A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report.

BACKGROUND: CHARGE syndrome (MIM# 214800)-which is characterised by a number of congenital anomalies including coloboma, ear anomalies, deafness, facial anomalies, heart defects, atresia choanae, genital hypoplasia, growth retardation, and developmental delay-is caused by a heterozygous variant in the CHD7 (MIM# 608892) gene located on chromosome 8q12. We report the identification of a novel c.5535-1G > A variant in CHD7 and provide the evaluation of its effect on pre-mRNA splicing. CASE PRESENTATION: In this study, we report on a female presenting features of CHARGE syndrome. A novel heterozygous CHD7 variant c.5535-1G > A located in the acceptor splice site of intron 26 was identified in the proband's DNA sample after analysis of whole exome sequencing data. In silico predictions indicating that the variant is probably pathogenic by affecting pre-mRNA splicing were verified by genetic analysis based on reverse transcription of the patient's RNA followed by PCR amplifications performed on synthesised cDNA and Sanger sequencing. Sanger sequencing of cDNA revealed that the c.5535-1G > A variant disrupts the original acceptor splice site and activates a cryptic splice site only one nucleotide downstream of the pathogenic variant site. This change causes the omission of the first nucleotide of exon 27, leading to a frameshift in the mRNA of the CHD7 gene. Our results suggest that the alteration induces the premature truncation of the CHD7 protein (UniProtKB: Q9P2D1), thus resulting in CHARGE syndrome. CONCLUSION: Genetic analysis of novel splice site variant underlines its importance for studying the pathogenic splicing mechanism as well as for confirming a diagnosis.

The high frequency of GJB2 gene mutation c.313_326del14 suggests its possible origin in ancestors of Lithuanian population.

BACKGROUND: Congenital hearing loss (CHL) is diagnosed in 1 - 2 newborns in 1000, genetic factors contribute to two thirds of CHL cases in industrialised countries. Mutations of the GJB2 gene located in the DFNB1 locus (13q11-12) are a major cause of CHL worldwide. The aim of this cross-sectional study was to assess the contribution of the DFNB1 locus containing the GJB2 and GJB6 genes in the development of early onset hearing loss in the affected group of participants, to determine the population-specific mutational profile and DFNB1-related HL burden in Lithuanian population. METHODS: Clinical data were obtained from a collection of 158 affected participants (146 unrelated probands) with early onset non-syndromic HL. GJB2 and GJB6 gene sequencing and GJB6 gene deletion testing were performed. The data of GJB2 and GJB6 gene sequencing in 98 participants in group of self-reported healthy Lithuanian inhabitants were analysed. Statistic summary, homogeneity tests, and logistic regression analysis were used for the assessment of genotype-phenotype correlation. RESULTS: Our findings show 57.5% of affected participants with two pathogenic GJB2 gene mutations identified. The most prevalent GJB2 mutations were c.35delG, p. (Gly12Valfs*2) (rs80338939) and c.313_326del14, p. (Lys105Glyfs*5) (rs111033253) with allele frequencies 64.7% and 28.3% respectively. GJB6 gene mutations were not identified in the affected group of participants. The statistical analysis revealed significant differences between GJB2(-) and GJB2(+) groups in disease severity (p = 0.001), and family history (p = 0.01). The probability of identification of GJB2 mutations in patients with various HL characteristics was estimated. The carrier rate of GJB2 gene mutations - 7.1% (~1 in 14) was identified in the group of healthy participants and a high frequency of GJB2-related hearing loss was estimated in our population. DISCUSSION: The results show a very high proportion of GJB2-positive individuals in the research group affected with sensorineural HL. The allele frequency of c.35delG mutation (64.7 %) is consistent with many previously published studies in groups of affected individuals of Caucasian populations. The high frequency of the c.313_326del14 (28.3 % of pathogenic alleles) mutation in affected group of participants was an unexpected finding in our study suggesting not only a high frequency of carriers of this mutation in our population but also its possible origin in Lithuanian ancestors. The high frequency of carriers of the c.313_326del14 mutation in the entire Lithuanian population is supported by it being identified twice in the ethnic Lithuanian group of healthy participants (a frequency 2.0 % of carriers in the study group). CONCLUSION: Analysis of the allele frequency of GJB2 gene mutations revealed a high proportion of c. 313_326del14 (rs111033253) mutations in the GJB2-positive group suggesting its possible origin in Lithuanian forebears. The high frequency of carriers of GJB2 gene mutations in the group of healthy participants corresponds to the substantial frequency of GJB2-associated HL in Lithuania. The observations of the study indicate the significant contribution of GJB2 gene mutations to the pathogenesis of the disorder in the Lithuanian population and will contribute to introducing principles to predict the characteristics of the disease in patients.

Thiamine responsive megaloblastic anemia syndrome: a novel homozygous SLC19A2 gene mutation identified.

