Alternative titles; symbols
HGNC Approved Gene Symbol: ARID1B
Cytogenetic location: 6q25.3 Genomic coordinates (GRCh38) : 6:156,776,026-157,210,779 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 6q25.3 | Coffin-Siris syndrome 1 | 135900 | Autosomal dominant | 3 |
SWI/SNF complexes contain a Swi2/Snf2-related DNA-dependent ATPase (e.g., SMARCA4; 603254) and function in the remodeling of chromatin. ARID1B is present in a small subset of SWI/SNF complexes (Hurlstone et al., 2002; Nie et al., 2003).
By sequencing clones obtained from a fetal brain cDNA library, Nagase et al. (1999) obtained a partial ARID1B clone, which they designated KIAA1235. The deduced 1,485-amino acid sequence contains an AT-rich DNA interaction domain (ARID). RT-PCR ELISA detected variable ARID1B expression in all tissues examined. Highest expression was in skeletal muscle, followed by ovary, kidney, and most specific adult brain regions examined, and lowest expression was in testis.
By searching databases for the human ortholog of Drosophila Eld/Osa, followed by screening a fetal brain cDNA library, Hurlstone et al. (2002) cloned ARID1B, which they called ELD/OSA1. The deduced protein contains 1,740 amino acids and has a predicted molecular mass of 189 kD. ELD/OSA1 contains an ARID in its N-terminal half and 2 Eld/Osa homology domains (EHD1 and EHD2) in its C-terminal half. The remainder of ELD/OSA1 is rich in proline and glutamine, and ELD/OSA1 contains a number of LxxLL motifs predicted to mediate interaction of ELD/OSA1 with liganded nuclear hormone receptors. The ARID, EHD1, and EHD2 domains of ELD/OSA1 share over 90% similarity with comparable domains of BAF250 (ARID1A; 603024). EST database analysis revealed ELD/OSA1 expression in a wide range of tissues. Western blot analysis detected ELD/OSA1 at an apparent molecular mass of 189 kD in all human tissues examined and in mouse brain. Immunocytochemical analysis showed that epitope-tagged ELD/OSA1 was expressed in nuclei of transfected COS-7 cells.
By searching databases for sequences similar to BAF250A (ARID1A), followed by screening a human T-cell cDNA library, Nie et al. (2003) cloned ARID1B, which they called BAF250B. The deduced 1,956-amino acid protein has N-terminal alanine- and glutamine-rich regions, followed by a central ARID, a second glutamine-rich region, and 2 conserved C-terminal regions corresponding to EHD1 and EHD2. Northern blot analysis detected variable expression of BAF250B transcripts of 7.5 and 9.5 kb in all tissues examined. In situ hybridization of day-16 mouse embryos showed that Baf250b was highly expressed in select regions of brain and in retina. BAF250B had an apparent molecular mass of nearly 230 kD by SDS-PAGE.
By yeast 2-hybrid analysis, Hurlstone et al. (2002) found that ELD/OSA1 interacted with BAF250 and BRG1 (SMARCA4), as well as with itself. ELD/OSA1 coprecipitated with wildtype and ATPase-dead BRG1 from transfected 293T cells. Size fractionation and immunoaffinity purification of mouse brain nuclear extracts confirmed that Eld/Osa1 purified with components of the mouse SWI/SNF complex.
By gel filtration, mass spectrometry, and Western blot analysis of human cell lines, Nie et al. (2003) found that BAF250B fractionated in a unique low-abundance SWI/SNF complex of 1 to 1.5 MD. This BAF250B-containing complex also contained ENL (MLLT1; 159556) and several common SWI/SNF subunits, but it did not contain BAF250A. Western blot analysis of HB(11;19) leukemia cells, which express the oncogenic MLL (159555)/ENL fusion protein, revealed that MLL/ENL also interacted with the BAF250B-containing complex. Both BAF250A- and BAF250B-containing complexes displayed ATP-dependent mononucleosome disruption activity in vitro.
Hurlstone et al. (2002) determined that the promoter region of the ARID1B gene is rich in CpG dinucleotides.
By radiation hybrid analysis, Nagase et al. (1999) mapped the ARID1B gene to chromosome 6.
By genomic sequence analysis, Hurlstone et al. (2002) mapped the ARID1B gene to chromosome 6q25.1, between the ESR1 (133430) and TCTEL1 (DYNLT1; 601554) genes.
