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Background X-linked spondyloepiphyseal dysplasia tarda (SEDT-XL) is a skeletal disorder characterized by defective structures of vertebral bodies and/or of epiphyses of the long bones, resulting in moderately short stature and early joint degeneration. TRAPPC2 gene, which is important for collagen secretion, has been reported as causative for SEDT-XL. Case presentation Here, we report two variants of TRAPPC2 gene of SEDT-XL patients, a missense variant of start codon, c.1A > T, and a deletion variant, c.40delG. To understand molecular consequence of the variants, we establish an in vitro gene expression assay system and demonstrate that both mutated genes are transcribed, but are not properly translated, indicative of the pathogenic nature of those TRAPPC2 variants. Conclusions In the current study, we provide additional experimental data showing that loss-of-function TRAPPC2 variants are probably causative for SEDT-XL phenotype. These findings further contribute to the understanding the clinical picture related to TRAPPC2 gene. ; TJC is supported by National Research Foundation (NRF) funded by the Ministry of Science, ICT & Future Planning of the Korean government (NRF2014M3C9A2064684: Genome Technology to Business Translation Program), which has been used for the patient recruitment and care, and determining genetic variants. YK is supported by NRF funded by the Ministry of Science, ICT & Future Planning of the Korean government (NRF-2014M3C9A2064688: Genome Technology to Business Translation Program and RF2016R1A5A1011974), which have been used for validation of the pathogenicity of identified variants and in vitro functional studies. All the decisions regarding to the current studies are made by authors, not by funders. The funders are not involved in the study design, data collection and analysis, performing experiments and in writing the manuscript.