ARID2

AT-rich interaction domain 2, the group of AT-rich interaction domain containing|PBAF complex|Armadillo like helical domain containing

Basic information

Region (hg38): 12:45729706-45908040

Links

ENSG00000189079NCBI:196528OMIM:609539HGNC:18037Uniprot:Q68CP9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Coffin-Siris syndrome (Strong), mode of inheritance: AD
  • Coffin-Siris syndrome (Supportive), mode of inheritance: AD
  • Coffin-Siris syndrome 6 (Strong), mode of inheritance: AD
  • Coffin-Siris syndrome (Definitive), mode of inheritance: AD
  • Coffin-Siris syndrome 6 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Coffin-Siris syndrome 6ADGeneralGenetic 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; Musculoskeletal; Neurologic26238514; 28124119; 28884947

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARID2 gene.

  • not_provided (204 variants)
  • Inborn_genetic_diseases (148 variants)
  • Coffin-Siris_syndrome_6 (109 variants)
  • ARID2-related_disorder (34 variants)
  • not_specified (31 variants)
  • ARID2-related_BAFopathy (8 variants)
  • See_cases (4 variants)
  • Coffin-Siris_syndrome (4 variants)
  • Neurodevelopmental_disorder (2 variants)
  • Dystonia,_early-onset,_and/or_spastic_paraplegia (1 variants)
  • Autism_spectrum_disorder (1 variants)
  • Castleman-Kojima_disease (1 variants)
  • Neurodevelopmental_delay (1 variants)
  • Desmoplastic/nodular_medulloblastoma (1 variants)
  • Microcephaly (1 variants)
  • Chronic_diarrhea (1 variants)
  • Neurodevelopmental_abnormality (1 variants)
  • Developmental_disorder (1 variants)
  • Coffin-Siris_syndrome_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152641.4. 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
3
clinvar
44
clinvar
6
clinvar
53
missense
1
clinvar
3
clinvar
243
clinvar
64
clinvar
8
clinvar
319
nonsense
17
clinvar
10
clinvar
2
clinvar
29
start loss
0
frameshift
44
clinvar
13
clinvar
4
clinvar
61
splice donor/acceptor (+/-2bp)
3
clinvar
7
clinvar
1
clinvar
11
Total 65 33 253 108 14

Highest pathogenic variant AF is 0.00000123914

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ARID2protein_codingprotein_codingENST00000334344 21178376
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.002.17e-11125692041256960.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.737209580.7520.000047511887
Missense in Polyphen208392.520.529914876
Synonymous-1.893863411.130.00001783767
Loss of Function8.00380.40.03730.00000394932

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00002650.0000264
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). Required for the stability of the SWI/SNF chromatin remodeling complex SWI/SNF-B (PBAF). May be involved in targeting the complex to different genes. May be involved in regulating transcriptional activation of cardiac genes. {ECO:0000269|PubMed:16782067, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.;
Disease
DISEASE: Coffin-Siris syndrome 6 (CSS6) [MIM:617808]: 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. CSS6 inheritance is autosomal dominant. {ECO:0000269|PubMed:26238514, ECO:0000269|PubMed:28124119, ECO:0000269|PubMed:28884947}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Hepatocellular carcinoma - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;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
0.102

Intolerance Scores

loftool
0.259
rvis_EVS
-1.76
rvis_percentile_EVS
2.33

Haploinsufficiency Scores

pHI
0.530
hipred
Y
hipred_score
0.775
ghis
0.648

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.485

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Arid2
Phenotype
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); 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); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype;

Gene ontology

Biological process
heart morphogenesis;nucleosome disassembly;regulation of transcription by RNA polymerase II;negative regulation of cell population proliferation;negative regulation of cell migration;homeostatic process;embryonic organ development;cardiac muscle cell proliferation;coronary artery morphogenesis
Cellular component
nucleoplasm;plasma membrane
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding