ARID1B
AT-rich interaction domain 1B, the group of Armadillo like helical domain containing|AT-rich interaction domain containing|BAF complex
Basic information
Region (hg38): 6:156776020-157210779
Links
Phenotypes
GenCC
Source:
- Coffin-Siris syndrome (Definitive), mode of inheritance: AD
- Coffin-Siris syndrome 1 (Definitive), mode of inheritance: AD
- Coffin-Siris syndrome 1 (Strong), mode of inheritance: AD
- Coffin-Siris syndrome 1 (Strong), mode of inheritance: AD
- Coffin-Siris syndrome (Supportive), mode of inheritance: AD
- Coffin-Siris syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Coffin-Siris syndrome 1 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Dermatologic; Musculoskeletal; Neurologic | 22405089; 22426308; 22426309 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (1803 variants)
- Inborn_genetic_diseases (569 variants)
- Coffin-Siris_syndrome_1 (469 variants)
- ARID1B-related_disorder (216 variants)
- not_specified (160 variants)
- ARID1B-related_BAFopathy (47 variants)
- Intellectual_disability (28 variants)
- Coffin-Siris_syndrome (20 variants)
- See_cases (9 variants)
- Long_eyelashes (4 variants)
- Blepharophimosis (4 variants)
- Thin_upper_lip_vermilion (4 variants)
- Intellectual_disability,_moderate (4 variants)
- Coffin_Siris/Intellectual_Disability (4 variants)
- Thick_lower_lip_vermilion (4 variants)
- Global_developmental_delay (4 variants)
- Absent_speech (4 variants)
- Severe_combined_immunodeficiency_due_to_DCLRE1C_deficiency (3 variants)
- Corpus_callosum,_agenesis_of (2 variants)
- Autism_spectrum_disorder (2 variants)
- Microcephaly (2 variants)
- Hypertrichosis (2 variants)
- Neurodevelopmental_disorder (2 variants)
- Neurodevelopmental_delay (2 variants)
- Marfanoid_habitus_and_intellectual_disability (2 variants)
- Developmental_disorder (2 variants)
- dysmorphy (1 variants)
- Pituitary_stalk_interruption_syndrome (1 variants)
- Abnormal_speech_pattern (1 variants)
- Delayed_speech_and_language_development (1 variants)
- Rare_genetic_intellectual_disability (1 variants)
- Nicolaides-Baraitser_syndrome (1 variants)
- Neonatal_hypotonia (1 variants)
- Seizure (1 variants)
- Constipation (1 variants)
- Hirsutism (1 variants)
- Noonan_syndrome (1 variants)
- Short_stature (1 variants)
- Medulloblastoma (1 variants)
- Wiedemann-Steiner_syndrome (1 variants)
- intellectual_deficiency (1 variants)
- Decreased_body_weight (1 variants)
- Epilepsy (1 variants)
- Schizophrenia (1 variants)
- Bilateral_cryptorchidism (1 variants)
- Recurrent_respiratory_infections (1 variants)
- Hereditary_ataxia (1 variants)
- Metabolic_disease (1 variants)
- Neurodevelopmental_abnormality (1 variants)
- Nail_dysplasia (1 variants)
- Astrocytoma (1 variants)
- Neurofibromatosis,_type_1 (1 variants)
- Congenital_cerebellar_hypoplasia (1 variants)
- Failure_to_thrive (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_001374828.1. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 12 | 409 | 41 | 467 | ||
| missense | 14 | 24 | 681 | 329 | 41 | 1089 |
| nonsense | 135 | 35 | 173 | |||
| start loss | 0 | |||||
| frameshift | 243 | 77 | 10 | 330 | ||
| splice donor/acceptor (+/-2bp) | 20 | 15 | 40 | |||
| Total | 414 | 154 | 710 | 739 | 82 |
Highest pathogenic variant AF is 0.000030956573
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARID1B | protein_coding | protein_coding | ENST00000346085 | 20 | 432851 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 3.04e-12 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.59 | 961 | 1.21e+3 | 0.791 | 0.0000708 | 14685 |
| Missense in Polyphen | 429 | 629.59 | 0.6814 | 7099 | ||
| Synonymous | -0.120 | 507 | 504 | 1.01 | 0.0000349 | 4450 |
| Loss of Function | 8.41 | 4 | 90.1 | 0.0444 | 0.00000481 | 980 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000626 | 0.0000626 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000529 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- 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 (By similarity). Binds DNA non-specifically (PubMed:14982958, PubMed:15170388). {ECO:0000250|UniProtKB:E9Q4N7, ECO:0000269|PubMed:14982958, ECO:0000269|PubMed:15170388, ECO:0000303|PubMed:12672490, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.;
- Disease
- DISEASE: 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. {ECO:0000269|PubMed:22405089, ECO:0000269|PubMed:22426308, ECO:0000269|PubMed:22426309}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Thermogenesis - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Androgen Receptor Network in Prostate Cancer;Tumor suppressor activity of SMARCB1;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;RNA Polymerase II Transcription;RMTs methylate histone arginines;Chromatin modifying enzymes;Chromatin organization;Transcriptional regulation by RUNX1
(Consensus)
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- loftool
- 0.343
- rvis_EVS
- -2.62
- rvis_percentile_EVS
- 0.8
Haploinsufficiency Scores
- pHI
- 0.152
- hipred
- Y
- hipred_score
- 0.646
- ghis
- 0.651
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.736
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arid1b
- Phenotype
- renal/urinary system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- chromatin remodeling;regulation of transcription by RNA polymerase II;nervous system development;chromatin-mediated maintenance of transcription
- Cellular component
- nucleoplasm;cytosol;plasma membrane;SWI/SNF complex;nBAF complex
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;transcription coactivator activity;protein binding