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ARID1A (AT rich interactive domain 1A (SWI-like))

Written2013-11Yohan Suryo Rahmanto, Tian-Li Wang
Departments of Gynecology/Obstetrics, Oncology Johns Hopkins Medical Institutions CRBII, Rm: 306, 1550 Orleans Street Baltimore, MD 21231, USA

(Note : for Links provided by Atlas : click)


Alias (NCBI)B120
HGNC Alias symbB120
HGNC Previous nameC1orf4
HGNC Previous nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1
 AT rich interactive domain 1A (SWI- like)
 AT rich interactive domain 1A (SWI-like)
LocusID (NCBI) 8289
Atlas_Id 44231
Location 1p36.11  [Link to chromosome band 1p36]
Location_base_pair Starts at 26696015 and ends at 26782104 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping ARID1A.png]
Local_order Gene orientation: telomere-3' ARID1A 5'-centromere.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ARID1A (1p36.11)::ARID1A (1p36.11)ARID1A (1p36.11)::BEND5 (1p33)ARID1A (1p36.11)::MAST2 (1p34.1)
ARID1A (1p36.11)::NIPBL (5p13.2)ARID1A (1p36.11)::PRKD1 (14q12)ARID1A (1p36.11)::RNF31 (14q12)
ARID1A (1p36.11)::RPS6KA1 (1p36.11)ARID1A (1p36.11)::SEC11A (15q25.2)ARID1A (1p36.11)::SEC11A (15q25.3)
ARID1A (1p36.11)::TFPI (2q32.1)ARID1A (1p36.11)::THBS3 (1q22)ARID1A (1p36.11)::WDTC1 (1p36.11)
ARID1A (1p36.11)::YTHDF2 (1p35.3)C1QC (1p36.12)::ARID1A (1p36.11)CIZ1 (9q34.11)::ARID1A (1p36.11)
DNAJA2 (16q11.2)::ARID1A (1p36.11)SLC15A4 (12q24.32)::ARID1A (1p36.11)TFPI (2q32.1)::ARID1A (1p36.11)
UACA (15q23)::ARID1A (1p36.11)


  DNA organization of ARID1A.
Description ARID1A gene is encoded by 20 exons spanning 86,08 Mb.
Transcription Human ARID1A has 2 transcript variants. The long variant (isoform 1) transcribed into 8585 bp mRNA, the coding sequence is from 374 bp - 7231 bp. The short variant (isoform 2) transcribed into 7934 bp mRNA, the coding sequence is from 374 bp - 6580 bp. Isoform 2 has a shorter exon 18 compared to isoform 1.


Note The longer isoform of ARID1A consists of 2285 amino acids (pI: 6.24), with predicted molecular mass of 242,04 kDa. The shorter isoform of ARID1A consists of 2068 amino acids (pI: 6.08), with predicted molecular mass of 218,33 kDa. Both isoforms contain a single "ARID" DNA binding domain and four "LXXLL" nuclear receptor coactivator motifs.
  ARID1A protein.
Description ARID1A is a member of the SWI/SNF family that can regulate genes transcription by chromatin structure alteration through its helicase and ATPase activities. The encoded ARID1A nuclear protein is part of the BRG/BRM chromatin remodeling complex that has been shown to play an integral role in controlling gene expression.
Expression Ubiquitously expressed in various normal tissues, with the highest expression seen in brain, blood and female tissues.
Localisation Mainly located at cell nucleus but not at nucleolus.
Function ARID1A contains a conserved DNA-binding domain (ARID) that could be important for its function and can specifically bind an AT-rich DNA sequence. ARID1A is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes. Changes in this SNF/SWI complex has been implicated in many cellular processes, including development, differentiation, proliferation, DNA repair, and tumor suppression.
ARID1A has been reported to act as tumor suppressor in gynecological cancers (Guan et al., 2011b). Molecular studies using over-expression and RNAi silencing models have demonstrated that ARID1A negatively regulates cellular proliferation and tumorigenicity. This negative regulation is achieved through molecular collaboration between ARID1A/BRG1 and p53, to regulate tumor-inhibiting p53-downstream target genes such as CDKN1A and SMAD3. Using mutational studies, Guan et al. (2012) have further confirmed ARID1A role as tumor suppressor, with all of the in-frame indel mutants have lost their ability to inhibit cellular proliferation.


Germinal ARID1A mutations have been implicated in Coffin-Siris syndrome, a rare genetic disorder that causes developmental delay and abnormities in 5th fingers or toes (Tsurusaki et al., 2012; Santen et al., 2013; Wieczorek et al., 2013).
Somatic ARID1A is located at chromosome 1p that is frequently deleted in tumours. ARID1A sequence mutations, deletions, and rearrangements were identified in ovarian, kidney, breast, lung, pancreatic and stomach cancer.

Implicated in

Entity Ovarian clear cell carcinoma
Oncogenesis ARID1A somatic mutations were identified in 57% of the 42 ovarian clear cell carcinomas (Jones et al., 2010). Maeda et al. (2010) has demonstrated that ARID1a genetic mutations resulted in loss of ARID1A protein expression in 59% of the 149 ovarian clear cell carcinomas.
Study with a larger cohort of 210 patient samples has also demonstrated that ARID1A somatic mutation were found in 46% of patients with ovarian clear-cell carcinoma and 30% of patients ovarian endometrioid carcinoma (Wiegand et al., 2010).
ARID1A inactivation by ARID1A mutations has been suggested as an early molecular event that can lead to tumor progression from benign ovarian endometroid cysts into an aggressive ovarian clear cell and endometrioid carcinoma (Ayhan et al., 2012).
Entity Uterine endometroid carcinoma
Oncogenesis ARID1A mutations were observed in 40% of uterine endometrioid carcinoma with none presented in uterine serous carcinomas (Guan et al., 2011a). All of the mutations in endometrioid carcinomas were the nonsense or insertion/deletion types (Guan et al., 2011a) and expected to result in complete loss or clonal loss of ARID1A expression. Immunostaining confirmed the relatively significant frequency of loss of ARID1A protein expression with 25-26% and 44% in uterine low-grade and high-grade endometrioid carcinomas, respectively (Guan et al., 2011a; Werner et al., 2013; Mao et al., 2013). Hence, mutation-related loss of ARID1A expression has also been hypothesized as an early event and played an important role in tumor progression of uterine endometrioid carcinoma (Ayhan et al., 2012; Werner et al., 2013; Mao et al., 2013).
Entity Cervical cancer
Oncogenesis Loss of ARID1A protein expression was observed in 31% (14/45) of cervical adenocarcinomas/adenosquamous carcinomas with no correlation to any clinicopathological features (Katagiri et al., 2012). Later studies using a large series of cervical cancer tissue specimens, ARID1A expression was found to be significantly decreased in cervical cancer tissues than in non-adjacent normal cervical epithelial tissues (Cho et al., 2013). The decrease of ARID1A expression was also found to be associated with transition from normal cells to cervical carcinoma and a more aggressive tumor phenotype (Cho et al., 2013). Overall survival was also found to be reduced in cervical cancer patients with loss of ARID1A (Cho et al., 2013).
Entity Breast cancer
Oncogenesis Low ARID1A expression was observed in 56% (63/112) of the breast cancers samples and was significantly associated with advanced tumor stage, higher P53 expression, increase Ki-67 and triple negative (ER-/PR-/Her-2-) molecular subtype (Zhang et al., 2012; Mamo et al., 2012). Low ARID1A expression was a predictor of poor overall survival of breast cancer patients (Zhang et al., 2012; Mamo et al., 2012). Breast cancer also exhibited a low rate (3-4%) of ARID1A mutations (Jones et al., 2010; Cornen et al., 2012).
Entity Gastric cancer
Oncogenesis Inactivating mutation of ARID1A has also been identified gastric cancer (Wang et al., 2011; Abe et al., 2012; Zhang et al., 2012). Loss of ARID1A expression has been correlated with increasing depth of tumor infiltration, higher tumor grade, and poor overall patient survival (Abe et al., 2012; Wang et al., 2012). Moreover, ARID1A expression has been shown as an independent prognostic factor of overall survival in multiple studies (Abe et al., 2012; Wang et al., 2012).
Entity Coffin-Siris syndrome
Prognosis Hepatoblastoma and multiple congenital anomalies.
Oncogenesis ARID1A mutations in individual with Coffin-Siris syndrome lead to a truncation and nonfunctional ARID1A protein (Tsurusaki et al., 2012; Santen et al., 2013; Wieczorek et al., 2013). As a result, affected individuals developed abnormalities, such as missing the fifth fingers or toes and coarse characteristic of facial features. Moreover, cancer was not detected in any of the individual with ARID1A mutation, reported in this study.


ARID1A expression loss in gastric cancer: pathway-dependent roles with and without Epstein-Barr virus infection and microsatellite instability.
Abe H, Maeda D, Hino R, Otake Y, Isogai M, Ushiku AS, Matsusaka K, Kunita A, Ushiku T, Uozaki H, Tateishi Y, Hishima T, Iwasaki Y, Ishikawa S, Fukayama M.
Virchows Arch. 2012 Oct;461(4):367-77. doi: 10.1007/s00428-012-1303-2. Epub 2012 Aug 23.
PMID 22915242
Loss of ARID1A expression is an early molecular event in tumor progression from ovarian endometriotic cyst to clear cell and endometrioid carcinoma.
Ayhan A, Mao TL, Seckin T, Wu CH, Guan B, Ogawa H, Futagami M, Mizukami H, Yokoyama Y, Kurman RJ, Shih IeM.
Int J Gynecol Cancer. 2012 Oct;22(8):1310-5.
PMID 22976498
Loss of ARID1A/BAF250a expression is linked to tumor progression and adverse prognosis in cervical cancer.
Cho H, Kim JS, Chung H, Perry C, Lee H, Kim JH.
Hum Pathol. 2013 Jul;44(7):1365-74. doi: 10.1016/j.humpath.2012.11.007. Epub 2013 Feb 18.
PMID 23427874
Mutations and deletions of ARID1A in breast tumors.
Cornen S, Adelaide J, Bertucci F, Finetti P, Guille A, Birnbaum DJ, Birnbaum D, Chaffanet M.
Oncogene. 2012 Sep 20;31(38):4255-6. doi: 10.1038/onc.2011.598. Epub 2012 Jan 16.
PMID 22249247
Functional analysis of in-frame indel ARID1A mutations reveals new regulatory mechanisms of its tumor suppressor functions.
Guan B, Gao M, Wu CH, Wang TL, Shih IeM.
Neoplasia. 2012 Oct;14(10):986-93.
PMID 23097632
Mutation and loss of expression of ARID1A in uterine low-grade endometrioid carcinoma.
Guan B, Mao TL, Panuganti PK, Kuhn E, Kurman RJ, Maeda D, Chen E, Jeng YM, Wang TL, Shih IeM.
Am J Surg Pathol. 2011a May;35(5):625-32. doi: 10.1097/PAS.0b013e318212782a.
PMID 21412130
ARID1A, a factor that promotes formation of SWI/SNF-mediated chromatin remodeling, is a tumor suppressor in gynecologic cancers.
Guan B, Wang TL, Shih IeM.
Cancer Res. 2011b Nov 1;71(21):6718-27. doi: 10.1158/0008-5472.CAN-11-1562. Epub 2011 Sep 7.
PMID 21900401
Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma.
Jones S, Wang TL, Shih IeM, Mao TL, Nakayama K, Roden R, Glas R, Slamon D, Diaz LA Jr, Vogelstein B, Kinzler KW, Velculescu VE, Papadopoulos N.
Science. 2010 Oct 8;330(6001):228-31. doi: 10.1126/science.1196333. Epub 2010 Sep 8.
PMID 20826764
Frequent loss of tumor suppressor ARID1A protein expression in adenocarcinomas/adenosquamous carcinomas of the uterine cervix.
Katagiri A, Nakayama K, Rahman MT, Rahman M, Katagiri H, Ishikawa M, Ishibashi T, Iida K, Otsuki Y, Nakayama S, Miyazaki K.
Int J Gynecol Cancer. 2012 Feb;22(2):208-12. doi: 10.1097/IGC.0b013e3182313d78.
PMID 22274316
Clinicopathological Significance of Loss of ARID1A Immunoreactivity in Ovarian Clear Cell Carcinoma.
Maeda D, Mao TL, Fukayama M, Nakagawa S, Yano T, Taketani Y, Shih IeM.
Int J Mol Sci. 2010;11(12):5120-8. doi: 10.3390/ijms11125120. Epub 2010 Dec 13.
PMID 21614196
An integrated genomic approach identifies ARID1A as a candidate tumor-suppressor gene in breast cancer.
Mamo A, Cavallone L, Tuzmen S, Chabot C, Ferrario C, Hassan S, Edgren H, Kallioniemi O, Aleynikova O, Przybytkowski E, Malcolm K, Mousses S, Tonin PN, Basik M.
Oncogene. 2012 Apr 19;31(16):2090-100. doi: 10.1038/onc.2011.386. Epub 2011 Sep 5.
PMID 21892209
Loss of ARID1A expression correlates with stages of tumor progression in uterine endometrioid carcinoma.
Mao TL, Ardighieri L, Ayhan A, Kuo KT, Wu CH, Wang TL, Shih IeM.
Am J Surg Pathol. 2013 Sep;37(9):1342-8. doi: 10.1097/PAS.0b013e3182889dc3.
PMID 24076775
Coffin-Siris syndrome and the BAF complex: genotype-phenotype study in 63 patients.
