ARID3B

Summary

ARID3B (AT-rich interaction domain 3B, HGNC:14350) is a protein-coding gene on chromosome 15q24.1, encoding AT-rich interactive domain-containing protein 3B (Q8IVW6). Transcription factor which may be involved in neuroblastoma growth and malignant transformation.

This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA-binding proteins. The encoded protein is homologous with two proteins that bind to the retinoblastoma gene product, and also with the mouse Bright and Drosophila dead ringer proteins. A pseudogene on chromosome 1p31 exists for this gene. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and possibly in chromatin structure modification.

Source: NCBI Gene 10620 — RefSeq curated summary.

At a glance

• GWAS associations: 19
• Clinical variants (ClinVar): 92 total — 2 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 1
• MANE Select transcript: NM_006465

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14350
Approved symbol	ARID3B
Name	AT-rich interaction domain 3B
Location	15q24.1
Locus type	gene with protein product
Status	Approved
Aliases	BDP, DRIL2
Ensembl gene	ENSG00000179361
Ensembl biotype	protein_coding
OMIM	612457
Entrez	10620

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000346246, ENST00000563567, ENST00000566147, ENST00000566468, ENST00000569680, ENST00000622429, ENST00000918002, ENST00000918003, ENST00000918004, ENST00000918005, ENST00000918006, ENST00000918007, ENST00000918008

RefSeq mRNA: 2 — MANE Select: NM_006465 NM_001307939, NM_006465

CCDS: CCDS10264, CCDS76777

Canonical transcript exons

ENST00000346246 — 9 exons

Exon	Start	End
ENSE00001258146	74591560	74591814
ENSE00001258149	74591151	74591434
ENSE00001258168	74541220	74541330
ENSE00001371732	74593138	74593236
ENSE00001661749	74573132	74573204
ENSE00001811829	74595611	74598131
ENSE00003621824	74572862	74572933
ENSE00003653335	74589820	74590003
ENSE00003658328	74543860	74544488

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 90.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1077 / max 74.3740, expressed in 1084 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
147700	3.8971	946
147699	1.0025	495
147701	0.2081	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	90.15	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.97	gold quality
type B pancreatic cell	CL:0000169	87.56	gold quality
blood	UBERON:0000178	87.44	gold quality
left testis	UBERON:0004533	87.26	gold quality
granulocyte	CL:0000094	87.25	gold quality
right testis	UBERON:0004534	87.24	gold quality
olfactory bulb	UBERON:0002264	87.08	gold quality
secondary oocyte	CL:0000655	87.00	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.62	gold quality
testis	UBERON:0000473	86.49	gold quality
bone marrow cell	CL:0002092	83.55	gold quality
triceps brachii	UBERON:0001509	83.40	gold quality
placenta	UBERON:0001987	83.39	gold quality
diaphragm	UBERON:0001103	83.35	gold quality
vena cava	UBERON:0004087	83.06	gold quality
tongue squamous epithelium	UBERON:0006919	82.66	silver quality
sperm	CL:0000019	82.06	silver quality
gluteal muscle	UBERON:0002000	81.98	gold quality
vastus lateralis	UBERON:0001379	81.90	gold quality
cardia of stomach	UBERON:0001162	81.88	silver quality
bone marrow	UBERON:0002371	81.75	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	81.70	gold quality
leukocyte	CL:0000738	81.00	gold quality
monocyte	CL:0000576	80.73	gold quality
embryo	UBERON:0000922	80.66	gold quality
mononuclear cell	CL:0000842	80.51	gold quality
quadriceps femoris	UBERON:0001377	80.34	gold quality
lateral globus pallidus	UBERON:0002476	80.06	silver quality
saphenous vein	UBERON:0007318	79.81	silver quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-75367	yes	335.10
E-ANND-3	yes	3.70
E-MTAB-6386	no	515.72

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

8 targets.

