Developmental Brain Disorder Gene Database

LoF Variant Gene

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Tier

1

ARID1B

HGNC:18040 (protein-coding gene)

AT-rich interaction domain 1B

Unique Cases:
92
Disorders:
ID, ASD, EP, ADHD, BD, CP
Last Updated:
January 24, 2024

Summary
Cases
Publications
External

Gene Summary:

DBD Genes Classification
ARID1B is a High Confidence candidate gene classified as Tier 1. Tier 1 genes have three or more de novo pathogenic loss-of-function variants.
Gene 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). Durin... (Source: Uniprot)
Previous symbols
No previous symbols
Alias symbols
KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5, SMARCF2
Chromosomal Location
6q25.3
Genomic Coordinates
GRCh37:chr6:157098989-157531913
GRCh38:chr6:156776026-157210779
Associated Disorders
Intellectual Disability, Autism, Epilepsy, Attention Deficit Hyperactivity Disorder, Cerebral Palsy

Predictive Scores:

HI Score (Decipher)

14.17

pLI (gnomAD)

1.00

LOEUF (gnomAD)

0.1

Classifications from External Sources:

SFARI Score (SFARI)

1

DDG2P Classification (DDG2P)

No Classification

ClinGen Classification (ClinGen)

Definitive1

GenCC Classification (GenCC)

Definitive3 Strong2 Supportive1

Publications:

Guo H et. al., Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes., Genet Med, 2019
Alsubaie L et. al., Genomic testing and counseling: The contribution of next-generation sequencing to epilepsy genetics., Ann Hum Genet, 2020
Santen GW et. al., Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome., Nat Genet, 2012
Thevenon J et. al., Diagnostic odyssey in severe neurodevelopmental disorders: toward clinical whole-exome sequencing as a first-line diagnostic test., Clin Genet, 2016
Hoyer J et. al., Haploinsufficiency of ARID1B, a member of the SWI/SNF-a chromatin-remodeling complex, is a frequent cause of intellectual disability., Am J Hum Genet, 2012
Dillon OJ et. al., Exome sequencing has higher diagnostic yield compared to simulated disease-specific panels in children with suspected monogenic disorders., Eur J Hum Genet, 2018
Ji J et. al., A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants., Cold Spring Harb Mol Case Stud, 2019
Trujillano D et. al., Clinical exome sequencing: results from 2819 samples reflecting 1000 families., Eur J Hum Genet, 2017
Deciphering Developmental Disorders Study. et. al., Large-scale discovery of novel genetic causes of developmental disorders., Nature, 2015
Coe BP et. al., Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity., Nat Genet, 2019
Ben-Salem S et. al., Gonadal mosaicism in ARID1B gene causes intellectual disability and dysmorphic features in three siblings., Am J Med Genet A, 2016
O'Roak BJ et. al., Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations., Nature, 2012
Coe BP et. al., Refining analyses of copy number variation identifies specific genes associated with developmental delay., Nat Genet, 2014
Wieczorek D et. al., A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling., Hum Mol Genet, 2013
Guo H et. al., Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model., Mol Autism, 2018
Chérot E et. al., Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients., Clin Genet, 2018
Halgren C et. al., Corpus callosum abnormalities, intellectual disability, speech impairment, and autism in patients with haploinsufficiency of ARID1B., Clin Genet, 2012
Wang T et. al., De novo genic mutations among a Chinese autism spectrum disorder cohort., Nat Commun, 2016
Beighley JS et. al., Clinical Phenotypes of Carriers of Mutations in CHD8 or Its Conserved Target Genes., Biol Psychiatry, 2020
Grozeva D et. al., Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability., Hum Mutat, 2015
Vals MA et. al., Coffin-Siris Syndrome with obesity, macrocephaly, hepatomegaly and hyperinsulinism caused by a mutation in the ARID1B gene., Eur J Hum Genet, 2014
Sweeney NM et. al., The case for early use of rapid whole-genome sequencing in management of critically ill infants: late diagnosis of Coffin-Siris syndrome in an infant with left congenital diaphragmatic hernia, congenital heart disease, and recurrent infections., Cold Spring Harb Mol Case Stud, 2018
Pranckėnienė L et. al., De novo splice site variant of ARID1B associated with pathogenesis of Coffin-Siris syndrome., Mol Genet Genomic Med, 2019
Natsume T et. al., Hepatomegaly in a boy with ARID1B-related Coffin-Siris syndrome., Pediatr Int, 2018
Melo Gomes S et. al., Inflammatory Arthritis as a Possible Feature of Coffin-Siris Syndrome., Pediatrics, 2019
Iglesias A et. al., The usefulness of whole-exome sequencing in routine clinical practice., Genet Med, 2014
Lu G et. al., Identification of de novo mutations for ARID1B haploinsufficiency associated with Coffin-Siris syndrome 1 in three Chinese families via array-CGH and whole exome sequencing., BMC Med Genomics, 2021
Jiang T et. al., Application of Trio-Whole Exome Sequencing in Genetic Diagnosis and Therapy in Chinese Children With Epilepsy., Front Mol Neurosci, 2021
Nishioka M et. al., Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder., Nat Commun, 2021
Moreno-De-Luca A et. al., Molecular Diagnostic Yield of Exome Sequencing in Patients With Cerebral Palsy., JAMA, 2021
Hiraide T et. al., Genetic and phenotypic analysis of 101 patients with developmental delay or intellectual disability using whole-exome sequencing., Clin Genet, 2021

NCBI: Gene

Integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
NCBI: Gene

Gene Reviews

An international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families.
Gene Reviews

DECIPHER

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient.
DECIPHER

SFARI

SFARI Gene is an evolving online database designed to permit quick entrée into the genetics of autism, and to help researchers track the ever-expanding genetic risk factors that emerge in the literature.
SFARI

ClinGen

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.
ClinGen

GenCC

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases.
GenCC

gnomAD

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
gnomAD
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