ARID1B

Summary

ARID1B (AT-rich interaction domain 1B, HGNC:18040) is a protein-coding gene on chromosome 6q25.3, encoding AT-rich interactive domain-containing protein 1B (Q8NFD5). Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). It is haploinsufficient (ClinGen: sufficient evidence).

This locus encodes an AT-rich DNA interacting domain-containing protein. The encoded protein is a component of the SWI/SNF chromatin remodeling complex and may play a role in cell-cycle activation. The protein encoded by this locus is similar to AT-rich interactive domain-containing protein 1A. These two proteins function as alternative, mutually exclusive ARID-subunits of the SWI/SNF complex. The associated complexes play opposing roles. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 57492 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Coffin-Siris syndrome (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 21
• Clinical variants (ClinVar): 2,839 total — 449 pathogenic, 148 likely-pathogenic
• Phenotypes (HPO): 155
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 20 cancer types
• Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
• MANE Select transcript: NM_001374828

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18040
Approved symbol	ARID1B
Name	AT-rich interaction domain 1B
Location	6q25.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5, SMARCF2
Ensembl gene	ENSG00000049618
Ensembl biotype	protein_coding
OMIM	614556
Entrez	57492

Gene structure

Transcript identifiers

Ensembl transcripts: 38 — 21 protein_coding, 14 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000319584, ENST00000346085, ENST00000350026, ENST00000400790, ENST00000414678, ENST00000452544, ENST00000478761, ENST00000493658, ENST00000494260, ENST00000635849, ENST00000635928, ENST00000635957, ENST00000636205, ENST00000636227, ENST00000636254, ENST00000636426, ENST00000636607, ENST00000636748, ENST00000636909, ENST00000636930, ENST00000636940, ENST00000637003, ENST00000637015, ENST00000637170, ENST00000637532, ENST00000637548, ENST00000637568, ENST00000637722, ENST00000637741, ENST00000637810, ENST00000637887, ENST00000637904, ENST00000637910, ENST00000637933, ENST00000638000, ENST00000674190, ENST00000674298, ENST00000938503

RefSeq mRNA: 5 — MANE Select: NM_001374828 NM_001363725, NM_001371656, NM_001374820, NM_001374828, NM_017519

CCDS: CCDS55072, CCDS87459, CCDS87460

Canonical transcript exons

ENST00000636930 — 20 exons

Exon	Start	End
ENSE00000765473	157133028	157133207
ENSE00000975824	157184231	157184435
ENSE00000975829	157200705	157201488
ENSE00001142049	157203866	157203996
ENSE00001142057	157198811	157198907
ENSE00001142064	157196165	157196315
ENSE00001142072	157190038	157190210
ENSE00001142078	157189642	157189780
ENSE00001332230	157148624	157148951
ENSE00001348846	157206167	157210779
ENSE00002467347	156935466	156935576
ENSE00002535311	156901376	156901525
ENSE00003502633	157084662	157084905
ENSE00003534281	157167040	157167185
ENSE00003539964	157174008	157174117
ENSE00003587385	157110472	157110561
ENSE00003655341	157174847	157175005
ENSE00003677647	156829227	156829421
ENSE00003786123	157180969	157181178
ENSE00003898582	156777378	156779471

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 96.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.0848 / max 462.9354, expressed in 1814 samples.

FANTOM5 promoters (18 alternative TSS)

Promoter ID	TPM avg	Samples expressed
70728	8.8439	1752
70737	5.5194	1679
70725	4.6321	1365
70734	3.0596	1284
70724	2.9615	1238
70727	2.2947	899
70731	2.2912	1123
70733	0.9661	557
70736	0.6824	365
70726	0.6306	353

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	96.37	gold quality
colonic epithelium	UBERON:0000397	96.14	gold quality
sural nerve	UBERON:0015488	95.74	gold quality
buccal mucosa cell	CL:0002336	95.21	gold quality
upper arm skin	UBERON:0004263	94.49	gold quality
calcaneal tendon	UBERON:0003701	94.34	gold quality
tonsil	UBERON:0002372	94.29	gold quality
seminal vesicle	UBERON:0000998	93.31	gold quality
superior surface of tongue	UBERON:0007371	93.31	gold quality
cortical plate	UBERON:0005343	93.05	gold quality
left ovary	UBERON:0002119	92.86	gold quality
ganglionic eminence	UBERON:0004023	92.83	gold quality
adrenal tissue	UBERON:0018303	92.81	gold quality
uterine cervix	UBERON:0000002	92.73	gold quality
corpus callosum	UBERON:0002336	92.72	gold quality
skin of abdomen	UBERON:0001416	92.55	gold quality
skin of leg	UBERON:0001511	92.55	gold quality
ileal mucosa	UBERON:0000331	92.51	gold quality
renal medulla	UBERON:0000362	92.48	gold quality
zone of skin	UBERON:0000014	92.43	gold quality
right ovary	UBERON:0002118	92.39	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.38	gold quality
tibialis anterior	UBERON:0001385	92.24	gold quality
skin of hip	UBERON:0001554	92.20	gold quality
caput epididymis	UBERON:0004358	92.11	gold quality
pigmented layer of retina	UBERON:0001782	91.87	gold quality
cauda epididymis	UBERON:0004360	91.58	gold quality
muscle of leg	UBERON:0001383	91.55	gold quality
ovary	UBERON:0000992	91.52	gold quality
tendon	UBERON:0000043	91.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-119	yes	28.92
E-ANND-3	yes	9.09
E-GEOD-137537	yes	5.97

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

5 targets.

