Whole exome sequencing identified two homozygous ALMS1 mutations in an Iranian family with Alström syndrome

Genotype-phenotype associations in Alström syndrome: a systematic review and meta-analysis

BACKGROUND

Alström syndrome (ALMS; #203800) is an ultrarare monogenic recessive disease. This syndrome is associated with variants in the ALMS1 gene, which encodes a centrosome-associated protein involved in the regulation of several ciliary and extraciliary processes, such as centrosome cohesion, apoptosis, cell cycle control and receptor trafficking. The type of variant associated with ALMS is mostly complete loss-of-function variants (97%) and they are mainly located in exons 8, 10 and 16 of the gene. Other studies in the literature have tried to establish a genotype-phenotype correlation in this syndrome with limited success. The difficulty in recruiting a large cohort in rare diseases is the main barrier to conducting this type of study.

METHODS

In this study we collected all cases of ALMS published to date. We created a database of patients who had a genetic diagnosis and an individualised clinical history. Lastly, we attempted to establish a genotype-phenotype correlation using the truncation site of the patient's longest allele as a grouping criteria.

RESULTS

We collected a total of 357 patients, of whom 227 had complete clinical information, complete genetic diagnosis and meta-information on sex and age. We have seen that there are five variants with high frequency, with p.(Arg2722Ter) being the most common variant, with 28 alleles. No gender differences in disease progression were detected. Finally, truncating variants in exon 10 seem to be correlated with a higher prevalence of liver disorders in patients with ALMS.

CONCLUSION

Pathogenic variants in exon 10 of the ALMS1 gene were associated with a higher prevalence of liver disease. However, the location of the variant in the ALMS1 gene does not have a major impact on the phenotype developed by the patient.

New pathogenic variants of ALMS1 gene in two Chinese families with Alström Syndrome

Purpose

Alström Syndrome (AS) is an autosomal recessive hereditary disease with the characteristics of multiorgan dysfunction. Due to the heterogeneity of clinical manifestations of AS, genetic testing is crucial for the diagnosis of AS. Herein, we used whole-exome sequencing (WES) to determine the genetic causes and characterize the clinical features of three affected patients in two Chinese families with Alström Syndrome.

Materials and methods

Three affected patients (initially diagnosed as achromatopsia). and five asymptomatic members were recruited for both genetic and clinical tests. The complete ophthalmic examinations and systemic examinations were performed on all participants. Whole exome sequencing (WES) was performed for mutation detection. The silico analysis was also applied to predict the pathogenesis of identified pathogenic variants.

Results

In family 1, the proband showed low vision, hyperopia, photophobia, nystagmus, and total color blindness. DNA analysis revealed that she carried a compound heterozygote with two novel pathogenic variants in the ALMS1 gene NM_015120.4:c.10379del (NP_055935.4:p.(Asp2252Tyr)) and NM_015120.4:c.11641_11642del (NP_055935.4:p.(Val3881ThrfsTer11)). Further systemic examinations showed short stature, acanthosis nigricans, and sensorineural hearing loss. In family 2, two affected siblings presented the low vision, hyperopia, photophobia, nystagmus, and total color blindness. DNA analysis revealed that they carried a same compound heterozygote with two novel pathogenic variants in the ALMS1 gene NM_015120.4:c.10379del (NP_055935.4:p.(Asn3460IlefsTer49)), NM_015120.4:c.10819C > T (NP_055935.4:p.(Arg3607Trp)). Further systemic examinations showed obesity and mild abnormalities of lipid metabolism. According to the genetic testing results and further systemic analysis, the three affected patients were finally diagnosed as Alström Syndrome (AS).

Conclusions

We found two new compound heterozygous pathogenic variants of the ALMS1 gene and determined the diagnosis as Alström Syndrome in three patients of two Chinese families. Our study extends the genotypic and phenotypic spectrums for ALMS1 -AS and emphasizes the importance of gene testing in assisting the clinical diagnosis for cases with phenotypic diversities, which would help the AS patients with early diagnosis and treatment to reduce future systemic damage.

