23823504:A:C	Y629D	1.000
2:23823515:A:G	L625P	1.000
2:23823554:T:A	D612V	1.000

dbSNP variants (sampled 300 via entrez): RS1000006475 (2:23773456 T>C,G), RS1000021922 (2:23903661 T>C,G), RS1000040584 (2:23686261 G>A), RS1000043481 (2:23882598 G>A), RS1000075843 (2:23697369 G>A), RS1000087184 (2:23771177 A>G), RS1000095907 (2:23924682 T>C), RS1000132752 (2:23758139 G>A,T), RS1000151384 (2:23682122 ACTTC>A), RS1000152987 (2:23840654 T>G), RS1000181567 (2:23906637 T>C), RS1000188605 (2:23809521 G>A), RS1000192119 (2:23822637 C>A,G,T), RS1000195234 (2:23855053 G>A), RS1000200725 (2:23897378 G>A,T)

Disease associations

OMIM: gene MIM:615347 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder	Moderate	Autosomal recessive

Mondo (1): neurodevelopmental disorder (MONDO:0700092)

Orphanet (0):

HPO phenotypes

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

GWAS associations

32 associations (top):

Study	Trait	p-value
GCST001762_400	Obesity-related traits	3.000000e-06
GCST002843_24	Sitting height ratio	1.000000e-08
GCST003124_26	Mild influenza (H1N1) infection	2.000000e-09
GCST003125_13	Influenza A (H1N1) infection	7.000000e-09
GCST004602_79	Mean corpuscular volume	2.000000e-19
GCST004610_40	White blood cell count	2.000000e-19
GCST004630_22	Mean corpuscular hemoglobin	5.000000e-12
GCST005146_19	Birth weight	6.000000e-11
GCST005316_316	Intelligence (MTAG)	4.000000e-08
GCST005316_317	Intelligence (MTAG)	3.000000e-09
GCST006922_5	Regular attendance at a religious group	8.000000e-09
GCST006976_116	Macular thickness	2.000000e-11
GCST007325_274	General risk tolerance (MTAG)	1.000000e-13
GCST007429_63	Lung function (FVC)	2.000000e-11
GCST007432_1	FEV1	4.000000e-11
GCST007954_43	Glycated hemoglobin levels	2.000000e-15
GCST008163_90	Height	6.000000e-06
GCST008839_199	Height	9.000000e-12
GCST90002385_116	High light scatter reticulocyte count	5.000000e-67
GCST90002385_117	High light scatter reticulocyte count	2.000000e-15
GCST90002386_235	High light scatter reticulocyte percentage of red cells	2.000000e-14
GCST90002387_250	Immature fraction of reticulocytes	3.000000e-64
GCST90002392_264	Mean corpuscular volume	3.000000e-39
GCST90002395_520	Mean platelet volume	1.000000e-17
GCST90002395_521	Mean platelet volume	2.000000e-12
GCST90002396_173	Mean reticulocyte volume	6.000000e-15
GCST90002396_199	Mean reticulocyte volume	9.000000e-10
GCST90002401_418	Platelet distribution width	7.000000e-09
GCST90002402_277	Platelet count	2.000000e-14
GCST90002405_111	Reticulocyte count	3.000000e-10

EFO canonical traits (16, from GWAS)

EFO ID	Trait name
EFO:0004730	hormone measurement
EFO:0007118	sitting height ratio
EFO:1001488	influenza A (H1N1)
EFO:0004527	mean corpuscular hemoglobin
EFO:0004344	birth weight
EFO:0004337	intelligence
EFO:0009592	social interaction measurement
EFO:0008579	risk-taking behaviour
EFO:0004312	vital capacity
EFO:0004314	forced expiratory volume
EFO:0004541	HbA1c measurement
EFO:0007986	reticulocyte count
EFO:0010701	mean reticulocyte volume
EFO:0007984	platelet component distribution width
EFO:0004309	platelet count
EFO:0007788	BMI-adjusted waist-hip ratio

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2176775 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

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

Target class: enzyme — 3.6.1.3 ATPases

Most potent curated ligand interactions (2 total), top 2:

Ligand	Action	Affinity	Parameter
GSK8814	Inhibition	7.7	pIC50
compound 23 [PMID: 31398032]	Inhibition	6.3	pIC50

ChEMBL bioactivities

10 potent at pChembl≥5 of 44 total, top 10 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
9.00	Kd	1	nM	CHEMBL4206758
8.10	Kd	7.943	nM	CHEMBL5079885
7.70	Kd	19.95	nM	CHEMBL4449894
7.70	IC50	20	nM	CHEMBL4536031
7.40	Ki	39.81	nM	CHEMBL3590408
7.00	Kd	100	nM	CHEMBL3590408
6.78	Kd	166.9	nM	CHEMBL3590405
6.30	IC50	501.2	nM	CHEMBL4583297
6.00	Kd	1000	nM	CHEMBL3823478
5.28	Kd	5200	nM	CHEMBL4786330