Target	Regulation
CR2
IL2RA
NCAM1
SMARCA4
TNFRSF10B

Upstream regulators (CollecTRI, top): BCL6

miRNA regulators (miRDB)

201 targeting ARID1B, 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-9-5P	100.00	72.28	2361
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-12118	100.00	65.88	1270
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-4533	100.00	69.48	2758
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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-363-3P	99.98	74.72	1821

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

• Cloning and characterization of hELD/OSA1, a novel BRG1 interacting protein. (PMID:11988099)
• 6A3-5 expression is associated with alpha-smooth muscle cell actin in mesangial cells, arteriolar smooth muscle cells, and interstitial myofibroblasts.could potentially be a novel early vascular marker of acute and chronic renal ischemic stress (PMID:14633620)
• Analysis of DNA-binding behaviour indicates that ARID1B binds DNA in a non-sequence-specific manner similar to ARID1A (PMID:15170388)
• The chromatin remodeling factor ARID1B had a very similar pattern of expression with an incremental increase in HPFH and decreased expression in deltabeta-thalassemia. (PMID:16952470)
• A subset of mammalian SWI/SNF complexes, specifically including the ARID1B subunit, is required for efficient cell cycle re-entry and for the association of activating factors with the c-myc promoter. (PMID:17255939)
• For a number of genes affected by de novo copy number variants CNVs in autism (CNTNAP2, ZNF214, ARID1B, Proline Dehydrogenase), reduced transcript expression may be a mechanism of pathogenesis during neurodevelopment. (PMID:21448237)
• ARID1B is important in human brain development and function in general, and in the development of CC and in speech development in particular. (PMID:21801163)
• Haploinsufficiency of ARID1B, a member of the SWI/SNF-A chromatin-remodeling complex, is a common cause of ID. (PMID:22405089)
• these results indicate that haploinsufficiency of the ARID1B gene, which encodes an epigenetic modifier of chromatin structure, is an important cause of CSS and is potentially a common cause of intellectual disability and speech impairment. (PMID:22426309)
• Identification of recurrent somatic mutations in the chromatin-remodeling gene ARID1B in the childhood cancer neuroblastoma. (PMID:23202128)
• A possible tumour-suppressor function for ARID1B in pancreatic cancer. (PMID:23660946)
• SMARCB1, SMARCA4, or ARID1B were mutated in 20 out of 49 Coffin-Siris syndrome patients. (PMID:23815551)
• associations revealed between genetic polymorphisms located in the flanking region of the ARID1B genes and hypoesthesia (PMID:23834954)
• Loss of ARID1B gene is associated with Waldenstrom macroglobulinemia. (PMID:24366360)
• Mutations in ARID1B gene is associated with microsatellite unstable colorectal cancer. (PMID:24382590)
• loss of ARID1A and ARID1B alleles cooperatively promotes cancer formation but also results in a unique functional dependence (PMID:24562383)
• The BAF complex, including both ARID1A and ARID1B, contributes to DNA repair and cellular resistance to ionizing radiation and cisplatin. (PMID:24788099)
• BAF complex gene ARID1B is mutated in Coffin-Siris syndrome patients. (PMID:25081545)
• Phenotype of Coffin-Siris syndrome patients with ARID1B mutations (PMID:25169814)
• The most prominent and consistent clinical findings in patients with ARID1B haploinsufficiency are developmental delay, speech impairment and intellectual disability. (PMID:25250687)
• ARID1B potentially serves as a valuable prognostic and predictive biomarker as well as a therapeutic target in breast cancer. (PMID:25817822)
• Results show the crystal structure and binding site of SWI1 protein and identify loop L1 and L2 regions of SWI1 ARID likely play key roles in ARID-DNA interactions. (PMID:26223912)
• Chromatin-Remodeling-Factor ARID1B Represses Wnt/beta-Catenin Signaling. (PMID:26340334)
• De novo mutations in ARID1B associated with both syndromic and non-syndromic short stature (PMID:26376624)
• Gonadal mosaicism in ARID1B gene causes intellectual disability and dysmorphic features in three siblings. (PMID:26395437)
• This study provide the evidence ARID1B mutation releate to Autism Spectrum Disorder. (PMID:26637798)
• ARID1B role in genome-wide transcriptional regulation by SWI/SNF complexes. (PMID:26716708)
• Chromosome analysis by array-CGH revealed a small interstitial 6q deletion spanning approximately 1.1 Mb of DNA and containing only one coding gene, ARID1B. We suggest that ARID1B is the key gene behind 6q microdeletion syndrome, and we discuss its possible role in the phenotypic manifestations (PMID:26754677)
• This study demonstrate that ARID1B is required for neuronal differentiation in the developing brain, such as in dendritic arborization and synapse formation. (PMID:26937011)
• We report two teenagers with ID whose molecular diagnosis of a SMARC2A or ARID1B mutation, respectively, was established through clinical exome analysis. (PMID:27112773)
• The ARID1B gene, commonly mutated in multiple types of cancer, was identified as an additional ZNF384 gene fusion partner. (PMID:27392123)
• HSCR was observed in a patient with a truncating mutation in ARID1B, further expanding the phenotypic spectrum of Coffin-Siris syndrome. This suggests that the BAF complex does not only play a role in the enteric system of Drosophila, but also in humans. (PMID:27511161)
• we identified concurrent ARID1A and ARID1B inactivating mutations with consequent loss of protein expression in the undifferentiated component of approximately one-quarter of dedifferentiated endometrial and ovarian carcinomas (PMID:27562491)
• The clinical features of both patients are felt to be consistent with an ARID1B-related disorder. To our knowledge, this is the first report of a pathogenic mutation in ARID1B being passed from an affected parent to their offspring. (PMID:27570168)
• knockdown of the SWI/SNF component ARID1B prevents OIS and cooperates with RAS to induce liver tumors (PMID:27737960)
• findings establish mutations in ARID1B as the underlying genetic defect in the HHID syndrome in two of three patients. (PMID:28323383)
• these results highlighted the significant genetic contribution of the ARID1B variant, rs73013281, to susceptibility for HCC, especially in interaction with physical activity. (PMID:28415691)
• we identified a subgroup of neuroblastoma with ARID1B mutation shows an aggressive behavior. These findings may provide a new biomarker to identify another subgroup of neuroblastoma with high-risk features. (PMID:28521285)
• We report here the clinical, genetic, and proteomic phenotypes of an individual with a unique apparent de novo mutation of ARID1B due to an intragenic duplication (PMID:28691782)
• Of the 34 undifferentiated endometrial carcinomas examined, 17 (50%) exhibited SWI/SNF complex inactivation, with 11 tumors showing complete loss of both ARID1A and ARID1B, 5 showing complete loss of BRG1 and 1 showing complete loss of INI1. Ten of the remaining 17 undifferentiated carcinomas showed the following alterations: 5 tumors (15%) showed loss of ARID1A only with intact ARID1B, BRG1, and INI1 expression. (PMID:28863077)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	arid1b	ENSDARG00000092503
mus_musculus	Arid1b	ENSMUSG00000069729
rattus_norvegicus	Arid1b	ENSRNOG00000017030
drosophila_melanogaster	osa	FBGN0261885
caenorhabditis_elegans	let-526	WBGENE00002717