Target	Regulation
ERVW-4
EZH2
MAPK8
MAPK9
MIR208B
RNH1
TBP
TENT4A

Upstream regulators (CollecTRI, top): CBX8

miRNA regulators (miRDB)

154 targeting ARID3B, 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-6867-5P	100.00	82.21	3464
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-6077	99.99	68.04	2299
HSA-LET-7I-5P	99.98	72.37	1788
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-22-3P	99.93	68.13	917

Literature-anchored findings (GeneRIF, showing 15)

• We identify AT-rich interactive domain 3B (ARID3B) as a target of miR-125a and demonstrate that ARID3B is overexpressed in human ovarian cancer (PMID:19881956)
• Among possible numerous targets of miR-125b, we showed ARID3B (AT-rich interactive domain 3B) to be a novel target with roles in cell motility in breast cancer cells. (PMID:22307404)
• Epigenetic regulation of the neuroblastoma genes, Arid3b and Mycn. (PMID:22751132)
• ARID3B Fl induces death receptor mediated apoptosis while the novel splice form ARID3B Sh does not induce cell death (PMID:22860069)
• The different patterns of ARID3B in normal tissues translate into different roles for ARID3B in carcinomas. (PMID:24704276)
• Data report a positive correlation between ER positivity and nuclear ARID3B expression in primary breast cancers, along with a negative correlation with the ERBB2 status. (PMID:25120063)
• ARID3B boosts production CD133+ tumor stem cells and increases ovarian cancer progression in vivo. (PMID:25327563)
• Although ARID3B and ARID3A share overlapping functions, ARID3B play a key role in the expression of pro-apoptotic p53-target genes and apoptosis. (PMID:26519881)
• Data indicate that the most prominent proteins associating with Gab2 are PTPN11, PIK3R1 and ARID3B. (PMID:27025927)
• A novel cellular protein (AT-rich interacting domain protein 3B [ARID3B]) that we show is able to temper lytic reactivation. (PMID:27512077)
• Knockout of LIN28A and LIN28B in ACH-3P cells not only significantly increased amounts of let-7 miRNAs but also led to significant reduction in ARID3B-complex proteins, potentially because of increased targeting by let-7 miRNAs. (PMID:31415216)
• Study provides a comprehensive list of genes and pathways regulated by ARID3A and ARID3B in ovarian cancer cells. (PMID:32061921)
• Harnessing stemness and PD-L1 expression by AT-rich interaction domain-containing protein 3B in colorectal cancer. (PMID:32483441)
• Genotype-Based Gene Expression in Colon Tissue-Prediction Accuracy and Relationship with the Prognosis of Colorectal Cancer Patients. (PMID:33142733)
• Distinct and overlapping roles of ARID3A and ARID3B in regulating E2Fdependent transcription via direct binding to E2F target genes. (PMID:33649863)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	arid3b	ENSDARG00000104034
mus_musculus	Arid3b	ENSMUSG00000004661
rattus_norvegicus	Arid3b	ENSRNOG00000019677
drosophila_melanogaster	retn	FBGN0004795
caenorhabditis_elegans	cfi-1	WBGENE00000476

Paralogs (2): ARID3A (ENSG00000116017), ARID3C (ENSG00000205143)

Protein

Protein identifiers

AT-rich interactive domain-containing protein 3B — Q8IVW6 (reviewed: Q8IVW6)

Alternative names: Bright and dead ringer protein, Bright-like protein

All UniProt accessions (2): Q8IVW6, H3BQ92

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor which may be involved in neuroblastoma growth and malignant transformation. Favors nuclear targeting of ARID3A.

Subunit / interactions. Heterodimer with ARID3A. Interacts with unphosphorylated RB1.

Subcellular location. Nucleus.

Tissue specificity. Expressed in placenta, testis and leukocytes. Expressed in neuroblastoma. Present in K-562 erythrocytic leukemia cell line (at protein level).

