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

Summary

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

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma.
Title: Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma.
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	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 EBI GWAS CatalogPubMed
Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SHGC-78670 (e-PCR)
- UniSTS:101965

MARC_21821-21822:1025098890:1 (e-PCR)
- UniSTS:268639

G33057 (e-PCR)
- UniSTS:117633

WI-14321 (e-PCR)
- UniSTS:76196

WI-16568 (e-PCR)
- UniSTS:74917

G54245 (e-PCR)
- UniSTS:109512

G54246 (e-PCR)
- UniSTS:109513

G54248 (e-PCR)
- UniSTS:109515

ARID2_3730 (e-PCR)
- UniSTS:462036

A010A40 (e-PCR)
- UniSTS:62939

G54266 (e-PCR)
- UniSTS:109533

WI-13379 (e-PCR)
- UniSTS:83427

RH69395 (e-PCR)
- UniSTS:9463

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

NG_052800.1 RefSeqGene

Range

5042..183373

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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