Paralogs (1): ARID1A (ENSG00000117713)

Protein

Protein identifiers

AT-rich interactive domain-containing protein 1B — Q8NFD5 (reviewed: Q8NFD5)

Alternative names: BRG1-associated factor 250b, BRG1-binding protein hELD/OSA1, Osa homolog 2, p250R

All UniProt accessions (21): A0A1B0GTE8, A0A1B0GTI6, A0A1B0GTJ8, A0A1B0GU09, A0A1B0GU65, A0A1B0GUC6, A0A1B0GUG2, A0A1B0GV63, A0A1B0GV92, Q8NFD5, A0A1B0GVH0, A0A1B0GVK1, A0A1B0GWI8, A0A1B0GWJ2, A0A3F2YNW7, A0A6I8PTU7, A0A6Q8NVI4, A0A8J9GB59, H0Y2R3, H0Y3S9, H0Y7H8

UniProt curated annotations — full annotation on UniProt →

Function. Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth. Binds DNA non-specifically.

Subunit / interactions. Component of SWI/SNF chromatin remodeling complexes, in some of which it can be mutually exclusive with ARID1B/BAF250B. The canonical complex contains a catalytic subunit (either SMARCA4/BRG1/BAF190A or SMARCA2/BRM/BAF190B) and at least SMARCE1, ACTL6A/BAF53, SMARCC1/BAF155, SMARCC2/BAF170, and SMARCB1/SNF5/BAF47. Other subunits specific to each of the complexes may also be present permitting several possible combinations developmentally and tissue specific. Component of the BAF (SWI/SNF-A) complex, which includes at least actin (ACTB), ARID1A/BAF250A, ARID1B/BAF250B, SMARCA2/BRM, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin. Component of a SWI/SNF-like EBAFb complex, at least composed of SMARCA4/BRG1/BAF190A, SMARCB1/BAF47/SNF5, ACTL6A/BAF53A, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, SMARCC1/BAF155, SMARCC2/BAF170, ARID1B/BAF250B, MLLT1/ENL and actin. Interacts through its C-terminus with SMARCA2/BRM/BAF190B and SMARCA4/BRG1/BAF190A. Interacts with SMARCC1/BAF155.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed with high levels in heart, skeletal muscle and kidney.

Disease relevance. Coffin-Siris syndrome 1 (CSS1) [MIM:135900] A form of Coffin-Siris syndrome, a congenital multiple malformation syndrome with broad phenotypic and genetic variability. Cardinal features are intellectual disability, coarse facial features, hypertrichosis, and hypoplastic or absent fifth digit nails or phalanges. Additional features include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Sucking/feeding difficulties, poor growth, ophthalmologic abnormalities, hearing impairment, and spinal anomalies are common findings. Both autosomal dominant and autosomal recessive inheritance patterns have been reported. The disease is caused by variants affecting the gene represented in this entry.

Polymorphism. The poly-Gln region is polymorphic and the number of Gln varies in the population (from 17 to 23).