Isoforms (3)

UniProt ID	Names	Canonical?
Q8IVW6-1	1	yes
Q8IVW6-3	3
Q8IVW6-4	4

RefSeq proteins (2): NP_001294868, NP_006456* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001606	ARID_dom	Domain
IPR023334	REKLES_domain	Domain
IPR036431	ARID_dom_sf	Homologous_superfamily
IPR045147	ARI3A/B/C	Family

Pfam: PF01388

UniProt features (26 total): region of interest 7, compositionally biased region 5, modified residue 5, splice variant 3, domain 2, mutagenesis site 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IVW6-F1	59.11	0.22

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 (5): 1, 89, 165, 311, 361

Mutagenesis-validated functional residues (2):

Position	Phenotype
240	impairs binding to rb1.
271	impairs binding to rb1.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 227 (showing top): ATACCTC_MIR202, LHX3_01, MUELLER_PLURINET, JAZAG_TGFB1_SIGNALING_DN, TGANTCA_AP1_C, AACTTT_UNKNOWN, MULLIGHAN_NPM1_SIGNATURE_3_DN, CHEN_ETV5_TARGETS_SERTOLI, TAATTA_CHX10_01, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, MARTENS_BOUND_BY_PML_RARA_FUSION, VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP, DUAN_PRDM5_TARGETS

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (2): DNA binding (GO:0003677), 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
transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1126 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARID3B	RBL2	Q08999	589
ARID3B	ARID5A	Q03989	572
ARID3B	LIN28B	Q6ZN17	536
ARID3B	SOX2	P48431	530
ARID3B	IGHV4-38-2	P0DP08	510
ARID3B	TCHP	Q9BT92	419
ARID3B	ARID5B	Q14865	403
ARID3B	LIN28A	Q9H9Z2	395
ARID3B	F5H6H0	F5H6H0	389
ARID3B	PHTF2	Q8N3S3	385
ARID3B	WDR18	Q9BV38	371
ARID3B	UBL7	Q96S82	370
ARID3B	LGR6	Q9HBX8	353
ARID3B	CLTCL1	P53675	353
ARID3B	GPR142	Q7Z601	349

IntAct

87 interactions, top by confidence:

A	B	Type	Score
NFIC	NFIB	psi-mi:“MI:2364”(proximity)	0.690
NEUROG3	GXYLT2	psi-mi:“MI:0914”(association)	0.640
JUN	NFATC1	psi-mi:“MI:0914”(association)	0.610
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
FHL2	CNOT1	psi-mi:“MI:0914”(association)	0.530
ARID3A	ARID3C	psi-mi:“MI:0914”(association)	0.530
PRR20E	SIAH2	psi-mi:“MI:0914”(association)	0.530
PPP3CC	NFATC1	psi-mi:“MI:0914”(association)	0.530
BCAT1	ARNT	psi-mi:“MI:0914”(association)	0.530
ARID3B	TINF2	psi-mi:“MI:0915”(physical association)	0.510
HCN1	ARID3B	psi-mi:“MI:0915”(physical association)	0.500
FOS	MYO1C	psi-mi:“MI:2364”(proximity)	0.480
EN1	NFIB	psi-mi:“MI:2364”(proximity)	0.470
ARID3B	H3-4	psi-mi:“MI:0915”(physical association)	0.400
POT1	ARID3B	psi-mi:“MI:0915”(physical association)	0.370
IRF9	ARID3B	psi-mi:“MI:0915”(physical association)	0.370
FOXB1	DDX39A	psi-mi:“MI:0914”(association)	0.350
FOXE1	DDX39A	psi-mi:“MI:0914”(association)	0.350
FOXH1	DDX39A	psi-mi:“MI:0914”(association)	0.350
FOXL1	DDX39A	psi-mi:“MI:0914”(association)	0.350
RBPJ	SAMD1	psi-mi:“MI:0914”(association)	0.350
TEAD2	DDX39A	psi-mi:“MI:0914”(association)	0.350
MKI67	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
ARHGEF19	NUP42	psi-mi:“MI:0914”(association)	0.350
ARID3A	PTMA	psi-mi:“MI:0914”(association)	0.350
SOX2	CBX4	psi-mi:“MI:0914”(association)	0.350
	BANF1	psi-mi:“MI:0914”(association)	0.350
GRHL1	POLRMT	psi-mi:“MI:0914”(association)	0.350
HCN1	USP27X	psi-mi:“MI:0914”(association)	0.350

