Identification of 13 novel pathogenic SLC25A13 variants and comparison of the genetic spectrum among different geographic regions: Molecular characterization of a large cohort of citrin deficiency in China

Objective

Citrin deficiency (CD), caused by biallelic pathogenic variants in SLC25A13, remains underdiagnosed due to allelic heterogeneity, variants of uncertain significance (VUS), and technical limitations. This study aimed to improve the diagnosis of CD by identifying novel pathogenic SLC25A13 variants and characterizing the variant spectrum and geographic distribution in a large Chinese pediatric cohort.

Methods

Polymerase chain reaction (PCR)-based methods and Sanger sequencing were performed to identify pathogenic SLC25A13 variants in 220 pediatric patients with clinically suspected CD and their parents from 2016 to 2024. We functionally validated novel missense and splice-site variants using agc1-knockout yeast modeling and minigene assays, respectively. Data from these 191 newly diagnosed CD patients (2016–2024) were combined with data from 274 previously reported CD cases (2005–2016) and from 186 additional CD patients diagnosed via next-generation sequencing since 2016. The SLC25A13 variant spectrum and geographic distribution were then analyzed in this combined cohort. Statistical analyses were performed using Chi-square/Fisher's exact tests and one-way analysis of variance, as appropriate.

Results

A large cohort of 651 CD patients was assembled, and 13 novel pathogenic SLC25A13 variants were identified, including c.177_189del, c.188del, c.212 + 3 A > G, c.889G > T, c.1193 T > A, c.1210G > T, c.1352 T > A, c.1620del, c.1722del, c.1799_1800insAAA, c.1853_1855dup, c.1603_1609dup, and c.819-16 T > A. The most frequent variants were c.852_855del (57.56 %), c.1751-5_1751–4ins(2684) (10.06 %), c.1638_1660dup (8.42 %), and c.615 + 5G > A (7.93 %). The variant c.329-3_329-2ins(6072) ranked fifth at 2.13 %. In the Chinese mainland, the variant c.852_855del was most prevalent in southern and southwestern provinces, c.1638_1660dup was enriched in eastern coastal regions, and c.1751-5_1751–4ins(2684) reached its highest frequency in Sichuan Province (29.7 %).

Conclusions

The study established the largest CD cohort to date, expanded the SLC25A13 variant spectrum, and delineated the distinct geographic distribution of these variants. These findings refined diagnostic protocols and emphasized the necessity for population-tailored genetic screening to optimize early diagnosis of CD.