ARID2, a milder cause of Coffin‐Siris Syndrome? Broadening the phenotype with 17 additional individuals

Coffin‐Siris Syndrome (CSS, MIM 135900) is now a well‐described genetic condition caused by pathogenic variants in the Bromocriptine activating factor (BAF) complex, including ARID1B, ARID1A, ARID2, SMARCA4, SMARCE1, SMARCB1, SOX11, SMARCC2, DPF2, and more recently, BICRA. Individuals with CSS have a spectrum of various medical challenges, most often evident at birth, including feeding difficulties, hypotonia, organ‐system anomalies, and learning and developmental differences. The classic finding of fifth digit hypo‐ or aplasia is seen variably. ARID2, previously described, is one of the less frequently observed gene changes in CSS. Although individuals with ARID2 have been reported to have classic features of CSS including hypertrichosis, coarse facial features, short stature, and fifth digit anomalies, as with many of the other CSS genes, there appears to be a spectrum of phenotypes. We report here a cohort of 17 individuals with ARID2 variants from the Coffin‐Siris/BAF clinical registry and detail their medical challenges as well as developmental progress. Feeding difficulties, hypotonia, and short stature occur often, and hip dysplasia appears to occur more often than with other genes, however more severe medical challenges such as significant brain and cardiac malformations are rarer. Individuals appear to have mild to moderate intellectual impairment and may carry additional diagnoses such as ADHD. Further phenotypic description of this gene will aid clinicians caring for individuals with this rarer form of CSS.


| INTRODUCTION
Coffin-Siris Syndrome (CSS, MIM 135900), first described in 1970 by Drs.Coffin and Siris, detailed three individuals with developmental delay, coarse facial features, hypertrichosis, and hypoplasia of the fifth digit phalanges (Coffin & Siris, 1970), now generally regarded as the "classic" features of CSS.In 2012, genes associated with the BAF complex were shown to be causative for a cohort of individuals with a phenotype consistent with CSS (Tsurusaki et al., 2012).Since that time, over 300 individuals have been described in the literature and likely there are several thousand with "BAFopathies" throughout the world.ARID1B is the most commonly affected gene (Hoyer et al., 2012;Sim et al., 2014), and individuals with ARID1B tend to have more of the classic features of CSS which were originally described (Mannino et al., 2018).Although there is a phenotypic spectrum within every gene seen in CSS, in general, individuals with "ARID" changes appear to have more neurodevelopmental phenotypes and less severe organ system anomalies.Individuals with "SMARC" changes tend to have more significant organ anomalies in addition to learning and developmental differences (Bogershausen & Wollnik, 2018;Mannino et al., 2018).Currently, there are 485 individuals in the International CSS/BAF complex registry.We report here 17 individuals with pathogenic variants in the ARID2 gene (including microdeletions) to further add to the phenotypic spectrum.As ARID2 changes represent approximately 4% of the various BAF genes in this particular registry, gaining a better understanding of the presentation will aid clinicians in providing better guidance for patients and families.

| METHODS
Individuals who were enrolled in the CSS/BAF registry were consented and enrolled through the EVMS IRB Protocol (EVMS IRB #15-03-EX-0058).Online consent forms were obtained and an electronic registry survey was completed by the legal guardian.
Additional medical records were obtained and compared with information provided from caregivers through the survey.In Table 1, individuals were noted with an "X" to have a feature or "(À)" if the feature was specifically noted as negative or normal in the medical records.

| RESULTS
Twenty-two individuals were identified as having pathogenic variants in ARID2 in the registryFull information and medical records were available for 17; complete records were considered to be genetic test results, available subspecialist clinic visits, information regarding growth, and imaging studies.As outlined in Table 1, nonspecific findings previously reported in CSS, including hypotonia, feeding difficulties, autism, and learning and developmental challenges were not uncommon.Hypotonia was reported in 8 of 17 individuals, feeding difficulties in 12 of 17, and GE reflux or evidence of gastritis in 6 of 17.Only three individuals needed a gastrostomy tube, and two of them have since had those removed.Autism was not reported frequently, although some individuals may not have been old enough to have had a full neurodevelopmental assessment at the time of the last chart review.ADHD was reported in nearly half of the individuals.Not all children had records of IQ/DQ assessments, but of the four who did, IQs were in the mild intellectual disability range, from 70 to 85. Ages of walking ranged from 18 months to 33 months, and speech acquisition ranged from 12 months to beyond the age of 3 years.
Other common findings included eye abnormalities (10/17), most commonly strabismus.A minority of individuals had reported ENT anomalies including laryngomalacia.Hip dysplasia was reported in 4 of the 17 individuals, which was not previously frequently reported with CSS.Short stature occurred in over half of the individuals (12/17).
Only two individuals reported the use of growth hormone supplementation.