Miscellaneous. Produced by alternative initiation at Met-84 of isoform 5.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8NFD5-5	5	yes
Q8NFD5-1	1
Q8NFD5-2	2
Q8NFD5-3	3

RefSeq proteins (5): NP_001350654, NP_001358585, NP_001361749, NP_001361757, NP_059989 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001606	ARID_dom	Domain
IPR021906	BAF250/Osa	Family
IPR033388	BAF250_C	Domain
IPR036431	ARID_dom_sf	Homologous_superfamily
IPR038040	ARID_ARID1B	Domain

Pfam: PF01388, PF12031

UniProt features (126 total): sequence variant 39, compositionally biased region 37, region of interest 12, sequence conflict 11, modified residue 11, helix 7, short sequence motif 3, splice variant 3, chain 1, domain 1, initiator methionine 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
2CXY	X-RAY DIFFRACTION	1.6
2EH9	X-RAY DIFFRACTION	2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NFD5-F1	47.16	0.18

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 (11): 2, 487, 585, 599, 608, 640, 1625, 1638, 1642, 1798, 1860

Function

Pathways and Gene Ontology

Reactome pathways

17 pathways

ID	Pathway
R-HSA-3214858	RMTs methylate histone arginines
R-HSA-8939243	RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-9824585	Regulation of MITF-M-dependent genes involved in pigmentation
R-HSA-9845323	Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs)
R-HSA-9933937	Formation of the canonical BAF (cBAF) complex
R-HSA-9934037	Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)
R-HSA-1266738	Developmental Biology
R-HSA-212165	Epigenetic regulation of gene expression
R-HSA-212436	Generic Transcription Pathway
R-HSA-3247509	Chromatin modifying enzymes
R-HSA-4839726	Chromatin organization
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)
R-HSA-8878171	Transcriptional regulation by RUNX1
R-HSA-9730414	MITF-M-regulated melanocyte development
R-HSA-9842860	Regulation of endogenous retroelements
R-HSA-9856651	MITF-M-dependent gene expression

MSigDB gene sets: 680 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_CHROMOSOME_ORGANIZATION, RRAGTTGT_UNKNOWN, GOBP_POSITIVE_REGULATION_OF_HEMOPOIESIS, PEREZ_TP63_TARGETS, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_REGULATION_OF_DNA_REPAIR, CEBPB_01, RODRIGUES_NTN1_TARGETS_DN, ATGTTAA_MIR302C, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_CELL_CELL_ADHESION, GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION, chr6q25

GO Biological Process (14): chromatin remodeling (GO:0006338), regulation of transcription by RNA polymerase II (GO:0006357), nervous system development (GO:0007399), regulation of mitotic metaphase/anaphase transition (GO:0030071), positive regulation of T cell differentiation (GO:0045582), positive regulation of cell differentiation (GO:0045597), positive regulation of myoblast differentiation (GO:0045663), transcription initiation-coupled chromatin remodeling (GO:0045815), positive regulation of DNA-templated transcription (GO:0045893), regulation of G0 to G1 transition (GO:0070316), regulation of G1/S transition of mitotic cell cycle (GO:2000045), positive regulation of double-strand break repair (GO:2000781), regulation of nucleotide-excision repair (GO:2000819), chromatin organization (GO:0006325)

GO Molecular Function (4): DNA binding (GO:0003677), transcription coactivator activity (GO:0003713), protein binding (GO:0005515), nucleosome binding (GO:0031491)

GO Cellular Component (10): chromatin (GO:0000785), nucleoplasm (GO:0005654), cytosol (GO:0005829), plasma membrane (GO:0005886), SWI/SNF complex (GO:0016514), brahma complex (GO:0035060), npBAF complex (GO:0071564), nBAF complex (GO:0071565), bBAF complex (GO:0140092), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-12 pathways:

Category	Pathways
SWI/SNF chromatin remodelers	2
Gene expression (Transcription)	2
Chromatin modifying enzymes	1
Transcriptional regulation by RUNX1	1
MITF-M-dependent gene expression	1
Regulation of endogenous retroelements	1
RNA Polymerase II Transcription	1
Chromatin organization	1
Generic Transcription Pathway	1
Developmental Biology	1
Epigenetic regulation of gene expression	1
MITF-M-regulated melanocyte development	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
SWI/SNF superfamily-type complex	5
cellular anatomical structure	3
regulation of DNA-templated transcription	2
regulation of mitotic cell cycle phase transition	2
chromatin organization	1
transcription by RNA polymerase II	1
system development	1
metaphase/anaphase transition of mitotic cell cycle	1
regulation of metaphase/anaphase transition of cell cycle	1
T cell differentiation	1
regulation of T cell differentiation	1
positive regulation of lymphocyte differentiation	1
positive regulation of T cell activation	1
cell differentiation	1
regulation of cell differentiation	1
positive regulation of cellular process	1
positive regulation of developmental process	1
myoblast differentiation	1
positive regulation of cell differentiation	1
regulation of myoblast differentiation	1
transcription initiation at RNA polymerase II promoter	1
positive regulation of gene expression, epigenetic	1
DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
regulation of cell cycle process	1
G0 to G1 transition	1
G1/S transition of mitotic cell cycle	1
regulation of cell cycle G1/S phase transition	1
double-strand break repair	1
positive regulation of DNA repair	1
regulation of double-strand break repair	1
regulation of DNA repair	1
nucleotide-excision repair	1
cellular component organization	1
nucleic acid binding	1
transcription coregulator activity	1
positive regulation of DNA-templated transcription	1
binding	1
chromatin binding	1
protein-containing complex binding	1

Protein interactions and networks

STRING

1570 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARID1B	SMARCA4	P51532	997
ARID1B	SMARCB1	Q12824	995
ARID1B	PBRM1	Q86U86	993
ARID1B	DPF2	Q92785	989
ARID1B	ARID2	Q68CP9	985
ARID1B	ARID1A	O14497	983
ARID1B	SMARCA2	P51531	980
ARID1B	SMARCE1	Q969G3	968
ARID1B	SMARCC1	Q92922	965
ARID1B	SMARCC2	Q8TAQ2	957
ARID1B	DPF1	Q92782	948
ARID1B	BRD7	Q9NPI1	936
ARID1B	ACTL6A	O96019	873
ARID1B	BRD9	Q9H8M2	856
ARID1B	ACTL6B	O94805	819

