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): 12:45729705-45908040

Links

ENSG00000189079 ∙ NCBI:196528 ∙ OMIM:609539 ∙ HGNC:18037 ∙ Uniprot:Q68CP9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the ARID2 gene.

• not provided (147 variants)
• Coffin-Siris syndrome 6 (74 variants)
• Inborn genetic diseases (50 variants)
• not specified (24 variants)
• ARID2-related BAFopathy (8 variants)
• ARID2-related condition (6 variants)
• See cases (4 variants)
• Neurodevelopmental disorder (2 variants)
• Chronic diarrhea (1 variants)
• Developmental disorder (1 variants)
• Microcephaly (1 variants)
• Neurodevelopmental delay (1 variants)
• Autism spectrum disorder (1 variants)
• Desmoplastic/nodular medulloblastoma (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	32	7	40
missense		2	110	32	11	155
nonsense	14	7				21
start loss						0
frameshift	31	9				40
inframe indel			1			1
splice donor/acceptor (+/-2bp)	3	6				9
splice region			3	4		7
non coding		1			7	8
Total	48	25	112	64	25

Highest pathogenic variant AF is 0.00000657

Variants in ARID2

This is a list of pathogenic ClinVar variants found in the ARID2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-45729823-C-G			Benign (May 20, 2021)
12-45729843-A-C		Coffin-Siris syndrome 6	Uncertain significance (Jul 12, 2019)
12-45729852-G-C			Uncertain significance (Apr 01, 2024)
12-45729858-G-T		ARID2-related disorder	Uncertain significance (Jul 13, 2023)
12-45729864-C-A		not specified • Microcephaly	Likely benign (Dec 01, 2023)
12-45729906-C-T			Uncertain significance (May 01, 2023)
12-45729925-G-C			Uncertain significance (Feb 01, 2024)
12-45729935-G-A			Likely benign (Jul 16, 2018)
12-45730053-T-TA		Coffin-Siris syndrome 6	Likely pathogenic (Sep 24, 2021)
12-45730061-T-G			Uncertain significance (Sep 12, 2022)
12-45730067-C-CG		Coffin-Siris syndrome 6	Pathogenic (Jan 01, 2021)
12-45730071-G-T			Likely benign (Mar 01, 2024)
12-45730072-G-C		Coffin-Siris syndrome 6	Uncertain significance (Nov 09, 2020)
12-45730075-G-C			Uncertain significance (Mar 16, 2022)
12-45730076-G-A		Inborn genetic diseases	Uncertain significance (Nov 07, 2022)
12-45730105-AC-A		Coffin-Siris syndrome 6	Pathogenic (Dec 13, 2017)
12-45730106-CCA-C		ARID2-related BAFopathy	Pathogenic (Jun 10, 2021)
12-45730113-C-G			Likely benign (Mar 01, 2023)
12-45730115-CTACTT-C		Inborn genetic diseases	Pathogenic (Jun 26, 2023)
12-45730131-C-T		Coffin-Siris syndrome 6	Benign/Likely benign (Feb 25, 2022)
12-45730137-G-C		Coffin-Siris syndrome 6	Uncertain significance (Sep 08, 2021)
12-45731213-C-T		Inborn genetic diseases	Likely benign (Aug 08, 2023)
12-45731257-T-G		not specified	not provided (Sep 19, 2013)
12-45731276-T-G			Uncertain significance (Jun 01, 2020)
12-45731314-G-A			Uncertain significance (Dec 15, 2019)

GnomAD

Source: gnomAD

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: 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

	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