A very early diagnosis of Alstrӧm syndrome by next generation sequencing

Background

Alström syndrome is a rare recessively inherited disorder caused by variants in the ALMS1 gene. It is characterized by multiple organ dysfunction, including cone-rod retinal dystrophy, dilated cardiomyopathy, hearing loss, obesity, insulin resistance, hyperinsulinemia, type 2 diabetes mellitus and systemic fibrosis. Heterogeneity and age-dependent development of clinical manifestations make it difficult to obtain a clear diagnosis, especially in pediatric patients.

Case presentation

Here we report the case of a girl with Alström syndrome. Genetic examination was proposed at age 22 months when suspected macular degeneration was the only major finding. Next generation sequencing of a panel of genes linked to eye-related pathologies revealed two compound heterozygous variants in the ALMS1 gene. Frameshift variants c.1196_1202del, p.(Thr399Lysfs*11), rs761292021 and c.11310_11313del, (p.Glu3771Trpfs*18), rs747272625 were detected in exons 5 and 16, respectively. Both variants cause frameshifts and generation of a premature stop-codon that probably leads to mRNA nonsense-mediated decay. Validation and segregation of ALMS1 variants were confirmed by Sanger sequencing.

Conclusions

Genetic testing makes it possible, even in childhood, to increase the number of correct diagnoses of patients who have ambiguous phenotypes caused by rare genetic variants. The development of high-throughput sequencing technologies offers an exceptionally valuable screening tool for clear genetic diagnoses and ensures early multidisciplinary management and treatment of the emerging symptoms.

A homozygous missense mutation of WFS1 gene causes Wolfram's syndrome without hearing loss in an Iranian family (a report of clinical heterogeneity)

Background

Wolfram's syndrome (WFS) is a hereditary (autosomal recessive) neurodegenerative disorder. The clinical features are related to diabetes insipidus, diabetes mellitus, optic atrophy, and deafness (DIDMOAD) with other variable clinical manifestations. Pathogenic variants in the WFS1 gene, encoding wolframin, are known to be the main cause of Wolfram's syndrome. In this study, we present the clinical and genetic characteristics of two WFS patients from an Iranian family.

Methods

The mutation screening was performed by polymerase chain reaction (PCR) followed by direct Sanger sequencing of all exons from two affected WFS.

Results

The complete Sanger sequencing of the WFS1 gene detected a homozygous missense variant, c.2207G>A (p.Gly736Asp), in the eighth exon of the WFS1 gene. Both cases developed all the major symptoms of the disease, interestingly, except hearing loss.

Conclusions

Because of the rarity and clinical heterogeneity of WFS, the molecular genetic assay is essential to confirm the diagnosis and management of the WFS patients.

The novel homozygous p.Asn197_Ser201del mutation in BTD gene is associated with profound biotinidase deficiency in an Iranian consanguineous family

BACKGROUND

Biotinidase deficiency is an autosomal recessive inherited inborn error of biotin metabolism. Biotin as a water-soluble vitamin is the prosthetic group of biotin-dependent carboxylase enzymes, and by enhancing their function plays a key role in amino acid catabolism, fatty acid synthesis, and gluconeogenesis. Beyond its prosthetic group role, it has been recognized that biotin regulates the level of gene transcription in the eukaryotic cells, therefore any defect in these pathways causes a multisystem metabolic disorder characterized by neurological and cutaneous symptoms.

METHODS AND RESULTS

We report the identification of a novel pathogenic variant in the BTD gene, c.528_542del15 (p.Asn197_Ser201del, UniProt P43251-1) in an Iranian consanguineous family with a severe form of the disease. The segregation analysis in the family was consistent with phenotype and the identified variant was predicated as a pathogenic mutation by the in-silico prediction tools. Computer structural modeling suggests the deleted amino acid residues are located near the biotinidase active site and disrupt the special conformations which are critical for the enzyme activity, and also N-glycosylation.

CONCLUSIONS

This study further expands the mutation spectrum of the BTD gene underlying cause of profound biotinidase deficiency.