Santen GW, Aten E, Vulto-van Silfhout AT, Pottinger C, van Bon BW, van Minderhout IJ, Snowdowne R, van der Lans CA, Boogaard M, Linssen MM, Vijfhuizen L, van der Wielen MJ, Vollebregt MJ; Coffin-Siris consortium, Breuning MH, Kriek M, van Haeringen A, den Dunnen JT, Hoischen A, Clayton-Smith J, de Vries BB, Hennekam RC, van Belzen MJ.
Hum Mutat. 2013 Nov;34(11):1519-28. doi: 10.1002/humu.22394. Epub 2013 Aug 30.
PMID 23929686
Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome.
Tsurusaki Y, Okamoto N, Ohashi H, Kosho T, Imai Y, Hibi-Ko Y, Kaname T, Naritomi K, Kawame H, Wakui K, Fukushima Y, Homma T, Kato M, Hiraki Y, Yamagata T, Yano S, Mizuno S, Sakazume S, Ishii T, Nagai T, Shiina M, Ogata K, Ohta T, Niikawa N, Miyatake S, Okada I, Mizuguchi T, Doi H, Saitsu H, Miyake N, Matsumoto N.
Nat Genet. 2012 Mar 18;44(4):376-8. doi: 10.1038/ng.2219.
PMID 22426308
Decreased expression of the ARID1A gene is associated with poor prognosis in primary gastric cancer.
Wang DD, Chen YB, Pan K, Wang W, Chen SP, Chen JG, Zhao JJ, Lv L, Pan QZ, Li YQ, Wang QJ, Huang LX, Ke ML, He J, Xia JC.
PLoS One. 2012;7(7):e40364. doi: 10.1371/journal.pone.0040364. Epub 2012 Jul 13.
PMID 22808142
Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer.
Wang K, Kan J, Yuen ST, Shi ST, Chu KM, Law S, Chan TL, Kan Z, Chan AS, Tsui WY, Lee SP, Ho SL, Chan AK, Cheng GH, Roberts PC, Rejto PA, Gibson NW, Pocalyko DJ, Mao M, Xu J, Leung SY.
Nat Genet. 2011 Oct 30;43(12):1219-23. doi: 10.1038/ng.982.
PMID 22037554
ARID1A loss is prevalent in endometrial hyperplasia with atypia and low-grade endometrioid carcinomas.
Werner HM, Berg A, Wik E, Birkeland E, Krakstad C, Kusonmano K, Petersen K, Kalland KH, Oyan AM, Akslen LA, Trovik J, Salvesen HB.
Mod Pathol. 2013 Mar;26(3):428-34. doi: 10.1038/modpathol.2012.174. Epub 2012 Oct 19.
PMID 23080032
A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling.
Wieczorek D, Bogershausen N, Beleggia F, Steiner-Haldenstatt S, Pohl E, Li Y, Milz E, Martin M, Thiele H, Altmuller J, Alanay Y, Kayserili H, Klein-Hitpass L, Bohringer S, Wollstein A, Albrecht B, Boduroglu K, Caliebe A, Chrzanowska K, Cogulu O, Cristofoli F, Czeschik JC, Devriendt K, Dotti MT, Elcioglu N, Gener B, Goecke TO, Krajewska-Walasek M, Guillen-Navarro E, Hayek J, Houge G, Kilic E, Simsek-Kiper PO, Lopez-Gonzalez V, Kuechler A, Lyonnet S, Mari F, Marozza A, Mathieu Dramard M, Mikat B, Morin G, Morice-Picard F, Ozkinay F, Rauch A, Renieri A, Tinschert S, Utine GE, Vilain C, Vivarelli R, Zweier C, Nurnberg P, Rahmann S, Vermeesch J, Ludecke HJ, Zeschnigk M, Wollnik B.
Hum Mol Genet. 2013 Dec 20;22(25):5121-35. doi: 10.1093/hmg/ddt366. Epub 2013 Aug 1.
PMID 23906836
ARID1A mutations in endometriosis-associated ovarian carcinomas.
Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, Miller D, Jones SJ, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih IeM, Mes-Masson AM, Bowtell DD, Hirst M, Gilks B, Marra MA, Huntsman DG.
N Engl J Med. 2010 Oct 14;363(16):1532-43. doi: 10.1056/NEJMoa1008433. Epub 2010 Sep 8.
PMID 20942669
Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes.
Zang ZJ, Cutcutache I, Poon SL, Zhang SL, McPherson JR, Tao J, Rajasegaran V, Heng HL, Deng N, Gan A, Lim KH, Ong CK, Huang D, Chin SY, Tan IB, Ng CC, Yu W, Wu Y, Lee M, Wu J, Poh D, Wan WK, Rha SY, So J, Salto-Tellez M, Yeoh KG, Wong WK, Zhu YJ, Futreal PA, Pang B, Ruan Y, Hillmer AM, Bertrand D, Nagarajan N, Rozen S, Teh BT, Tan P.
Nat Genet. 2012 May;44(5):570-4. doi: 10.1038/ng.2246.
PMID 22484628
Frequent low expression of chromatin remodeling gene ARID1A in breast cancer and its clinical significance.
Zhang X, Zhang Y, Yang Y, Niu M, Sun S, Ji H, Ma Y, Yao G, Jiang Y, Shan M, Zhang G, Pang D.
Cancer Epidemiol. 2012 Jun;36(3):288-93. doi: 10.1016/j.canep.2011.07.006. Epub 2011 Sep 1.
PMID 21889920