BioGRID (146): ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Affinity Capture-MS), ARID3B (Proximity Label-MS)

ESM2 similar proteins: A1Z6W3, A1Z9P3, A8X633, B3MT31, B3P851, B4G2G5, B4IC49, B4M140, B4NFJ7, B4PRU6, E1JIT7, P08155, P10070, P10181, P17671, P18490, P22293, P27715, P29776, P91620, Q05A36, Q09103, Q0VGT2, Q17308, Q174I2, Q21227, Q23977, Q24459, Q292U2, Q292U5, Q4LBB6, Q5IS79, Q7JXG9, Q7KTX8, Q7QJT4, Q8IVW6, Q8MQW8, Q91661, Q92858, Q93560

Diamond homologs: A2BEA6, A2BH40, A2CG63, A6NKF2, A6PWV5, E1BLP6, E2R9X2, E7F888, E9Q4N7, F8VPQ2, O02326, O14497, O74365, P29374, P29375, P41229, P41230, Q03214, Q03989, Q14865, Q24573, Q30DN6, Q38JA7, Q3SWY1, Q3U108, Q3UXZ9, Q4H3P5, Q4LE39, Q5F3R2, Q5XGD9, Q5XUN4, Q5ZJ69, Q62431, Q6GQD7, Q6IQX0, Q8BM75, Q8IN94, Q8IVW6, Q8MQH7, Q8NFD5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 111 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
RNA Polymerase III Transcription Termination	5	31.0×	5e-05
Deactivation of the beta-catenin transactivating complex	7	20.4×	7e-06
RNA Polymerase III Abortive And Retractive Initiation	5	17.4×	5e-04
Gastrulation	5	16.2×	7e-04
TCF dependent signaling in response to WNT	8	11.8×	4e-05
Signaling by WNT	7	9.8×	4e-04
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)	5	9.2×	7e-03

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of miRNA transcription	9	24.4×	3e-08
outflow tract morphogenesis	5	14.3×	2e-03
somatic stem cell population maintenance	6	13.9×	5e-04
positive regulation of transcription initiation by RNA polymerase II	5	12.7×	4e-03
retina development in camera-type eye	5	11.9×	5e-03
transcription by RNA polymerase II	15	9.9×	1e-08
anatomical structure morphogenesis	6	7.8×	7e-03
neuron migration	6	7.5×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	1
Uncertain significance	72
Likely benign	2
Benign	3

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
1808735	GRCh37/hg19 15q24.1-24.3(chr15:74353736-77884397)x1	Pathogenic
980532	GRCh37/hg19 15q24.1-24.2(chr15:74398162-76054094)x1	Pathogenic
545183	Single allele	Likely pathogenic

SpliceAI

1562 predictions. Top by Δscore:

Variant	Effect	Δscore
15:74541327:ACAG:A	donor_gain	1.0000
15:74541327:ACAGG:A	donor_loss	1.0000
15:74541328:CAG:C	donor_gain	1.0000
15:74541329:AG:A	donor_gain	1.0000
15:74541330:GG:G	donor_gain	1.0000
15:74541330:GGT:G	donor_loss	1.0000
15:74541331:G:GA	donor_loss	1.0000
15:74541331:G:GG	donor_gain	1.0000
15:74572857:TTTA:T	acceptor_loss	1.0000
15:74572859:TAGAA:T	acceptor_loss	1.0000
15:74572860:AGA:A	acceptor_loss	1.0000
15:74572860:AGAAT:A	acceptor_gain	1.0000
15:74572861:GA:G	acceptor_gain	1.0000
15:74572861:GAATG:G	acceptor_gain	1.0000
15:74573113:T:A	acceptor_gain	1.0000
15:74573122:G:A	acceptor_gain	1.0000
15:74573200:GAGGG:G	donor_gain	1.0000
15:74589804:C:A	acceptor_gain	1.0000
15:74589807:T:TA	acceptor_gain	1.0000
15:74589808:G:A	acceptor_gain	1.0000
15:74589998:G:GT	donor_gain	1.0000
15:74590001:GCA:G	donor_gain	1.0000
15:74590004:G:GG	donor_gain	1.0000
15:74591801:G:GT	donor_gain	1.0000
15:74591812:GGG:G	donor_gain	1.0000
15:74591813:GG:G	donor_gain	1.0000
15:74591813:GGG:G	donor_gain	1.0000
15:74591814:G:T	donor_gain	1.0000
15:74591814:GG:G	donor_gain	1.0000
15:74591815:G:GA	donor_loss	1.0000