Thiamine responsive megaloblastic anemia syndrome (TRMAS) is a rare autosomal recessive disorder especially in countries where consanguinity is uncommon. Three main features are characteristic of the disease - megaloblastic anemia, early onset deafness, and non-type I diabetes. TRMAS is a Mendelian disorder; a gene SLC19A2 coding high affinity thiamine transporter mediating vitamin B1 uptake through cell membrane has been identified. We present the first patient with TRMAS in Lithuania - a 3-year-old boy born to a non-consanguineous family with a novel homozygous SLC19A2 gene mutation. The patient had insulin dependent diabetes (onset 11 months), respiratory illness (onset 11 months), bilateral profound hearing loss (onset at 7 months, verified at 20 months), refractory anemia (onset 2 years), and decreased vision acuity and photophobia (onset 2.5 years). The psychomotor abilities developed according to age. Phenotypic evaluation did not reveal any dysmorphic features. The clinical diagnosis of TRMAS was suspected and daily supplementation with thiamine 100 mg was started. The condition of the patient markedly improved several days after the initiation of treatment. The results of SLC19A2 gene molecular testing confirmed the clinical diagnosis - novel homozygous c.[205G>T], p.[(Val69Phe)] mutation changing conserved amino acid residue or even interfering the mRNA splicing. Clinical heterogeneity, diverse dynamics, and wide spectrum of symptoms are aggravating factors in the diagnosis. The possibility of treatment demands early recognition of disorder to facilitate the improvement of the patient's condition.

Etiological profile of hearing loss amongst Lithuanian pediatric cochlear implant users.

INTRODUCTION: Congenital sensorineural hearing loss is a heterogeneous disorder; its etiological profile varies between populations. Pathogenic variants of GJB2 gene are the major cause of non-syndromic hearing loss. Congenital cytomegalovirus infection (cCMV) is the most important prenatal etiological factor causing hearing loss and other disorders. Perinatal events, syndromes, postnatal infections or traumas are less common. Causes of the remaining one third of hearing loss cases are unknown. OBJECTIVES: To determine the etiological profile of hearing loss in pediatric cochlear implant users in Lithuanian population. METHODS: The data of 122 children (70 male/52 female; aged 7.6 ± 3.3 years) cochlear implant users were analysed. Medical records of all children recruited in Santaros Clinics (Vilnius, Lithuania) were analysed to identify prenatal, perinatal, or postnatal risk factors based on the adapted list proposed by the Joint Committee of Infant Hearing. Genetic counselling and testing according to the scheme were performed to 101 children. DNA of 117 children was extracted from the DBS on Guthrie cards and CMV DNA detected using real time PCR. RESULTS: Non-syndromic hearing loss was diagnosed in 65 cases (53.3%), 58 of which were GJB2 gene-associated; syndromic hearing loss was diagnosed to 8 children (6.6%). Perinatal (prematurity, low birth weight, hypoxia, hyperbilirubinemia, sepsis, ototoxicity, and meningitis) and postnatal (meningitis) risk factors were associated with hearing loss in 16 (13.1%) and 4 (3.3%) study participants respectively. CMV DNA was detected in 12 samples (9.8%). The cause of hearing loss remained unknown only for 17 (13.9%) children. CONCLUSIONS: The major cause of HL in the current study was GJB2 gene alterations. Only 14% of the cohort had congenital hearing loss of unknown origin.

Evaluation of quality of life after paediatric cochlear implantation.

BACKGROUND: Cochlear implantation (CI) is the main treatment method for deaf children. CI influences not only communication, but also psychosocial outcomes in children with severe to profound hearing loss. Focusing on issues specific to CI (e.g., self-reliance, social relations, education) may provide a more accurate and relative view of functional status of paediatric cochlear implant users. The objectives of this study were to translate into Lithuanian and adapt an international questionnaire of the quality of life after cochlear implantation and to evaluate parental perspectives regarding CI and the child's progress after a minimum of two years after surgery. MATERIALS AND METHODS: The parental questionnaire The Children with Cochlear Implants: Parental Perspectives CCIPP was used to evaluate the quality of life following cochlear implantation. The questionnaire includes 74 items covering two main domains: decision-making (26 items) and the outcomes of implantation (48 items). Quality of life is estimated according to the scores of eight sub-domains: communication, general functioning, well-being, self-reliance, social relations, education, effects of implantation, and supporting the child. RESULTS: The paediatric sample consisted of 11 (39%) girls and 17 (61%) boys, whose mean age at the time of cochlear implantation was 2.41 ± 2.25 years, mean duration of the implant use 3.7 ± 1.3 years. All the grand means in the outcomes of implantation domain exceeded 3 on the 5-point scale, meaning that parents viewed the quality of life of their children as either average or better. Parents rated the sub-domains of communication (3.90 ± 0.77 points), social relations (4.05 ± 0.41), and supporting the child (3.89 ± 0.49) most positively. CONCLUSIONS: According to parents, the quality of life improves after the cochlear implantation, especially in the fields of communication, social relations and supporting the child.