IntAct

167 interactions, top by confidence:

A	B	Type	Score
ARID1B	SMARCB1	psi-mi:“MI:0914”(association)	0.890
SMARCB1	ARID1A	psi-mi:“MI:0914”(association)	0.860
SMARCE1	ARID1A	psi-mi:“MI:0914”(association)	0.840
SMARCC1	ARID1A	psi-mi:“MI:0914”(association)	0.790
SMARCD1	ARID1A	psi-mi:“MI:0914”(association)	0.790
SMARCC2	ARID1A	psi-mi:“MI:0914”(association)	0.790
ARID1B	SMARCC2	psi-mi:“MI:0915”(physical association)	0.770
SS18	ARID1A	psi-mi:“MI:0914”(association)	0.760
DPF2	ARID1A	psi-mi:“MI:0914”(association)	0.730
RPRD1B	POLR2D	psi-mi:“MI:0914”(association)	0.730

BioGRID (394): ARID1B (Affinity Capture-MS), ARID1B (Affinity Capture-MS), ARID1B (Affinity Capture-MS), ARID1B (Affinity Capture-MS), ARID1B (Affinity Capture-MS), ARID1B (Affinity Capture-MS), ARID1A (Co-fractionation), ARID1B (Co-fractionation), ARID1B (Co-fractionation), ARID1B (Co-fractionation), ARID1B (Co-fractionation), ARID1B (Co-fractionation), ARID1B (Co-fractionation), ARID1B (Co-fractionation), ARID1B (Co-fractionation)

ESM2 similar proteins: A1YFU7, A2AJK6, A2BH40, B2RWS6, D3YWE6, E9Q4N7, M9NEY8, O00512, O14497, O35126, O42368, O43365, O57401, P02831, P02833, P22810, P23441, P23512, P25822, P32182, P34545, P35582, P35583, P43698, P43699, P50220, P50901, P54258, P54259, P54269, P55317, Q06A37, Q08DG7, Q08E31, Q09472, Q0VCT9, Q10571, Q1KKX7, Q24248, Q24645

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

4 interactions.

A	Effect	B	Mechanism
ARID1B	“form complex”	“SWI/SNF complex”	binding
ARID1B	“form complex”	“Muscle cell-specific SWI/SNF ARID1B variant”	binding
ARID1B	“form complex”	“BAF250b E3 ligase”	binding
ARID1B	“down-regulates activity”	“Histone H2B”	ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 154 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
Formation of the canonical BAF (cBAF) complex	14	81.5×	1e-23
Formation of the embryonic stem cell BAF (esBAF) complex	14	77.2×	4e-23
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)	17	71.2×	8e-27
Formation of the polybromo-BAF (pBAF) complex	12	69.8×	5e-19
Formation of the non-canonical BAF (ncBAF) complex	11	67.8×	3e-17
Regulation of endogenous retroelements	14	47.3×	5e-19
Regulation of MITF-M-dependent genes involved in pigmentation	19	46.3×	2e-25
MITF-M-dependent gene expression	17	28.3×	8e-19

GO biological processes:

GO term	Partners	Fold	FDR
regulation of G0 to G1 transition	16	74.4×	3e-25
regulation of nucleotide-excision repair	16	66.4×	3e-24
regulation of mitotic metaphase/anaphase transition	16	54.7×	2e-22
nucleosome disassembly	9	49.8×	4e-12
positive regulation of double-strand break repair	16	38.0×	2e-19
positive regulation of T cell differentiation	12	37.7×	1e-14
regulation of G1/S transition of mitotic cell cycle	16	33.8×	1e-18
positive regulation of myoblast differentiation	13	32.8×	7e-15

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 20 cancer types — ANGS, BLCA, BRCA, CCRCC, CEAD, COADREAD, DLBCLNOS, HCC, LGGNOS, LUSC, MBL, MLYM…(+8 more).

Clinical variants and AI predictions

ClinVar

2839 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	449
Likely pathogenic	148
Uncertain significance	918
Likely benign	800
Benign	138

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1033954	NM_001374828.1(ARID1B):c.3126del (p.Met1043fs)	Pathogenic
1069782	NM_001374828.1(ARID1B):c.4453C>T (p.Gln1485Ter)	Pathogenic
1074286	NM_001374828.1(ARID1B):c.5070del (p.Met1690fs)	Pathogenic
1075235	NC_000006.11:g.(?157405796)(157406039_?)del	Pathogenic
1098402	NM_001374828.1(ARID1B):c.1681del (p.Asp561fs)	Pathogenic
1164017	NM_001374828.1(ARID1B):c.6497dup (p.Ser2166fs)	Pathogenic
1164018	NM_001374828.1(ARID1B):c.3247_3248del (p.Leu1083fs)	Pathogenic
1172514	NM_001374828.1(ARID1B):c.5840del (p.Gly1947fs)	Pathogenic
1174076	NM_001374828.1(ARID1B):c.3345G>C (p.Lys1115Asn)	Pathogenic
1174809	NM_001374828.1(ARID1B):c.2595dup (p.Thr866fs)	Pathogenic
1176847	GRCh37/hg19 6q25.3(chr6:157405796-157406039)x1	Pathogenic
1177310	NM_001374828.1(ARID1B):c.4444_4445dup (p.Gly1483fs)	Pathogenic
1177311	NM_001374828.1(ARID1B):c.4530dup (p.Glu1511fs)	Pathogenic
1177312	NM_001374828.1(ARID1B):c.4593_4594del (p.Gly1532fs)	Pathogenic
1177313	NM_001374828.1(ARID1B):c.5285_5294delinsAGA (p.Val1762fs)	Pathogenic
1177314	NM_001374828.1(ARID1B):c.5633_5636del (p.Thr1878fs)	Pathogenic
1177315	NM_001374828.1(ARID1B):c.6058del (p.Gln2020fs)	Pathogenic
1177316	NM_001374828.1(ARID1B):c.6085_6086del (p.Gly2029fs)	Pathogenic
1177317	NM_001374828.1(ARID1B):c.6412del (p.Asp2138fs)	Pathogenic
1177331	NM_001374828.1(ARID1B):c.6567del (p.Pro2191fs)	Pathogenic
1177332	NM_001374828.1(ARID1B):c.6997G>T (p.Glu2333Ter)	Pathogenic
1177347	NM_001374828.1(ARID1B):c.2002G>T (p.Gly668Ter)	Pathogenic
1177348	NM_001374828.1(ARID1B):c.2086dup (p.Gln696fs)	Pathogenic
1177349	NM_001374828.1(ARID1B):c.2239dup (p.Ser747fs)	Pathogenic
1177350	NM_001374828.1(ARID1B):c.2729dup (p.Tyr910Ter)	Pathogenic
1177357	NM_001374828.1(ARID1B):c.2844del (p.Asn949fs)	Pathogenic
1177358	NM_001374828.1(ARID1B):c.2875C>T (p.Gln959Ter)	Pathogenic
1177359	NM_001374828.1(ARID1B):c.3505-2A>G	Pathogenic
1177360	NM_001374828.1(ARID1B):c.3527del (p.Thr1176fs)	Pathogenic
1177361	NM_001374828.1(ARID1B):c.3585G>A (p.Trp1195Ter)	Pathogenic

SpliceAI

8293 predictions. Top by Δscore:

Variant	Effect	Δscore
6:156829224:CAG:C	acceptor_loss	1.0000
6:156829225:A:AG	acceptor_gain	1.0000
6:156829225:A:C	acceptor_loss	1.0000
6:156829225:AG:A	acceptor_gain	1.0000
6:156829225:AGG:A	acceptor_gain	1.0000
6:156829226:G:GA	acceptor_gain	1.0000
6:156829226:GG:G	acceptor_gain	1.0000
6:156829226:GGG:G	acceptor_gain	1.0000
6:156829226:GGGC:G	acceptor_gain	1.0000
6:156829226:GGGCA:G	acceptor_gain	1.0000
6:156844371:G:GG	donor_gain	1.0000
6:156870256:G:T	donor_gain	1.0000
6:156870264:G:GG	donor_gain	1.0000
6:156901371:GACA:G	acceptor_loss	1.0000
6:156901373:CAGA:C	acceptor_loss	1.0000
6:156901374:A:AG	acceptor_gain	1.0000
6:156901374:A:G	acceptor_loss	1.0000
6:156901375:G:A	acceptor_loss	1.0000
6:156901375:G:GG	acceptor_gain	1.0000
6:156933487:G:GT	donor_gain	1.0000
6:156935464:A:AG	acceptor_gain	1.0000
6:156935465:G:GG	acceptor_gain	1.0000
6:156935465:GGAC:G	acceptor_gain	1.0000
6:156935577:G:GG	donor_gain	1.0000
6:157110556:A:T	donor_gain	1.0000
6:156790791:T:G	acceptor_gain	0.9900
6:156790802:T:G	acceptor_gain	0.9900
6:156829223:A:AG	acceptor_gain	0.9900
6:156829223:ACAG:A	acceptor_gain	0.9900
6:156829223:ACAGG:A	acceptor_gain	0.9900

AlphaMissense

15619 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:156779185:T:A	L419H	1.000
6:157181040:A:C	R1056S	1.000
6:157181040:A:T	R1056S	1.000
6:157181047:T:A	W1059R	1.000
6:157181047:T:C	W1059R	1.000
6:157181049:G:C	W1059C	1.000
6:157181049:G:T	W1059C	1.000
6:157181051:T:A	V1060D	1.000
6:157181057:G:C	R1062P	1.000
6:157181059:T:G	Y1063D	1.000
6:157181063:T:C	L1064P	1.000
6:157181068:T:C	F1066L	1.000
6:157181069:T:C	F1066S	1.000
6:157181070:C:A	F1066L	1.000
6:157181070:C:G	F1066L	1.000
6:157181126:T:A	L1085Q	1.000
6:157181126:T:C	L1085P	1.000
6:157181141:T:C	L1090P	1.000
6:157181153:T:A	V1094D	1.000
6:157181164:G:T	G1098W	1.000
6:157181165:G:A	G1098E	1.000
6:157181167:G:C	G1099R	1.000
6:157181171:T:C	L1100S	1.000
6:157184232:T:A	V1103D	1.000
6:157184234:A:G	N1104D	1.000
6:157184236:T:A	N1104K	1.000
6:157184236:T:G	N1104K	1.000
6:157184237:A:G	K1105E	1.000
6:157184238:A:T	K1105I	1.000
6:157184239:A:C	K1105N	1.000

dbSNP variants (sampled 300 via entrez): RS1000032568 (6:157196966 A>ATGC), RS1000036690 (6:157053356 G>A), RS1000038324 (6:157092856 CAT>C), RS1000050124 (6:157171123 T>A,G), RS1000057022 (6:156964080 G>A), RS1000057768 (6:157007956 G>A), RS1000059553 (6:157163087 T>G), RS1000060206 (6:157136735 G>A), RS1000061002 (6:156807888 G>A), RS1000063457 (6:157203420 T>C), RS1000071660 (6:157124171 A>G), RS1000085319 (6:157053090 G>C), RS1000099309 (6:156848689 T>C), RS1000123378 (6:156889494 C>G,T), RS1000124883 (6:156990645 GAACAAACA>G,GAACA,GAACAAACAAACA)