Hoyer et al. (2012) performed Sanger sequencing of candidate genes, including ARID1B, in a region on chromosome 6q25 that was deleted in a patient with mental retardation (see 612863). A total of 8 mutations in the ARID1B gene (see, e.g., 614556.0001-614556.0005) were found in 8 (0.9%) of 887 individuals with mental retardation (Coffin-Siris syndrome-1; CSS1; 135900). All mutations were in the heterozygous state, occurred de novo, and resulted in haploinsufficiency of the ARID1B gene. All patients presented with moderate to severe psychomotor retardation, and most showed evidence of muscular hypotonia. In many of the patients, expressive speech was reported to be more severely affected than receptive function. Although there was no distinct recognizable facial gestalt, common findings included short stature, abnormal head shape and low-set, posteriorly rotated, and abnormally shaped ears, downslanting palpebral fissures, a bulbous nasal tip, a thin upper lip, minor teeth anomalies, and brachydactyly or single palmar creases. Only 1 patient had autistic features. Given the known function of ARID1B, the findings indicated that chromatin-remodeling defects are an important contributor to neurodevelopmental disorders.
In 5 patients with Coffin-Siris syndrome, Tsurusaki et al. (2012) identified 4 truncating (nonsense or frameshift; e.g., 614556.0006, 614556.0007) mutations in ARID1B and a microdeletion involving the ARID1B gene. The truncating mutations occurred de novo in 3 patients. Overall, Tsurusaki et al. (2012) screened 16 SWI/SNF complex subunit genes in 23 affected individuals and found that 20 individuals (87%) had a germline mutation in 1 of 6 subunit SWI/SNF complex subunit genes.
By exome sequencing, Santen et al. (2012) identified 3 de novo truncating mutations in the ARID1B gene (614556.0008-614556.0010) in individuals with Coffin-Siris syndrome. Array-based copy number variation analysis in 2,000 individuals with intellectual disability revealed an additional 3 subjects with a deletion affecting ARID1B.
In 2 unrelated Finnish women (P2 and P3) with CSS1, Zweier et al. (2017) identified de novo heterozygous frameshift mutations in the ARID1B gene (614556.0011 and 614556.0012). The mutations, which were found by trio-based exome sequencing of the patients and their parents, were confirmed by Sanger sequencing. Functional studies of the variants were not performed, but both were predicted to result in a loss of function and haploinsufficiency. The patients had previously been reported by Poyhonen et al. (2004) as having a different disorder, but the findings of Zweier et al. (2017) confirmed the diagnosis of CSS1.
In a 3.5-year-old German boy with Coffin-Siris syndrome-1 (CSS1; 135900), Hoyer et al. (2012) identified a de novo heterozygous 3919C-T transition in exon 16 of the ARID1B gene, resulting in a gln1307-to-ter (Q1307X) substitution. The patient had severe developmental delay, delayed motor development, hypotonia, and mild dysmorphic features, including prominent forehead, low-set, posteriorly rotated and abnormally shaped ears, downslanting palpebral fissures, thin upper lip, pointed teeth, and brachydactyly. He also had autistic features.
In a 7-year-old German boy with Coffin-Siris syndrome-1 (CSS1; 135900), Hoyer et al. (2012) identified a de novo heterozygous 11-bp deletion (6463_6473del) in exon 20 of the ARID1B gene, resulting in a frameshift and premature termination. He had short stature, hypotonia, cleft palate, abnormally shaped ears, downslanting palpebral fissures, strabismus, bulbous nasal tip, thin upper lip, small teeth, sandal gaps, hypoplastic nails, cryptorchidism, and myopia.
In a 12-year-old girl with Coffin-Siris syndrome-1 (CSS1; 135900), Hoyer et al. (2012) identified a de novo heterozygous 3304C-T transition in exon 12 of the ARID1B gene, resulting in an arg1102-to-ter (R1102X) substitution. She had short stature, severe developmental delay, delayed walking, poor speech, and hypotonia. She also had 1 seizure, unilateral hearing loss, brachycephaly and low forehead, low-set, posteriorly rotated, and abnormal ears, downslanting palpebral fissures, thin upper lip, cleft palate, sandal gaps, myopia, and wide mouth, among other minor dysmorphisms.
