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

ENSG00000049618NCBI:57492OMIM:614556HGNC:18040Uniprot:Q8NFD5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Coffin-Siris syndrome 1ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Dermatologic; Musculoskeletal; Neurologic22405089; 22426308; 22426309

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARID1B gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
3
clinvar
12
clinvar
409
clinvar
41
clinvar
467
missense
14
clinvar
24
clinvar
681
clinvar
329
clinvar
41
clinvar
1089
nonsense
135
clinvar
35
clinvar
3
clinvar
173
start loss
0
frameshift
243
clinvar
77
clinvar
10
clinvar
330
splice donor/acceptor (+/-2bp)
20
clinvar
15
clinvar
4
clinvar
1
clinvar
40
Total 414 154 710 739 82

Highest pathogenic variant AF is 0.000030956573

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ARID1Bprotein_codingprotein_codingENST00000346085 20432851
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.003.04e-12125742061257480.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.599611.21e+30.7910.000070814685
Missense in Polyphen429629.590.68147099
Synonymous-0.1205075041.010.00003494450
Loss of Function8.41490.10.04440.00000481980

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006260.0000626
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00005290.0000352
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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