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ARID2 AT-rich interaction domain 2 [ Homo sapiens (human) ]

Gene ID: 196528, updated on 27-Nov-2024

Summary

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Official Symbol
ARID2provided by HGNC
Official Full Name
AT-rich interaction domain 2provided by HGNC
Primary source
HGNC:HGNC:18037
See related
Ensembl:ENSG00000189079 MIM:609539; AllianceGenome:HGNC:18037
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CSS6; p200; BAF200; ZIPZAP; SMARCF3
Summary
This gene encodes a member of the AT-rich interactive domain (ARID)-containing family of DNA-binding proteins. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and chromatin structure modification. This protein functions as a subunit of the polybromo- and BRG1-associated factor or PBAF (SWI/SNF-B) chromatin remodeling complex which facilitates ligand-dependent transcriptional activation by nuclear receptors. Mutations in this gene are associated with hepatocellular carcinomas. A pseudogene of this gene is found on chromosome1. [provided by RefSeq, Dec 2016]
Expression
Broad expression in testis (RPKM 13.8), thyroid (RPKM 5.2) and 25 other tissues See more
Orthologs
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Genomic context

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See ARID2 in Genome Data Viewer
Location:
12q12
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (45729706..45908037)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (45688334..45867621)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (46123489..46301820)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369744 Neighboring gene Sharpr-MPRA regulatory region 8796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4374 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:46090484-46090652 Neighboring gene H3K27ac hESC enhancers GRCh37_chr12:46120332-46121294 and GRCh37_chr12:46121295-46122257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4376 Neighboring gene long intergenic non-protein coding RNA 938 Neighboring gene NANOG hESC enhancer GRCh37_chr12:46161969-46162913 Neighboring gene uncharacterized LOC105369745 Neighboring gene MPRA-validated peak1713 silencer Neighboring gene RNA, 7SL, cytoplasmic 246, pseudogene Neighboring gene lysine rich nucleolar protein 1 pseudogene 2 Neighboring gene SR-related CTD associated factor 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46384079-46384792 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6233 Neighboring gene ribosomal protein L13a pseudogene 21

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Confirmation of an ARID2 defect in SWI/SNF-related intellectual disability. Van Paemel R, et al. Am J Med Genet A, 2017 Nov. PMID 28884947
  2. ARID2 suppression promotes tumor progression and upregulates cytokeratin 8, 18 and β-4 integrin expression in TP53-mutated tobacco-related oral cancer and has prognostic implications. Shukla P, et al. Cancer Gene Ther, 2022 Dec. PMID 35869277
  3. Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. Carcamo S, et al. Cell Rep, 2022 Apr 5. PMID 35385731, Free PMC Article
  4. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Li M, et al. Nat Genet, 2011 Aug 7. PMID 21822264, Free PMC Article
  5. ARID2: a new tumor suppressor gene in hepatocellular carcinoma. Zhao H, et al. Oncotarget, 2011 Nov. PMID 22095441, Free PMC Article