This paper should be referenced as such :
Suryo, Rahmanto Y ; Wang, TL
ARID1A (AT rich interactive domain 1A (SWI-like))
Atlas Genet Cytogenet Oncol Haematol. 2014;18(6):368-371.
Free journal version : [ pdf ]   [ DOI ]

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  Burkitt's lymphoma (BL)
Waldenstrom macroglobulinemia

External links

HGNC (Hugo)ARID1A   11110
LRG (Locus Reference Genomic)LRG_875
Entrez_Gene (NCBI)ARID1A    AT-rich interaction domain 1A
AliasesB120; BAF250; BAF250a; BM029; 
C1orf4; CSS2; ELD; MRD14; OSA1; P270; SMARCF1; hELD; hOSA1
GeneCards (Weizmann)ARID1A
Ensembl hg19 (Hinxton)ENSG00000117713 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000117713 [Gene_View]  ENSG00000117713 [Sequence]  chr1:26696015-26782104 [Contig_View]  ARID1A [Vega]
ICGC DataPortalENSG00000117713
Genatlas (Paris)ARID1A
SOURCE (Princeton)ARID1A
Genetics Home Reference (NIH)ARID1A
Genomic and cartography
GoldenPath hg38 (UCSC)ARID1A  -     chr1:26696015-26782104 +  1p36.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)ARID1A  -     1p36.11   [Description]    (hg19-Feb_2009)
GoldenPathARID1A - 1p36.11 [CytoView hg19]  ARID1A - 1p36.11 [CytoView hg38]
Genome Data Viewer NCBIARID1A [Mapview hg19]  
OMIM603024   614607   
Gene and transcription
Genbank (Entrez)AB001895 AB210022 AF217506 AF219114 AF231056
RefSeq transcript (Entrez)NM_006015 NM_018450 NM_139135
Consensus coding sequences : CCDS (NCBI)ARID1A
Gene ExpressionARID1A [ NCBI-GEO ]   ARID1A [ EBI - ARRAY_EXPRESS ]   ARID1A [ SEEK ]   ARID1A [ MEM ]
Gene Expression Viewer (FireBrowse)ARID1A [ Firebrowse - Broad ]
GenevisibleExpression of ARID1A in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8289
GTEX Portal (Tissue expression)ARID1A
Human Protein AtlasENSG00000117713-ARID1A [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)ARID1A
Human Protein Atlas [tissue]ENSG00000117713-ARID1A [tissue]
Protein Interaction databases
Ontologies - Pathways
PubMed308 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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