ARID2
Basic information
Region (hg38): 12:45729706-45908040
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Coffin-Siris syndrome 6 | 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; Musculoskeletal; Neurologic | 26238514; 28124119; 28884947 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 44 | 53 | ||||
missense | 243 | 64 | 319 | |||
nonsense | 17 | 10 | 29 | |||
start loss | 0 | |||||
frameshift | 44 | 13 | 61 | |||
splice donor/acceptor (+/-2bp) | 11 | |||||
Total | 65 | 33 | 253 | 108 | 14 |
Highest pathogenic variant AF is 0.00000123914
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ARID2 | protein_coding | protein_coding | ENST00000334344 | 21 | 178376 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 2.17e-11 | 125692 | 0 | 4 | 125696 | 0.0000159 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.73 | 720 | 958 | 0.752 | 0.0000475 | 11887 |
Missense in Polyphen | 208 | 392.52 | 0.52991 | 4876 | ||
Synonymous | -1.89 | 386 | 341 | 1.13 | 0.0000178 | 3767 |
Loss of Function | 8.00 | 3 | 80.4 | 0.0373 | 0.00000394 | 932 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000265 | 0.0000264 |
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). 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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