AlphaMissense

3638 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:74573161:G:C	R218S	1.000
15:74573161:G:T	R218S	1.000
15:74573168:T:C	F221L	1.000
15:74573169:T:C	F221S	1.000
15:74573170:C:A	F221L	1.000
15:74573170:C:G	F221L	1.000
15:74573172:T:C	L222P	1.000
15:74573181:T:C	L225P	1.000
15:74589835:G:C	R238P	1.000
15:74589840:C:A	P240T	1.000
15:74589840:C:T	P240S	1.000
15:74589841:C:A	P240H	1.000
15:74589841:C:G	P240R	1.000
15:74589847:T:A	M242K	1.000
15:74589847:T:C	M242T	1.000
15:74589847:T:G	M242R	1.000
15:74589850:C:A	A243D	1.000
15:74589852:A:G	K244E	1.000
15:74589853:A:T	K244I	1.000
15:74589854:A:C	K244N	1.000
15:74589854:A:T	K244N	1.000
15:74589862:T:A	L247Q	1.000
15:74589862:T:C	L247P	1.000
15:74589877:T:C	L252P	1.000
15:74589886:T:C	L255P	1.000
15:74589933:T:A	W271R	1.000
15:74589933:T:C	W271R	1.000
15:74589934:G:C	W271S	1.000
15:74589935:G:C	W271C	1.000
15:74589935:G:T	W271C	1.000

dbSNP variants (sampled 300 via entrez): RS1000037959 (15:74574752 C>G), RS1000082438 (15:74540030 C>A,G,T), RS1000170769 (15:74568334 G>C), RS1000181948 (15:74598274 T>G), RS1000306825 (15:74555923 C>G), RS1000362502 (15:74561019 A>G), RS1000415285 (15:74574442 C>G), RS1000421088 (15:74553997 A>G), RS1000472700 (15:74569285 T>C), RS1000491997 (15:74569584 A>G), RS1000515889 (15:74585941 A>G), RS1000537946 (15:74580927 C>A), RS1000722813 (15:74562970 A>C,G), RS1000749473 (15:74555444 C>T), RS1000797214 (15:74561326 G>A)

Disease associations

OMIM: gene MIM:612457 | disease phenotypes: MIM:181500

GenCC curated gene-disease

Mondo (1): schizophrenia (MONDO:0005090)

Orphanet (1): NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0100753	Schizophrenia

GWAS associations

19 associations (top):

Study	Trait	p-value
GCST000394_3	Diastolic blood pressure	1.000000e-23
GCST003846_10	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	5.000000e-18
GCST003846_11	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	1.000000e-20
GCST003846_7	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	1.000000e-11
GCST003846_8	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	2.000000e-16
GCST003846_9	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	3.000000e-09
GCST003848_1	Caffeine metabolism (plasma 1,3-dimethylxanthine (theophylline) level)	1.000000e-07
GCST003848_2	Caffeine metabolism (plasma 1,3-dimethylxanthine (theophylline) level)	1.000000e-08
GCST003848_3	Caffeine metabolism (plasma 1,3-dimethylxanthine (theophylline) level)	2.000000e-07
GCST003848_4	Caffeine metabolism (plasma 1,3-dimethylxanthine (theophylline) level)	1.000000e-07
GCST003851_4	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	3.000000e-07
GCST003851_5	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	3.000000e-14
GCST003851_6	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	3.000000e-11
GCST003851_7	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	4.000000e-15
GCST003851_8	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	9.000000e-22
GCST004412_7	Craniofacial microsomia	1.000000e-23
GCST004865_16	Itch intensity from mosquito bite adjusted by bite size	6.000000e-08
GCST008555_2	Breakfast cereal skipping frequency	4.000000e-10
GCST008839_564	Height	2.000000e-15