See all (136) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Revealing the clinical impact of MTOR and ARID2 gene mutations on MALT lymphoma of the alimentary canal using targeted sequencing.
    Title: Revealing the clinical impact of MTOR and ARID2 gene mutations on MALT lymphoma of the alimentary canal using targeted sequencing.
  2. ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals.
    Title: ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals.
  3. ARID2 mutations may relay a distinct subset of cutaneous melanoma patients with different outcomes.
    Title: ARID2 mutations may relay a distinct subset of cutaneous melanoma patients with different outcomes.
  4. Coffin-Siris Syndrome: Case Series of Three Patients and a Novel ARID2 Variant.
    Title: Coffin-Siris Syndrome: Case Series of Three Patients and a Novel ARID2 Variant.
  5. miR-29a-5p regulates the malignant biological process of liver cancer cells through ARID2 regulation of EMT.
    Title: miR-29a-5p regulates the malignant biological process of liver cancer cells through ARID2 regulation of EMT.
  6. ARID2, a rare cause of Coffin-Siris syndrome: A novel microdeletion at 12q12q13.11 causing severe short stature and literature review.
    Title: ARID2, a rare cause of Coffin-Siris syndrome: A novel microdeletion at 12q12q13.11 causing severe short stature and literature review.
  7. USP2 Inhibits Lung Cancer Pathogenesis by Reducing ARID2 Protein Degradation via Ubiquitination.
    Title: USP2 Inhibits Lung Cancer Pathogenesis by Reducing ARID2 Protein Degradation via Ubiquitination.
  8. ARID2 suppression promotes tumor progression and upregulates cytokeratin 8, 18 and beta-4 integrin expression in TP53-mutated tobacco-related oral cancer and has prognostic implications.
    Title: ARID2 suppression promotes tumor progression and upregulates cytokeratin 8, 18 and β-4 integrin expression in TP53-mutated tobacco-related oral cancer and has prognostic implications.
  9. Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma.
    Title: Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma.
  10. BRD4 inhibition induces synthetic lethality in ARID2-deficient hepatocellular carcinoma by increasing DNA damage.
    Title: BRD4 inhibition induces synthetic lethality in ARID2-deficient hepatocellular carcinoma by increasing DNA damage.
Submit: New GeneRIF Correction See all GeneRIFs (36)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Coffin-Siris syndrome 6
MedGen: C4540499 OMIM: 617808 GeneReviews: Coffin-Siris Syndrome
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2019-06-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2019-06-26)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat A PBAF-specific component BAF200 is required for HIV-1 Tat-mediated activation of HIV LTR PubMed
tat Acetylated HIV-1 Tat binds efficiently to BRG1 and BAF200 (component of PBAF complex) and weakly to BAF250 (component of BAF complex) PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ30619, KIAA1557, DKFZp686G052, DKFZp779P0222

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in coronary artery morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic organ development IEA
Inferred from Electronic Annotation
more info
  
involved_in heart morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in homeostatic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cell population proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nucleosome disassembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of T cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of double-strand break repair NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of myoblast differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of G0 to G1 transition NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of G1/S transition of mitotic cell cycle NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of mitotic metaphase/anaphase transition NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of nucleotide-excision repair NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of RSC-type complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of SWI/SNF complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromatin NAS
Non-traceable Author Statement
more info
 PubMed 
located_in kinetochore NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nuclear matrix NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
AT-rich interactive domain-containing protein 2
Names
ARID domain-containing protein 2
AT rich interactive domain 2 (ARID, RFX-like)
BRG1-associated factor 200
zinc finger protein with activation potential
zipzap/p200

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_052800.1 RefSeqGene

    Range
    5042..183373
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001347839.2 → NP_001334768.1  AT-rich interactive domain-containing protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and 3' coding region compared to isoform 1. The encoded isoform (2) has a shorter C-terminus compared to isoform 1.
    Source sequence(s)
    AC008124, AC009464, CR749833
    UniProtKB/TrEMBL
    F8WCU9
    Related
    ENSP00000415650.3, ENST00000422737.7

  2. NM_152641.4 → NP_689854.2  AT-rich interactive domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_689854.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform 1.
    Source sequence(s)
    AC008124, AC009464, BX537879, DQ096628
    Consensus CDS
    CCDS31783.1
    UniProtKB/Swiss-Prot
    Q15KG9, Q5EB51, Q645I3, Q68CP9, Q6ZRY5, Q7Z3I5, Q86T28, Q96SJ6, Q9HCL5
    Related
    ENSP00000335044.6, ENST00000334344.11
    Conserved Domains (2) summary
    pfam01388
    Location:19 → 101
    ARID; ARID/BRIGHT DNA binding domain
    pfam02257
    Location:521 → 601
    RFX_DNA_binding; RFX DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    45729706..45908037
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428489.1 → XP_047284445.1  AT-rich interactive domain-containing protein 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    45688334..45867621
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371390.1 → XP_054227365.1  AT-rich interactive domain-containing protein 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q68CP9.2 GenPept UniProtKB/Swiss-Prot:Q68CP9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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