| DISCUSSION
ARID2 variants causing CSS appear to have phenotypes that to fall on the "milder" end of the spectrum in regards to other genes in the BAF complex, and even within the ARID genes themselves."Mild" is a subjective term in some sense, as even minor medical challenges may create significant struggles for families, but in general, individuals are less medically complex, with fewer organ systems affected, and tend to achieve developmental milestones a little closer to the typical time than others.Individuals with ARID2 variant (CSS6, MIM 617808) have been previously reported in the literature, first in 2015 (Shang et al., 2015).Most subsequent reports have detailed physical exam findings and dysmorphic features, but also noted cognitive and behavioral challenges.Gazdagh et al. (2019) reported seven individuals with pathogenic variants in ARID2, including two with microdeletions of 12q12.The majority did not have the classic findings seen with CSS, although they did have moderate to severe intellectual disability.Kang et al. (2021) reported a comprehensive review of 22 individuals with either ARID2 microdeletions or intragenic mutations.All individuals had some degree of learning and developmental differences, and the majority had short stature.Skeletal anomalies were also reported in the majority of individuals (Kang et al., 2021).Additional ARID2 individuals have been reported (Khazanchi et al., 2019;Van Paemel et al., 2017).In the report by Wang et al. (2022), a seemingly unaffected parent was found to have a pathogenic ARID2 change which was passed on to their child; this suggests that there may be additional individuals with ARID2 changes who have few or no symptoms.Van der Sluijs et al. ( 2021) reported ARID1B variants that appeared to be inherited from unaffected or mildly affected parents, further highlighting that this may be the case in other BAFopathy genes.The use of methylation "signatures" is being increasingly utilized to help identify the pathogenicity of certain variants of uncertain significance in BAFopathy genes as well as other genes (Aref-Eshghi et al., 2020;Haghshenas et al., 2020;Kerkhof et al., 2021).This may be of help when determining, for example, if an ARID2 change is at play in a very mildly affected or unaffected individual.
Short stature is common, as has been reported previously (Xia et al., 2023;van Paemel et al., 2017), but two individuals in this cohort had reports of growth hormone supplementation.An additional individual was identified as having growth hormone deficiency but has not yet been treated with growth hormone.One individual with short stature also harbored a pathogenic variant in GNAS, which may be contributing to her slower growth.It is assumed that individuals were plotted on the typical CDC growth charts rather than CSS-specific curves (McCague et al., 2020).
The minority of individuals in this registry cohort had feeding difficulties severe enough to necessitate a feeding tube, and no individuals required respiratory support beyond the neonatal period.Of the individuals with microdeletions, the size of the microdeletion appears to correlate with the degree of developmental delay; the largest microdeletion of 2.9 Mb had the most delayed milestones of this group.x (discontinued age 7) Abnormal brain MRI Intracranial white matter loss, areas of T2 hyperintensity and pallor within the supratentorial white matter.Other Short stature x (19th% @ 7 years 4 months) x (2% @ 6 years 5 months) x (2% @ 4 years 8 months) x (<5th% @ 21 months) x (~3rd% @ 7 years) Growth hormone supplementation   x (<1% @ 8 years 6 months) x (% unknown) x (25% @ 32 months) x (<1% @ 9 years) x (5th-10th% @ 14 months) x (% unknown) x (% unknown) Few individuals had reports of "classic" CSS findings, although it is possible these were not noted in the medical records reviewed.Hip dysplasia occurred in 4 of the 17 individuals, which appears to be at a higher proportion for CSS in general as well as in ARID2 (Mannino et al., 2018).Subluxation of the hip was previously reported in an individual with a SMARCA4 variant (Kosho et al., 2013).An ARID2 female was reported to have hip dysplasia at birth (van Paemel et al., 2017).In Gazdagh's (2019) ARID2 cohort, an additional individual was reported to have "dislocatable hips" at birth.Given the higher numbers of individuals reported with this finding in the cohort, clinicians may want to consider imaging or a referral to orthopedics if their patients with ARID2 variants have any pain, gait anomalies, or abnormal hip exams as infants.
There  (Vasko et al., 2022), which included 14 individuals with ARID2 changes, noted that 60% of individuals in that study had "severe" language impairment (first word after 25 months) and 13% had "moderate" language impairment (first word between 22 and 25 months).The majority of individuals with ARID2 changes in this study would be classified as having "mild" language impairment (first word between 19 and 21) months or normal language development (first word before 18 months) (8 individuals).Five individuals would be classified as "severe" language delay.
As with any caregiver-completed survey, information is limited by what is known to the guardians and what is available or completed in the medical record.Some individuals may not be old enough to have had certain assessments, and it is possible that there are further updates for some of these individuals that were not able to be obtained.This is especially true for some of the developmental evaluations as well as autism evaluations.The phenotypic features outlined in Table 1 were chosen based on what appeared to be noted most frequently in all of the individuals' medical records and their registry survey.
Surveillance recommendations have been published previously for individuals with CSS (Mannino et al., 2018); care still appears to be primarily supportive, although for individuals with ARID2, we would recommend emphasis on early intervention therapies and appropriate school supports as they grow older.Individuals who have are having significant delays with walking (understanding that motor delays are not uncommon in this group in general), gait anomalies, or abnormal hip exams in infancy, may benefit from an orthopedic evaluation for possible hip dysplasia if not picked up previously.
This report further broadens the phenotype of individuals with pathogenic variants in ARID2, and offers some additional guidance for families and clinicians who care for these individuals.
T A B L E 1 Genotypic and phenotypic features of 17 individuals.
has not been a comprehensive analysis of average IQs or developmental quotients in individuals with Coffin-Siris Syndrome.A large study of individuals with ARID1B changes by van der Sluijs et al (including what was characterized as ARID1B-Coffin Siris syndrome and ARID1B-related intellectual disability) noted that virtually all individuals had both motor (gross and fine) and speech delays, but specific neuropsychiatric assessments were not detailed.A study on language impairments in all Coffin-Siris individuals from the same registry as in this manuscript