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

    Gene ID: 196528, updated on 7-Apr-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
    mouse all
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    Genomic context

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    Location:
    12q12
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (45729706..45908037)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (45688334..45867621)
    105.20220307 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. ARID2, a rare cause of Coffin-Siris syndrome: A novel microdeletion at 12q12q13.11 causing severe short stature and literature review. Xia D, et al. Am J Med Genet A, 2023 May. PMID 36756859
    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. Association between ARID2 and RAS-MAPK pathway in intellectual disability and short stature. Kang E, et al. J Med Genet, 2021 Nov. PMID 33051312
    5. Extending the clinical and genetic spectrum of ARID2 related intellectual disability. A case series of 7 patients. Gazdagh G, et al. Eur J Med Genet, 2019 Jan. PMID 29698805

    See all (118) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma.
      Title: Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma.
    8. 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.
    9. Association between ARID2 and RAS-MAPK pathway in intellectual disability and short stature.
      Title: Association between ARID2 and RAS-MAPK pathway in intellectual disability and short stature.
    10. ARID2 Deficiency Correlates with the Response to Immune Checkpoint Blockade in Melanoma.
      Title: ARID2 Deficiency Correlates with the Response to Immune Checkpoint Blockade in Melanoma.
    Submit: New GeneRIF Correction See all GeneRIFs (34)

    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
    		Compare labs

    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)

    Genotypes

    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 IEA
    Inferred from Electronic Annotation
    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 
    part_of 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
    		  
    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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    NEW Try the new Transcript table

    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_2023_10

    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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