Tsurusaki et al. (2012) identified this mutation occurring de novo in a patient (Patient 23) with Coffin-Siris syndrome.
In a 4-year-old girl with Coffin-Siris syndrome-1 (CSS1; 135900), Hoyer et al. (2012) identified a de novo heterozygous 2-bp deletion (3323delAA) in exon 12 of the ARID1B gene, resulting in a frameshift and premature termination. She had delayed psychomotor development, hypotonia, and mild dysmorphic features, such as frontal bossing, low-set ears, thin upper lip, retrognathia, and long toes.
In a 17-year-old boy with Coffin-Siris syndrome-1 (CSS1; 135900), Hoyer et al. (2012) identified a de novo heterozygous 4038T-A transition in exon 17 of the ARID1B gene, resulting in a tyr1346-to-ter (Y1346X) substitution. He had moderate developmental delay, seizures, low-set and posteriorly rotated ears, malocclusion of the teeth, hypertelorism, myopia, and retrognathia.
In a patient with Coffin-Siris syndrome-1 (CSS1; 135900), Tsurusaki et al. (2012) identified a heterozygous de novo C-to-T transition at nucleotide 1903 of the ARID1B gene, resulting in a glu-to-ter substitution at codon 635 (Q635X). This occurred as a de novo event. Tsurusaki et al. (2012) characterized the phenotype of this patient (Patient 15) as Coffin-Siris syndrome (135900).
In a patient with Coffin-Siris syndrome-1 (CSS1; 135900), Tsurusaki et al. (2012) identified a heterozygous single-basepair deletion of G at nucleotide 5632 of the ARID1B gene, resulting in frameshift at codon 1878 and premature termination 96 codons downstream (Arg1878MetfsTer96). This patient also carried a missense mutation, pro715-to-leu (P715L), on the opposite allele of ARID1B that the authors considered a rare polymorphism rather than deleterious. Tsurusaki et al. (2012) characterized the phenotype of this patient (Patient 10) as Coffin-Siris syndrome (135900).
In a patient with Coffin-Siris syndrome-1 (CSS1; 135900), Santen et al. (2012) detected a heterozygous A-to-T transition at nucleotide 5329 in exon 20 of the ARID1B gene, resulting in a lys-to-ter substitution at codon 1777 (K1777X). Santen et al. (2012) characterized the phenotype of this patient (Patient 1) as Coffin-Siris syndrome (135900). The patient had severe intellectual disability, severe speech delay, and coarse facial features with thick eyebrows, but not hypoplastic fifth fingernails.
In a patient with Coffin-Siris syndrome-1 (CSS1; 135900), Santen et al. (2012) detected a heterozygous de novo C-to-T transition at nucleotide 3223 in exon 12 of the ARID1B gene, resulting in an arg-to-ter substitution at codon 1075 (R1075X). The patient had severe intellectual disability and severe speech delay. Santen et al. (2012) characterized the phenotype of this patient (Patient 2) as Coffin-Siris syndrome (135900).
In a 3-year-old female (Patient 3) with Coffin-Siris syndrome-1 (CSS1; 135900), Santen et al. (2012) identified a heterozygous de novo 10-bp deletion in exon 18 of the ARID1B gene (4619_4628del) resulting in frameshift and premature termination 35 amino acids downstream from codon 1541 in exon 18 of the ARID1B gene (Gln1541ArgfsTer35). The phenotype of this patient was characterized as Coffin-Siris syndrome (135900).
In a 26-year-old Finnish woman (P2) with Coffin-Siris syndrome-1 (CSS1; 135900), Zweier et al. (2017) identified a de novo heterozygous 4-bp deletion (c.5570_5573del, NM_020732.3) in the last coding exon of the ARID1B gene, predicted to result in a frameshift and premature termination (Lys1857SerfsTer17). The mutation, which was found by trio-based exome sequencing of the patient and her parents, was confirmed by Sanger sequencing. Functional studies of the variant and studies of patient cells were not performed. The patient had previously been reported by Poyhonen et al. (2004) as having a different disorder, but the findings of Zweier et al. (2017) confirmed the diagnosis of CSS1.
