Missense SLC25A38 variations play an important role in autosomal recessive inherited sideroblastic anemia

Abstract

Background: Congenital sideroblastic anemias are rare disorders with several genetic causes; they are characterized by erythroblast mitochondrial iron overload, differ greatly in severity and some occur within a syndrome. The most common cause of non-syndromic, microcytic sideroblastic anemia is a defect in the X-linked 5-aminolevulinate synthase 2 gene but this is not always present. Recently, variations in the gene for the mitochondrial carrier SLC25A38 were reported to cause a non-syndromic, severe type of autosomal-recessive sideroblastic anemia. Further evaluation of the importance of this gene was required to estimate the proportion of patients affected and to gain further insight into the range and types of variations involved.

Design and methods: In three European diagnostic laboratories sequence analysis of SLC25A38 was performed on DNA from patients affected by congenital sideroblastic anemia of a non-syndromic nature not caused by variations in the 5-aminolevulinate synthase 2 gene.

Results: Eleven patients whose ancestral origins spread across several continents were homozygous or compound heterozygous for ten different SLC25A38 variations causing premature termination of translation (p.Arg117X, p.Tyr109LeufsX43), predicted splicing alteration (c.625G>C; p.Asp209His) or missense substitution (p.Gln56Lys, p.Arg134Cys, p.Ile147Asn, p.Arg187Gln, p.Pro190Arg, p.Gly228Val, p.Arg278Gly). Only three of these variations have been described previously (p.Arg117X, p.Tyr109LeufsX43 and p.Asp209His). All new variants reported here are missense and affect conserved amino acids. Structure modeling suggests that these variants may influence different aspects of transport as described for mutations in other mitochondrial carrier disorders.

Conclusions: Mutations in the SLC25A38 gene cause severe, non-syndromic, microcytic/hypochromic sideroblastic anemia in many populations. Missense mutations are shown to be of importance as are mutations that affect protein production. Further investigation of these mutations should shed light on structure-function relationships in this protein.

Figure 1.

Multiple amino acid sequence alignment obtained using Clustalw2 for SLC25A38 from 14 species (7 mammalian, 1 bird, 1 frog, 1 fish and 4 yeast/fungi). Amino acids reported in this work to be substituted in congenital sideroblastic anemia patients are marked with a vertical arrow. Shaded bars represent the transmembrane regions as reported by Uniprot and are extended slightly by the structure modeling as shown in Figure 2. The mitochondrial carrier domains (Pfam) are shown as black boxes. Below the alignment a star indicates that the amino acid at this position is identical for all 14 species, dots indicate amino acids with similar but not identical properties.

Figure 2.

(A) The position of the substituted amino acids in the predicted secondary structure of human SLC25A38. Predicted helices are shown as blocks and predicted loops are shown as lines. The positions of the amino acid substitutions reported here are shown as white dots with respect to key glycine (black dot or half black-half white dot) and proline (gray dot or half gray-half white dot) residues. The latter were identified by their position in the amino acid sequence relative to the PX[D/E]XX[K/R]X[K/R] and [D/E]GXXXX[W/Y/F][K/R]G parts of the signature sequence for this class of proteins (shown in a hashed line here). The position of the previously-reported substituted amino acid Gly130 (gray text) is also shown. (B) Predicted structural model by SWISS-MODEL of SLC25A38 visualized with PyMol. The backbone helices and loops are shown in light gray and the side chains of the substituted amino acids are shown as dark gray spheres. The side chains of five of the seven substituted amino acids can be seen to point into the central channel. The side chains of the 190 proline and the 147 isoleucine can be seen as the uppermost and the furthest right of the side chains respectively. The view is from the mitochondrial inter-membrane space down the central channel but somewhat at an angle to show the 147 isoleucine side chain stretching away from the channel toward a short helical section that lies at the matrix side of the inner mitochondrial membrane. Please also refer to the Online Supplementary Figure S2.