Disease associations

OMIM: gene MIM:614556 | disease phenotypes: MIM:135900, MIM:609943, MIM:614562, MIM:213000, MIM:217990, MIM:181500, MIM:602450, MIM:601358, MIM:162200, MIM:163950, MIM:155255, MIM:219050, MIM:605130

GenCC curated gene-disease

Disease	Classification	Inheritance
Coffin-Siris syndrome 1	Definitive	Autosomal dominant
Coffin-Siris syndrome	Definitive	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
Coffin-Siris syndrome	Definitive	AD

Mondo (25): Coffin-Siris syndrome 1 (MONDO:0007617), Coffin-Siris syndrome (MONDO:0015452), isolated cerebellar hypoplasia/agenesis (MONDO:0008939), corpus callosum, agenesis of (MONDO:0009022), neurodevelopmental disorder (MONDO:0700092), intellectual disability (MONDO:0001071), schizophrenia (MONDO:0005090), autism spectrum disorder (MONDO:0005258), microcephaly (MONDO:0001149), constipation disorder (MONDO:0002203), epilepsy (MONDO:0005027), blepharophimosis (MONDO:0001008), hereditary ataxia (MONDO:0100309), metabolic disease (MONDO:0005066), severe combined immunodeficiency due to DCLRE1C deficiency (MONDO:0011225)

Orphanet (17): Coffin-Siris syndrome (Orphanet:1465), Isolated cerebellar agenesis (Orphanet:1398), Isolated corpus callosum agenesis (Orphanet:200), Cerebellar hypoplasia-tapetoretinal degeneration syndrome (Orphanet:2246), Hereditary ataxia (Orphanet:183518), Severe combined immunodeficiency due to DCLRE1C deficiency (Orphanet:275), Rare disorder with hypertrichosis (Orphanet:79365), Nicolaides-Baraitser syndrome (Orphanet:3051), Neurofibromatosis type 1 (Orphanet:636), Noonan syndrome (Orphanet:648), Medulloblastoma (Orphanet:616), Rare genetic intellectual disability (Orphanet:183757), Pituitary stalk interruption syndrome (Orphanet:95496), Wiedemann-Steiner syndrome (Orphanet:319182), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

155 total (30 of 155 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000023	Inguinal hernia
HP:0000028	Cryptorchidism
HP:0000047	Hypospadias
HP:0000072	Hydroureter
HP:0000085	Horseshoe kidney
HP:0000086	Ectopic kidney
HP:0000089	Renal hypoplasia
HP:0000119	Abnormality of the genitourinary system
HP:0000126	Hydronephrosis
HP:0000151	Aplasia of the uterus
HP:0000154	Wide mouth
HP:0000175	Cleft palate
HP:0000179	Thick lower lip vermilion
HP:0000218	High palate
HP:0000219	Thin upper lip vermilion
HP:0000248	Brachycephaly
HP:0000252	Microcephaly
HP:0000272	Malar flattening
HP:0000278	Retrognathia
HP:0000280	Coarse facial features
HP:0000286	Epicanthus
HP:0000289	Broad philtrum
HP:0000294	Low anterior hairline
HP:0000316	Hypertelorism
HP:0000322	Short philtrum
HP:0000331	Short chin
HP:0000343	Long philtrum
HP:0000347	Micrognathia
HP:0000358	Posteriorly rotated ears

GWAS associations

21 associations (top):

Study	Trait	p-value
GCST001350_1	Pancreatic cancer	7.000000e-07
GCST001868_7	Alzheimer’s disease biomarkers	3.000000e-06
GCST002090_4	Sensory disturbances after bilateral sagittal split ramus osteotomy	4.000000e-08
GCST002090_5	Sensory disturbances after bilateral sagittal split ramus osteotomy	2.000000e-06
GCST002201_10	Calcium levels	9.000000e-07
GCST002793_3	Vein graft stenosis in coronary artery bypass grafting	6.000000e-06
GCST003127_7	Lipoprotein (a) levels	1.000000e-09
GCST003783_5	Multiple system atrophy (pathologically confirmed)	4.000000e-06
GCST004640_5	Western dietary pattern	8.000000e-07
GCST004688_1	Psychosis proneness (perceptual aberration scale and revised physical anhedonia scale)	5.000000e-08
GCST005038_112	Allergic disease (asthma, hay fever or eczema)	1.000000e-08
GCST005912_3	Type 2 diabetes	3.000000e-06
GCST006193_96	Diastolic blood pressure x smoking status (current vs non-current) interaction (2df test)	2.000000e-08
GCST006979_716	Heel bone mineral density	3.000000e-12
GCST007096_171	Pulse pressure	4.000000e-08
GCST007097_37	Pulse pressure	7.000000e-06
GCST007204_8	Low density lipoprotein cholesterol levels	2.000000e-06
GCST007741_33	Iris color (b* coordinate)	7.000000e-06
GCST010083_186	Hemoglobin levels	1.000000e-10
GCST90002383_465	Hematocrit	3.000000e-09
GCST90002403_185	Red blood cell count	1.000000e-10

EFO canonical traits (16, from GWAS)

