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Background  Human height is a complex trait with a strong genetic basis. Recently, a significant association between rare copy number variations (CNVs) and short stature has been identified, and candidate genes in these rare CNVs are being explored. This study aims to evaluate the association between mutations in  ARID1B  gene and short stature, both the syndromic and non-syndromic form.    Results  Based on a case-control study of whole genome chromosome microarray analysis (CMA), three overlapping CNVs were identified in patients with developmental disorders who exhibited short stature.  ARID1B , a causal gene for Coffin Siris syndrome, is the only gene encompassed by all three CNVs. A following retrospective genotype-phenotype analysis based on a literature review confirmed that short stature is a frequent feature in those Coffin-Siris syndrome patients with  ARID1B  mutations. Mutation screening of  ARID1B  coding regions was further conducted in a cohort of 48 non-syndromic short stature patients,andfour novel missense variants including two  de novo  mutations were found.    Conclusion  These results suggest that haploinsufficient mutations of  ARID1B  are associated with syndromic short stature including Coffin-Siris syndrome and intellectual disability, while rare missense variants in  ARID1B  are associated with non-syndromic short stature. This study supports the notion that mutations in genes related to syndromic short stature may exert milder effect and contribute to short stature in the general population.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1898-1) contains supplementary material, which is available to authorized users.

De novo mutations in ARID1B associated with both syndromic and non-syndromic short stature