Molecular diagnosis of citrin deficiency in an infant with intrahepatic cholestasis: identification of a 21.7kb gross deletion that completely silences the transcriptional and translational expression of the affected SLC25A13 allele

Abstract

Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency (NICCD) arises from biallelic SLC25A13 mutations, and SLC25A13 analysis provides reliable evidences for NICCD definite diagnosis. However, novel large insertions/deletions in this gene could not be detected just by conventional DNA analysis. This study aimed to explore definite diagnostic evidences for an infant highly-suspected to have NICCD. Prevalent mutation screening and Sanger sequencing of SLC25A13 gene just revealed a paternally-inherited mutation c.851_854del4. Nevertheless, neither citrin protein nor SLC25A13 transcripts of maternal origin could be detected on Western blotting and cDNA cloning analysis, respectively. On this basis, the hidden maternal mutation was precisely positioned using SNP analysis and semi-quantitative PCR, and finally identified as a novel large deletion c.-3251_c.15+18443del21709bp, which involved the SLC25A13 promoter region and the entire exon 1 where locates the translation initiation codon. Hence, NICCD was definitely diagnosed in the infant. To the best of our knowledge, the novel gross deletion, which silenced the transcriptional and translational expression of the affected SLC25A13 allele, is the hitherto largest deletion in SLC25A13 mutation spectrum. The Western blotting approach using mitochondrial protein extracted from expanded peripheral blood lymphocytes, of particular note, might be a new minimally-invasive and more-feasible molecular tool for NICCD diagnosis.

Sodium Taurocholate Cotransporting Polypeptide (NTCP) Deficiency Hidden Behind Citrin Deficiency in Early Infancy: A Report of Three Cases

“…Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency (NICCD) in neonates or infants (Ohura et al, 2001; Tazawa et al, 2001; Tomomasa et al, 2001), adult-onset citrullinemia type II (CTLN2) in adolescents or adults (Kobayashi et al, 1999), and Failure to Thrive and Dyslipidemia caused by Citrin Deficiency (FTTDCD) at pediatric age beyond 1 year (Song et al, 2011; Saheki and Song., 2017). To the best of our knowledge, although the clinical and molecular characteristics of NICCD has been studied for years (Ohura et al, 2007; Chen et al, 2013; Song et al, 2013; Ricciuto and Buhas, 2014; Zeng et al, 2014; Wang et al, 2015; Lin et al, 2016; Zhang et al, 2017), patients with NTCP deficiency complicated by NICCD have never been reported thus far.…”

Case report: Three novel variants on SLC25A13 in four infants with neonatal intrahepatic cholestasis caused by citrin deficiency

“…According to the ACMG guidelines, the pathogenicity analysis is PVS1 + PM2 + PP4, so it is likely pathogenic. Exon deletion is a rare variant type among SLC25A13 variants, which are mainly caused by large fragment deletion, including exon deletion, such as c.329–154_468 + 2352del2646bp (deletion of exon 5) ( 12 ), c.70–862_c.212 + 3527 del4532bp (deletion of exon 3) ( 13 ), Ex16 + 74_IVS17-32del516 (deletion of exon 17) ( 14 ), c.329–1687 -c.468 + 3865del5692bp (deletion of exon 5) ( 15 ), c.1019_1177 + 893del (deletion of exon 11) ( 16 ), c.1312–2860_1452 + 988del (deletion of exon 14) ( 17 ), c.1312–4144_1452 + 3373del (deletion of exon 14) ( 17 ) and c.3251 _c.15 + 18443del21709bp (deletion of exon 1) ( 18 ). Partial abnormal splicing of partially intron regions leads to exome deletions in mRNA, such as IVS4ins6 kb (skipping of exon 5) ( 19 ), IVS11+1 G > A (skipping of exon 11) ( 20 ), IVS15 + 1G > T (skipping of exon 15) ( 21 ) and IVS13+1G > A (skipping of exon 13) ( 22 ).…”

Neonatal Cholestasis: A Pandora’s Box

“…Presymptomatic testing is offered to individuals with a known genetic disorder in the family, whereas postsymptomatic genetic testing should be offered to individuals suspected clinically to be affected by genetic disease, ranging from gene specific to panel specific to WGS/WES. 37 Some of the disorders which can be unveiled with genomic testing are neonatal intrahepatic cholestasis caused by citrin deficiency (mutations in SLC25A13), 38 progressive familial intrahepatic cholestasis 39 (mutations in either ATP8B1 or ABCB11), Alagille syndrome (mutations in either JAG1 or NOTCH2), Alagille syndrome and Dubin-Johnson syndrome (mutations in ABCC2). In a recent study by Togawa et al, they analyzed 109 Japanese infants with cholestasis and made a molecular genetic diagnosis in 26% of their cohort (28/109).…”