EFO ID	Trait name
EFO:0005194	amyloid-beta measurement
EFO:0005324	post-operative sensory disturbance
EFO:0004838	calcium measurement
EFO:0007051	vein graft stenosis
EFO:0006925	lipoprotein A measurement
EFO:0008111	diet measurement
EFO:0008337	psychosis predisposition measurement
EFO:0006336	diastolic blood pressure
EFO:0006527	smoking status measurement
EFO:0009270	heel bone mineral density
EFO:0005763	pulse pressure measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0009764	eye colour measurement
EFO:0004509	hemoglobin measurement
EFO:0004348	hematocrit
EFO:0004305	erythrocyte count

MeSH disease descriptors (20)

Descriptor	Name	Tree numbers
D061085	Agenesis of Corpus Callosum	C10.500.034; C16.131.666.034; C23.300.008
D001254	Astrocytoma	C04.557.465.625.600.380.080; C04.557.470.670.380.080; C04.557.580.625.600.380.080
D016569	Blepharophimosis	C11.250.090; C11.338.190; C16.131.384.190
D003248	Constipation	C23.888.821.150
D003456	Cryptorchidism	C12.100.500.829.258; C12.200.294.829.258; C12.200.706.258; C12.800.258; C16.131.939.258; C19.391.829.258
D004827	Epilepsy	C10.228.140.490
D006983	Hypertrichosis	C17.800.329.875
D007037	Hypothyroidism	C19.874.482
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D008527	Medulloblastoma	C04.557.465.625.600.380.515; C04.557.465.625.600.590.500; C04.557.470.670.380.515; C04.557.470.670.590.500; C04.557.580.625.600.380.515; C04.557.580.625.600.590.500
D008659	Metabolic Diseases	C18.452
D008831	Microcephaly	C05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
D065886	Neurodevelopmental Disorders	F03.625
D009456	Neurofibromatosis 1	C04.557.580.600.580.590.650; C04.700.631.650; C10.562.600.500; C10.574.500.549.400; C10.668.829.675; C16.320.400.560.400; C16.320.700.633.650
D009634	Noonan Syndrome	C05.660.207.690; C14.240.400.787; C14.280.400.787; C16.131.240.400.784; C16.131.621.207.690; C17.300.690
C562568	Cerebellar Hypoplasia (supp.)
C536436	Coffin-Siris syndrome (supp.)
C531684	Hereditary spinal ataxia (supp.)
C536116	Nicolaides Baraitser syndrome (supp.)
C536704	Wiedemann Grosse Dibbern syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	6
Valproic Acid	affects expression, decreases expression, decreases methylation	3
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, affects expression	2
Cisplatin	affects cotreatment, decreases expression	2
Ozone	increases oxidation, increases abundance, affects expression, affects cotreatment	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
dicrotophos	increases expression	1
2,4,6-tribromophenol	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
bisphenol A	decreases expression	1
trichostatin A	affects expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
tetrabromobisphenol A	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	decreases methylation	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, decreases expression	1
Arsenic Trioxide	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Vehicle Emissions	decreases expression, increases abundance	1

Cellosaurus cell lines

28 cell lines: 13 induced pluripotent stem cell, 10 cancer cell line, 3 embryonic stem cell, 2 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_1320	JVM-3	Transformed cell line	Male
CVCL_5088	SNU-739	Cancer cell line	Male
CVCL_A1SF	VOA1066	Cancer cell line	Female
CVCL_B7JK	SCLC-J1	Cancer cell line	Male
CVCL_B8BG	Abcam HCT 116 ARID1B KO	Cancer cell line	Male
CVCL_B8SK	Abcam MCF-7 ARID1B KO	Cancer cell line	Female
CVCL_B9DJ	Abcam A-549 ARID1B KO	Cancer cell line	Male
CVCL_C1WE	SDQLCHi045-A	Induced pluripotent stem cell	Female
CVCL_C8TB	CUTO-9	Cancer cell line	Male
CVCL_D0UZ	HPS2822	Induced pluripotent stem cell	Female

Clinical trials (associated diseases)

212 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
NCT01678105	PHASE2	COMPLETED	A Phase II Study of Dovitinib in Recurrent and/or Metastatic Adenoid Cystic Carcinoma of the Salivary Glands
NCT06066333	PHASE2	RECRUITING	Study of Radiotherapy and Pembrolizumab in People With Adrenocortical Carcinoma
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
NCT01898715	PHASE1	COMPLETED	Phase 1 Study of ATR-101 in Subjects With Advanced Adrenocortical Carcinoma
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
NCT01262235	PHASE1/PHASE2	COMPLETED	A Dose Finding Study of TKM-080301 Infusion in Neuroendocrine Tumors (NET) and Adrenocortical Carcinoma (ACC) Patients
NCT00170326	Not specified	COMPLETED	Progressive Ventricular Dysfunction Prevention in Pacemaker Patients
NCT01117792	Not specified	COMPLETED	Subcutaneous Implantable Defibrillator (S-ICD) System - CE Clinical Investigation
NCT02267161	Not specified	COMPLETED	Infants With Agenesis of the Corpus Callosum
NCT02826824	Not specified	UNKNOWN	BECOME CHILDREN OF HOLDERS Corpus Callosum Agenesis Screened IN PERIOD Antenatal
NCT05843110	Not specified	UNKNOWN	Decision-making Process of Couples Confronted With Prenatal Diagnosis of an Isolated CCA
NCT06262152	Not specified	UNKNOWN	Sleep Profile of Patients With Septo-optic Dysplasia
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