In a 19-year-old Finnish woman (P3) with Coffin-Siris syndrome-1 (CSS1; 135900), Zweier et al. (2017) identified a de novo heterozygous c.4110G-A transition (c.4110G-A, NM_020732.3) in the last coding basepair of exon 17 of the ARID1B gene, which was predicted to result in a synonymous substitution, but was located in a conserved splice donor site. The mutation, which was found by trio-based exome sequencing of the patient and her parents, was confirmed by Sanger sequencing. Functional studies of the variant and studies of patient cells were not performed, but Zweier et al. (2017) noted that the mutation had previously been reported by Hoyer et al. (2012), who had demonstrated that it causes the skipping of exon 17. Thus, the c.4110G-A transition was predicted to cause a frameshift and premature termination (His1339IlefsTer77), and was likely subject to nonsense-mediated mRNA decay. The patient had previously been reported by Poyhonen et al. (2004) as having a different disorder, but the findings of Zweier et al. (2017) confirmed the diagnosis of CSS1.
Hoyer, J., Ekici, A. B., Endele, S., Popp, B., Zweier, C., Wiesener, A., Wohlleber, E., Dufke, A., Rossier, E., Petsch, C., Zweier, M., Gohring, I., Zink, A. M., Rappold, G., Schrock, E., Wieczorek, D., Riess, O., Engels, H., Rauch, A., Reis, A. Haploinsufficiency of ARID1B, a member of the SWI/SNF-A chromatin-remodeling complex, is a frequent cause of intellectual disability. Am. J. Hum. Genet. 90: 565-572, 2012. [PubMed: 22405089] [Full Text: https://doi.org/10.1016/j.ajhg.2012.02.007]
Hurlstone, A. F. L., Olave, I. A., Barker, N., van Noort, M., Clevers, H. Cloning and characterization of hELD/OSA1, a novel BRG1 interacting protein. Biochem. J. 364: 255-264, 2002. [PubMed: 11988099] [Full Text: https://doi.org/10.1042/bj3640255]
Nagase, T., Ishikawa, K., Kikuno, R., Hirosawa, M., Nomura, N., Ohara, O. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res. 6: 337-345, 1999. [PubMed: 10574462] [Full Text: https://doi.org/10.1093/dnares/6.5.337]
Nie, Z., Yan, Z., Chen, E. H., Sechi, S., Ling, C., Zhou, S., Xue, Y., Yang, D., Murray, D., Kanakubo, E., Cleary, M. L., Wang, W. Novel SWI/SNF chromatin-remodeling complexes contain a mixed-lineage leukemia chromosomal translocation partner. Molec. Cell. Biol. 23: 2942-2952, 2003. [PubMed: 12665591] [Full Text: https://doi.org/10.1128/MCB.23.8.2942-2952.2003]
Poyhonen, M. H., Peippo, M. M., Valanne, L. K., Kuokkanen, K. E., Koskela, S. M., Bartsch, O., Rasi, S., Wiebe, G. J., Kahkonen, M., Kaariainen, H. A. Hypertrichosis, hyperkeratosis, abnormal corpus callosum, mental retardation and dysmorphic features in three unrelated families. Clin. Dysmorph. 13: 85-90, 2004. [PubMed: 15057123]
Santen, G. W. E., Aten, E., Sun, Y., Almomani, R., Gilissen, C., Nielsen, M., Kant, S. G., Snoeck, I. N., Peeters, E. A. J., Hilhorst-Hofstee, Y., Wessels, M. W., den Hollander, N. S., Ruivenkamp, C. A. L., van Ommen, G.-J. B., Breuning, M. H., den Dunnen, J. T., van Haeringen, A., Kriek, M. Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome. Nature Genet. 44: 379-380, 2012. [PubMed: 22426309] [Full Text: https://doi.org/10.1038/ng.2217]
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., and 19 others. Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. Nature Genet. 44: 376-378, 2012. [PubMed: 22426308] [Full Text: https://doi.org/10.1038/ng.2219]
Zweier, M., Peippo, M. M., Poyhonen, M., Kaariainen, H., Begemann, A., Joset, P., Oneda, B., Rauch, A. The HHID syndrome of hypertrichosis, hyperkeratosis, abnormal corpus callosum, intellectual disability, and minor anomalies is caused by mutations in ARID1B. Am. J. Med. Genet. 173A: 1440-1443, 2017. [PubMed: 28323383] [Full Text: https://doi.org/10.1002/ajmg.a.38143]