Genotype-Phenotype Correlations in Ornithine Transcarbamylase Deficiency: A Mutation Update

Abstract

Ornithine transcarbamylase (OTC) deficiency is an X-linked trait that accounts for nearly half of all inherited disorders of the urea cycle. OTC is one of the enzymes common to both the urea cycle and the bacterial arginine biosynthesis pathway; however, the role of OTC has changed over evolution. For animals with a urea cycle, defects in OTC can trigger hyperammonemic episodes that can lead to brain damage and death. This is the fifth mutation update for human OTC with previous updates reported in 1993, 1995, 2002, and 2006. In the 2006 update, 341 mutations were reported. This current update contains 417 disease-causing mutations, and also is the first report of this series to incorporate information about natural variation of the OTC gene in the general population through examination of publicly available genomic data and examination of phenotype/genotype correlations from patients participating in the Urea Cycle Disorders Consortium Longitudinal Study and the first to evaluate the suitability of systematic computational approaches to predict severity of disease associated with different types of OTC mutations.

Keywords: Hyperammonemia; Mutation; Ornithine transcarbamylase; Ornithine transcarbamylase deficiency; Urea cycle.

Fig. 1

Schematic of a hepatocyte highlighting the various enzymes, transporters, and metabolites of the urea cycle. Shown in yellow is a mitochondrion containing the proximal enzymes N-acetylglutamate synthase (NAGS), carbamylphosphate synthetase 1 (CPS1), ornithine transcarbamylase (OTC), and the ornithine transporter (ORNT) and citrin transporters. Citrulline is transported out of the mitochondrion, and converted by argininosuccinate synthetase (ASS), argininosuccinate lyase (ASL), and arginase I (ARG1) to produce urea and regenerate ornithine that is reutilized by OTC.

Fig. 2

Missense and nonsense mutations in OTC and their overlap with CpG dinucleotides. The number of different missense and nonsense mutations that cause OTCD was plotted against their codon number. Blue symbols, missense mutations. Orange symbols, nonsense mutations. Gray bars, codons that overlap with CpG dinucleotides on sense and antisense strands.

Fig. 3

Conservation and solvent accessible area of amino acids affected by missense mutations in patients with OTCD. A: Conservation scores of amino acids affected by missense mutations found in females (green, n = 73) and males with either neonatal (red, n = 66) or late onset (blue, n = 57) OTCD. B: Frequency distribution of conservation scores of the amino acids affected by missense mutations that cause OTCD. C: Solvent accessible areas of amino acids affected by missense mutations found in females and males with either neonatal or late onset OTCD. D: Frequency distribution of the solvent accessible areas of amino acids affected by missense mutations that cause OTCD. E–G: Scatter plots of conservation scores vs. solvent accessible areas of amino acids affected by mutations that cause OTCD in female patients (E) and male patients with either neonatal (F) or late (G) onset OTCD.

Fig. 4

Destabilization of the OTC protein by amino acid replacements found in patients with OTCD. A: Calculated difference between stability of mutant and wild type OTC using support vector machines. B: Calculated difference between wild type and mutant OTC using force fields. C: Frequency distribution of ΔΔG values calculated using support vector machines. D: Frequency distribution of ΔΔG values calculated using force fields. Red, males with neonatal onset OTCD (n = 87). Blue, males with late onset OTCD (n = 70). Green, females with OTCD (n = 95)

Fig. 5

Recurrent mutations found in participants enrolled in the longitudinal study of OTCD. Number of study subjects with each missense and nonsense mutation and their overlap between affected codons and CpG dinucleotides on sense and antisense strands of the OTC coding region were plotted for each codon of the OTC open reading frame. Blue symbols, positions of missense and nonsense mutations in the OTC coding sequence. Gray bars, codons that overlap with CpG dinucleotides on sense and antisense strands.

Fig. 6

Neurocognitive outcomes in female and male participants of the longitudinal study of OTCD. A: IQ scores of the neonatal onset females (dark purple), late onset females (light purple), asymptomatic females (lavender) study subjects. B: IQ scores of the neonatal onset males (navy), late onet males (light blue), asymptomatic males (cyan) study subjects. Error bars represent median and interquartile ranges. Normal IQ ranges are shown in grey.

Fig. 7

Hyperammonemic and illness episodes experienced by the participants in the longitudinal study of the OTCD. Distribution of reported illness (gray) and hyperammonemic (cyan) episodes by the male study subjects with either neonatal onset (A) or late onset (B) OTCD and female study subjects with late onset OTCD (C). Frequency of hyperammonemic episodes reported by male study subjects with either neonatal onset (D) or late onset (E) OTCD and female study subjects with late onset OTCD (F) due to missense (blue), loss of function (orange) or intronic (magenta) mutations.

Fig. 8

Biomarkers of liver damage in participants of the longitudinal study of OTCD. Baseline values of plasma ALT in female (A) and male (B) study subjects; baseline INR values in female (C) and male (D) study subjects. Plasma ALT activities of 35–105 U/L and 40–120 U/L were considered mildly elevated in females and males, respectively. Plasma ALT activities of 105–175 U/L and 120–200 U/L were considered moderately elevated in females and males, respectively. Plasma ALT activities above 175 and 200 U/l were considered severely elevated in females and males, respectively. INR values between 1.2 and 1.5 were considered mildly elevated, while values between 1.5 and 2.5 were considered moderately elevated. Gray areas indicate normal ranges of plasma ALT and INR values. Neonatal onset females (dark purple), late onset females (light purple), asymptomatic females (lavender), neonatal onset males (navy), late onset males (light blue), asymptomatic males (cyan)