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0007872	caffeine metabolite measurement
EFO:0008377	mosquito bite reaction itch intensity measurement
EFO:0008378	mosquito bite reaction size measurement
EFO:0010129	breakfast skipping measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	increases expression, increases methylation	3
aristolochic acid I	increases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
sodium arsenate	increases abundance, increases expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	increases expression	1
beta-methylcholine	affects expression	1
avobenzone	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
bisphenol S	affects cotreatment, increases methylation	1
jinfukang	affects cotreatment, decreases expression	1
LDN 193189	affects cotreatment, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Bortezomib	increases expression, increases response to substance	1
Resveratrol	decreases expression, affects cotreatment	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Arsenic	increases expression, increases abundance	1
Cadmium	decreases expression	1
Caffeine	affects phosphorylation	1
Calcitriol	increases expression	1
Cisplatin	affects cotreatment, decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A0C4	SEES3-1V human ARID3B, clone1	Embryonic stem cell	Male
CVCL_A0C5	SEES3-1V human ARID3B, clone2	Embryonic stem cell	Male
CVCL_A0C6	SEES3-1V human ARID3B, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00000374	PHASE4	COMPLETED	Treatment for First-Episode Schizophrenia
NCT00001656	PHASE4	COMPLETED	Comparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774	PHASE4	COMPLETED	To Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001	PHASE4	COMPLETED	CATIE- Schizophrenia Trial
NCT00018668	PHASE4	COMPLETED	Antipsychotic Response in Schizophrenia
NCT00034801	PHASE4	COMPLETED	Olanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905	PHASE4	COMPLETED	A Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088	PHASE4	COMPLETED	Olanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187	PHASE4	COMPLETED	The Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655	PHASE4	COMPLETED	Switching Medication to Treat Schizophrenia
NCT00048828	PHASE4	COMPLETED	Treating Drug-Resistant Childhood Schizophrenia
NCT00053703	PHASE4	COMPLETED	Treatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498	PHASE4	COMPLETED	Risperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802	PHASE4	COMPLETED	Efficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327	PHASE4	COMPLETED	Study of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049	PHASE4	COMPLETED	Study of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012	PHASE4	COMPLETED	Comparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776	PHASE4	COMPLETED	Efficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571	PHASE4	COMPLETED	Olanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368	PHASE4	COMPLETED	The Effects of Risperidone and Olanzapine on Thinking
NCT00114595	PHASE4	COMPLETED	Ethyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923	PHASE4	COMPLETED	Risperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020	PHASE4	COMPLETED	Clinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166	PHASE4	COMPLETED	Treatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847	PHASE4	COMPLETED	Naltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564	PHASE4	COMPLETED	Energy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715	PHASE4	COMPLETED	Efficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223	PHASE4	COMPLETED	Effectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081	PHASE4	COMPLETED	One Year Drug Treatment in First-Episode Schizophrenia
NCT00159120	PHASE4	COMPLETED	Maintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133	PHASE4	COMPLETED	Prodrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757	PHASE4	TERMINATED	12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817	PHASE4	COMPLETED	Effect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026	PHASE4	TERMINATED	Alcoholism and Schizophrenia: Effects of Clozapine
NCT00169039	PHASE4	TERMINATED	Clozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065	PHASE4	COMPLETED	Effectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091	PHASE4	TERMINATED	Clozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423	PHASE4	COMPLETED	Efficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436	PHASE4	COMPLETED	Atomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008	PHASE4	COMPLETED	Aripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety