case_images: PMC11084280_01
case_images: (A) schematic presentation of mtDNA replication. RNR, ribonucleotide reductase; dNMP, deoxynucleoside monophosphate; dNDP, deoxynucleoside diphosphate; dNTP, deoxynucleoside triphosphate; NDP, nucleoside diphosphate; dTMP, deoxythymidine monophosphate. (B) Graphical representation of the RRM2B protein 3D structure and location of the altered amino acid. The identified c. 155T>C variant caused the p.Ile52Thr amino acid change. The pink coil represents the loop structure, blue depicts an alpha-helix and the purple region is a beta-strand. Each color represents a different atom; yellow-C atom, gray-H atom, blue-N atom, red-O atom and orange-S atom. The red dotted line represents the hydrogen bond. The red rectangles show areas of change.
case_images: fped-12-1363728-g001.jpg
case_images: PMC11084280_01_fped-12-1363728-g001.jpg
case_images: F1
case_images: The hematological parameters (Table 1) showed that the patient had aberrantly elevated lactate (Supplementary Figure S1), high-sensitivity cardiac troponin I (hs-cTnI), myohemoglobin, lactate dehydrogenase (LDH), creatine kinase (CK), aspartic transaminase (AST), alanine aminotransaminase (ALT), plus reduced uric acid and fibrinogen. AlphaFold artificial intelligence algorithm (Figure 1B). AlphaFold2 produced a per-residue confidence score >90, which indicated very high confidence in the model for most regions of the protein structure.
case_images: (A) MRI images obtained during hospitalization. The MRI showed a high water content in the white matter of the bilateral frontal, temporal, parietal and occipital lobes. Red arrows point to brain lesions. (B) Pedigree of the family. The father and mother were asymptomatic carriers of the pathogenic variant, while the patient showed clinical symptoms. (C) Reverse complementary sequences of the RRM2B variants showed an A>G nucleotide substitution at the 155th nucleotide, in exon 2. The patient carried a homozygous mutation, while both his father and mother had a heterozygous mutation at the same site. (D) A multispecies analysis showed that this site was highly conserved.
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case_images: PMC11084280_01_fped-12-1363728-g002.jpg
case_images: F2
case_images: The MRI showed a high water content in the white matter of the bilateral frontal, temporal, parietal and occipital lobes, and showed that the sulci of the bilateral cerebral hemispheres were wider and deeper than normal, which suggested abnormal brain development (Figure 2A). Urine gas chromatography-mass spectrometry (GC-MS) showed that a variety of urinary organic acids, such as lactate, pyruvic acid, hydroxybutyrate and 5-oxyproline, were elevated by varying degrees (Supplementary Figure S2). In accordance with the sequencing results from the family, the patient's two copies of the variant were inherited from his parents, who were both heterozygous for this variant (Figures 2B,C). Taster and GERP++, based on the evolutionary conservation. The analysis of conservation showed that the amino acids at this site were highly conserved across multiple species, from fish to mammals (Figure 2D).
case_images: (A) previously reported pathogenic RRM2B variants and the novel variant in the patient. The location of each variant is shown in the nine exons of RRM2B messenger RNA (mRNA). The P53R2 protein comprises 351 amino acid residues. Each exon is labeled with the segment of the amino acid chain that it encodes. Codon variant refers to an insertion or deletion of one or several codons. The yellow, blue and green fonts represent homozygous, heterozygous and compound heterozygous genotypes, respectively. The grey font indicates an unknown type of variant. Purple represents both homozygous and compound heterozygous genotypes. Red represents both heterozygous and complex heterozygous genotypes. & indicates that the variant was present in both MDDS and PEO. The red arrow represents the novel variant. (B) Distribution of genotypes in patients with MDDS and PEO. M, missense variant; PTV, protein-truncating variant, e.g., splice-site, nonsense, frameshift and codon variants. (C) The relationship between PTV and developmental delay in patients with MDDS. (D) Clinical features in patients with MDDS.
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case_images: PMC11084280_01_fped-12-1363728-g003.jpg
case_images: F3
case_images: This implied that functionalization of the protein was affected during polymerization (Supplementary Figure S3). Table S3). Single heterozygotes in PEO and homozygote or compound heterozygotes in MDDS were mostly found in exons 1, 3 and 9 (Figure 3A). The predominant variant types that were responsible for such diseases were the variants that altered the amino acids. These included 27 (64.29%) missense and four (9.52%) frameshift variants in patients with MDDS, and 19 (70.37%) missense and four (14.81%) frameshift variants in patients with PEO or other diseases. Figure 3B). For MDDS, almost all variants were found in homozygous or compound heterozygous genotypes, which may indicate that both copies of the gene were damaged. In contrast, the genotypes were mainly heterozygous or compound heterozygous in patients with PEO, which suggested a partially disrupted function of the gene (Figure 3A; Supplementary Table S1). The median age of onset was two months, with a range from 0 to 36 months, and 33 patients (84.62%) died. The most frequent clinical symptoms, such as hypotonia (36/39, 92.31%), developmental delay (23/39, 58.97%), renal disease (19/39, 48.72%), feeding difficulties (17/39, 43.59%), hearing loss (17/39, 43.59%), respiratory involvement (16/39, 41.03%), seizures (12/39, 30.77%) and eye abnormalities (9/39, 23.08%) (Figure 3C), involved multiple systems. As shown in Figure 3C, the number of PTVs (protein-truncating variants), such as splice-sites, nonsense, frameshift and codon variants, was positively associated with a higher risk of developmental delay (Chi squared test, chi2 = 7.337, p = 0.026).