PubChem BioAssay actives

10 with measured affinity, of 115 total; 9 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
8-[[(3R,4R,5S)-3-[(4,4-difluorocyclohexyl)methoxy]-5-methoxypiperidin-4-yl]amino]-3-methyl-5-(5-methyl-3-pyridinyl)-1H-1,7-naphthyridin-2-one	1376129: Binding affinity to partial length human ATAD2B (Q955 to R1082) expressed in bacterial expression system by Bromoscan method	kd	0.0010	uM
(1R,9S,12R)-13-[8-[[1-(2-fluoro-2-methylpropyl)piperidin-4-yl]amino]-3-methyl-[1,2,4]triazolo[4,3-b]pyridazine-6-carbonyl]-12-propan-2-yl-11,13-diazatricyclo[7.3.1.02,7]trideca-2,4,6-trien-10-one	1822989: Binding affinity to human ATAD2B bromodomain assessed as dissociation constant by BROMOscan method	kd	0.0079	uM
N-[4-bromo-3-[(3S)-3-methylpyrrolidin-1-yl]sulfonylphenyl]-2-[(4S)-4-cyclopropyl-4-methyl-2,5-dioxoimidazolidin-1-yl]acetamide	1561906: Binding affinity to human partial length ATAD2B (Q955 to R1082 residues) expressed in bacterial expression system by BROMOscan assay	kd	0.0199	uM
N-[(2R)-1-[(4-aminocyclohexyl)amino]-3-(4-cyanophenyl)propan-2-yl]-2-chloro-4-methoxy-5-[5-[[[(1R)-1-(4-methylphenyl)ethyl]amino]methyl]furan-2-yl]benzamide	2071883: Displacement of tetra-acetylated H4 peptide from ATAD2B (unknown origin)	ic50	0.0200	uM
8-[[(3R,4R)-3-[(1,1-dioxothian-4-yl)methoxy]-1-methylpiperidin-4-yl]amino]-3-methyl-5-(5-methyl-3-pyridinyl)-1H-1,7-naphthyridin-2-one	1234381: Binding affinity to ATAD2B (unknown origin) by BROMOscan panel based assay	ki	0.0398	uM
8-[[(3R,4R)-3-[(1,1-dioxothian-4-yl)methoxy]piperidin-4-yl]amino]-3-methyl-5-(5-methyl-3-pyridinyl)-1H-quinolin-2-one	1678125: Binding affinity to N-terminal GST tagged human ATAD2B (953-1085 residues) expressed in Escherichia coli by ITC analysis	kd	0.1669	uM
N-(4-bromo-3-piperidin-1-ylsulfonylphenyl)-2-(4-cyclopropyl-4-methyl-2,5-dioxoimidazolidin-1-yl)acetamide	1516814: Displacement of biotinylated H4 peptide from ATAD2B bromodomain (unknown origin) by TR-FRET assay	ic50	0.5012	uM
4-[4-[(dimethylamino)methyl]-3,5-dimethoxyphenyl]-2-methyl-2,7-naphthyridin-1-one	2191057: Binding affinity to KIAA1240 (unknown origin) assessed as dissociation constant by bromoKdselect analysis	kd	1.0000	uM
(2S)-2-[[2-[[2-[[(2S)-2-[[2-[[(2S)-2-[[2-[[(2S)-2-[[2-[[2-[[(2S)-6-acetamido-2-[[2-[[(2S)-2-[[2-[[(2S)-2-amino-3-hydroxypropanoyl]amino]acetyl]amino]-5-(diaminomethylideneamino)pentanoyl]amino]acetyl]amino]hexanoyl]amino]acetyl]amino]acetyl]amino]-6-aminohexanoyl]amino]acetyl]amino]-4-methylpentanoyl]amino]acetyl]amino]-6-aminohexanoyl]amino]acetyl]amino]acetyl]amino]propanoic acid	1678125: Binding affinity to N-terminal GST tagged human ATAD2B (953-1085 residues) expressed in Escherichia coli by ITC analysis	kd	5.2000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	4
Benzo(a)pyrene	affects methylation, decreases expression	3
epigallocatechin gallate	increases expression, affects cotreatment, decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
trichostatin A	affects expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
coumarin	affects phosphorylation	1
beta-glycerophosphoric acid	affects cotreatment, increases expression	1
lei gong teng	increases expression	1
entinostat	decreases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Vorinostat	decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	decreases methylation, increases abundance	1
Ascorbic Acid	affects cotreatment, increases expression	1
Caffeine	increases phosphorylation	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Lead	affects expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1

ChEMBL screening assays

52 unique, capped per target: 52 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL2187000	Binding	Inhibition of His6FLAG-tagged ATD2B expressed in Escherichia coli assessed as change in melting temperature at 100 uM by thermal shift assay	Fragment-based discovery of bromodomain inhibitors part 2: optimization of phenylisoxazole sulfonamides. — J Med Chem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SD81	HAP1 ATAD2B (-) 1	Cancer cell line	Male
CVCL_SD82	HAP1 ATAD2B (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	PHASE2/PHASE3	RECRUITING	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
NCT03148782	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice