A novel mutation in the cytochrome P450(27) (CYP27) gene caused cerebrotendinous xanthomatosis in a Japanese family

Clinical and Genetic Characteristics of Splicing Variant in CYP27A1 in an Iranian Family with Cerebrotendinous Xanthomatosis

Background:

CTX is a rare congenital lipid-storage disorder, leading to a progressive multisystem disease. CTX with autosomal recessive inheritance is caused by a defect in the CYP27A1 gene. Chronic diarrhea, tendon xanthomas, neurologic impairment, and bilateral cataracts are common symptoms of the disease.

Methods:

Three affected siblings with an initial diagnosis of non-syndromic intellectual disability were recruited for further molecular investigations. To identify the possible genetic cause(s), WES was performed on the proband. Sanger sequencing was applied to confirm the final variant. The clinical and molecular genetic features of the three siblings from the new CTX family and other patients with the same mutations, as previously reported, were analyzed. The CYP27A1 gene was also studied for the number of pathogenic variants and their location.

Results:

We found a homozygous splicing mutation, NM_000784: exon6: c.1184+1G>A, in CYP27A1 gene, which was confirmed by Sanger sequencing. Among the detected pathogenic variants, the splice site mutation had the highest prevalence, and the mutations were mostly found in exon 4.

Conclusion:

This study is the first to report the c.1184+1G>A mutation in Iran. Our findings highlight the other feature of the disease, which is the lack of relationship between phenotype and genotype. Due to nonspecific symptoms and delay in diagnosis, CYP27A1 genetic analysis should be the definitive method for CTX diagnosis.

Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations

Background

In the search for novel causal mutations, public and/or private variant databases are nearly always used to facilitate the search as they result in a massive reduction of putative variants in one step. Practically, variant filtering is often done by either using all variants from the variant database (called the absence-approach, i.e. it is assumed that disease-causing variants do not reside in variant databases) or by using the subset of variants with an allelic frequency > 1% (called the 1%-approach). We investigate the validity of these two approaches in terms of false negatives (the true disease-causing variant does not pass all filters) and false positives (a harmless mutation passes all filters and is erroneously retained in the list of putative disease-causing variants) and compare it with an novel approach which we named the quantile-based approach. This approach applies variable instead of static frequency thresholds and the calculation of these thresholds is based on prior knowledge of disease prevalence, inheritance models, database size and database characteristics.

Results

Based on real-life data, we demonstrate that the quantile-based approach outperforms the absence-approach in terms of false negatives. At the same time, this quantile-based approach deals more appropriately with the variable allele frequencies of disease-causing alleles in variant databases relative to the 1%-approach and as such allows a better control of the number of false positives.

We also introduce an alternative application for variant database usage and the quantile-based approach. If disease-causing variants in variant databases deviate substantially from theoretical expectancies calculated with the quantile-based approach, their association between genotype and phenotype had to be reconsidered in 12 out of 13 cases.

Conclusions

We developed a novel method and demonstrated that this so-called quantile-based approach is a highly suitable method for variant filtering. In addition, the quantile-based approach can also be used for variant flagging. For user friendliness, lookup tables and easy-to-use R calculators are provided.

Electronic supplementary material

The online version of this article (doi: 10.1186/s12859-017-1951-y) contains supplementary material, which is available to authorized users.

A novel mutation in the sterol 27-hydroxylase gene of a woman with autosomal recessive cerebrotendinous xanthomatosis

Article abstract

Mutations of the gene encoding the mitochondrial enzyme sterol 27-hydroxylase (CYP27A1 gene) cause defects in the cholesterol pathway to bile acids that lead to the storage of cholestanol and cholesterol in tendons, lenses and the central nervous system. This disorder is the cause of a clinical syndrome known as cerebrotendinous xanthomatosis (CTX). Since 1991 several mutations of the CYP27A1 gene have been reported. We diagnosed the clinical features of CTX in a caucasian woman. Serum levels of cholestanol and 7α-hydroxycholesterol were elevated and the concentration of 27-hydroxycholesterol was reduced. Bile alcohols in the urine and faeces were increased. The analysis of the CYP27A1 gene showed that the patient was a compound heterozygote carrying two mutations both located in exon 8. One mutation is a novel four nucleotide deletion (c.1330-1333delTTCC) that results in a frameshift and the occurrence of a premature stop codon leading to the formation of a truncated protein of 448 amino acids. The other mutation, previously reported, is a C - > T transition (c. c.1381C > T) that converts the glutamine codon at position 461 into a termination codon (p.Q461X). These truncated proteins are expected to have no biological function being devoid of the cysteine residue at position 476 of the normal enzyme that is crucial for heme binding and enzyme activity.

Cholestanol Metabolism, Molecular Pathology, and Nutritional Implications

Cholestanol, not cholesterol, is a minor component in the human body and in foods, but an increase in cholestanol concentration in serum induces a pathological condition named cerebrotendinous xanthomatosis (CTX). In our investigation of this disease for more than 25 years, a procedure for quantification of cholestanol by high-performance liquid chromatography and an assay method for sterol 27-hydroxylase were established, and several mutations of the CYP 27 gene in 10 CTX families were identified. We also established experimental animal models with symptoms of CTX by feeding a high cholestanol diet. Corneal dystrophy and gallstones were produced in mice, and an apoptosis of cerebellar neuronal cells was observed in rats. We propose the following underlying mechanism of CTX pathogenesis: When cholesterol in the plasma membrane is replaced by cholestanol to some extent, the membrane fluidity is reduced, and the calcium channel fails to open, inducing cell death. CTX patients are treated with oral administration of chenodeoxycholic acid, which reduces the cholestanol concentration in serum. Cholestanol has a toxic effect, and an imbalance of the cholesterol/cholestanol ratio in plasma membrane is suspected to cause the disturbance of calcium channel function of the membrane.

Pharmacogenomics of drugs affecting the cardiovascular system

The variability in drug response originates partly from genetics, with possible consequences for drug efficacy, adverse effects, and toxicity. Until now, pharmacogenetics mainly indicated the best known source of variability, that is, the variability caused by drug metabolism. However, simultaneous progress in the knowledge of biochemical targets of drugs and of the human genome, together with the development of new technologies, revealed many new sources of human genetic variation, e.g., in receptors or transporters. Drugs are metabolized by various polymorphic phase I enzymes, including cytochromes P450 (CYP). Among them, the most relevant for the metabolism of cardiovascular drugs are CYP3A4, CYP2C9 or CYP2C19, and CYP2D6. The role of phase II enzymes is limited with regard to cardiovascular drugs biotransformation, but some polymorphisms (glutathion-S-transferase; GSH-T) are linked to cardiovascular risk. Phase III proteins or transporters, especially from the ABC family, must also be considered, as their polymorphisms affect cholesterol and other sterols transport. Among pharmacological targets, some proteins were identified as involved in interindividual variations in the response to cardiovascular drugs. Some examples are apolipoprotein E, angiotensin-converting enzyme, and the beta-adrenergic receptor. From the risk concept emphasizing impaired metabolism and adverse effects, we now moved to an approach, which is a personalized, genotype-dependent adaptation of therapy.

Clinical and molecular genetic characteristics of patients with cerebrotendinous xanthomatosis

Cerebrotendinous xanthomatosis (CTX) is a lipid storage disease caused by a deficiency of the mitochondrial enzyme 27-sterol hydroxylase (CYP 27), due to mutations in its gene. In this study we report on mutations in 58 patients with CTX out of 32 unrelated families. Eight of these were novel mutations, two of which were found together with two already known pathogenic mutations. Twelve mutations found in this patient group have been described in the literature. In the patients from 31 families, mutations were found in both alleles. In the literature, 28 mutations in 67 patients with CTX out of 44 families have been described. Pooling our patient group and the patients from the literature together, 37 different mutations in 125 patients out of 74 families were obtained. Identical mutations have been found in families from different ethnic backgrounds. In 41% of all the patients, CYP 27 gene mutations are found in the region of exons 6-8. This region encodes for adrenodoxin and haem binding sites of the protein. Of these 125 patients, a genotype-phenotype analysis was done for 79 homozygous patients harbouring 23 different mutations, out of 45 families. The patients with compound heterozygous mutations were left out of the genotype-phenotype analysis. The genotype-phenotype analysis did not reveal any correlation.