Structural, Functional, and Clinical Characterization of a Novel PTPN11 Mutation Cluster Underlying Noonan Syndrome

Germline mutations in PTPN11, the gene encoding the Src-homology 2 (SH2) domain-containing protein tyrosine phosphatase (SHP2), cause Noonan syndrome (NS), a relatively common, clinically variable, multisystem disorder. Here, we report on the identification of five different PTPN11 missense changes affecting residues Leu²⁶¹ , Leu²⁶² , and Arg²⁶⁵ in 16 unrelated individuals with clinical diagnosis of NS or with features suggestive for this disorder, specifying a novel disease-causing mutation cluster. Expression of the mutant proteins in HEK293T cells documented their activating role on MAPK signaling. Structural data predicted a gain-of-function role of substitutions at residues Leu²⁶² and Arg²⁶⁵ exerted by disruption of the N-SH2/PTP autoinhibitory interaction. Molecular dynamics simulations suggested a more complex behavior for changes affecting Leu²⁶¹ , with possible impact on SHP2's catalytic activity/selectivity and proper interaction of the PTP domain with the regulatory SH2 domains. Consistent with that, biochemical data indicated that substitutions at codons 262 and 265 increased the catalytic activity of the phosphatase, while those affecting codon 261 were only moderately activating but impacted substrate specificity. Remarkably, these mutations underlie a relatively mild form of NS characterized by low prevalence of cardiac defects, short stature, and cognitive and behavioral issues, as well as less evident typical facial features.

Y chromosome azoospermia factor region microdeletions and recurrent pregnancy loss

OBJECTIVE

This study was undertaken to determine the prevalence of Y-chromosome microdeletions in couples with recurrent pregnancy loss (RPL) as compared with fertile couples.

STUDY DESIGN

Forty-three men from couples with recurrent pregnancy loss, and 43 men from couples with a live birth and no history of miscarriages were recruited from Zekai Tahir Burak Woman Health, Education and Research Hospital. The DNA was tested for the presence of 4 sequence tagged sites (STSs) spanning 4 AZF regions: DYS220 (AZFb), DYS235, DYS236, and DYS237 (AZFd).

RESULTS

Seven (7) of the 43 men (16%) from couples with recurrent pregnancy loss had microdeletions in 1 or more of the 4 segments studied, whereas none of the fertile men had any microdeletions (P < .05). Their microdeletions were all found specifically at locus DYS 220 (AZFb).

CONCLUSION

The prevalence of the Y chromosome microdeletion in AZF region was much higher in men from couples with recurrent pregnancy loss than men in fertile couples. This study showed that Y chromosome microdeletion in AZF region may be a possible etiologic factor of recurrent pregnancy loss.

Early-Onset Mild Type Leukoencephalopathy Caused by a Homozygous EARS2 Mutation

Childhood leukoencephalopathies are a broad class of diseases, which are extremely rare. The treatment and classification of these disorders are both challenging. Nearly half of children presenting with a leukoencephalopathy remain without a specific diagnosis. Leukoencephalopathy with thalamus and brain stem involvement and high lactate (LTBL) is a newly described childhood leukoencephalopathy caused by mutations in the gene encoding a mitochondrial aminoacyl-tRNA synthetase specific for glutamate, EARS2 Magnetic resonance images show a characteristic leukoencephalopathy with thalamic and brain stem involvement. Here, we report a different clinical course of LTBL supported by typical MRI features in a Turkish patient who presented with a history of failure to walk. The EARS2 gene mutation analysis identified a c.322C>T transition, predicting a p.R108W change. This is the first reported early-onset mild type LTBL caused by a homozygous EARS2 mutation case in the literature.

An unexpected finding in a child with neurological problems: mosaic ring chromosome 18

Major neurological disorders may accompany rare chromosomal abnormalities. As an example of this rare condition, we present a case with microcephaly, mental retardation, developmental delay, hyperactivity, stereotypic movements, seizures and dysmorphic facial appearance in whom a mosaic ring chromosome 18 was found [45,XX,-18/46,XX,r(18)/46,XX,dicr(18)]. Although ring chromosome 18 phenotype has been known for a long time, this is the third reported patient with a dicentric ring chromosome 18 mosaicism. The presented case will contribute to the identification of the genotype-phenotype correlation in chromosome 18 anomalies.

Gorlin-Chaudhry-Moss syndrome revisited: expanding the phenotype

Gorlin-Chaudhry-Moss syndrome (OMIM 233500) is a rare congenital malformation syndrome with the cardinal manifestations of craniofacial dysostosis, hypertrichosis, underdeveloped genitalia, ocular, and dental anomalies. Since 1960, only six affected individuals have been reported. We report a 4-year and 6-month-old female patient with this phenotype and review the clinical presentation of all patients known so far. Previously unreported malformations of the extremities, larynx, and nose are also described, expanding the phenotype of this rare syndrome. Array-CGH analysis did not show pathological deletions or duplications.

17βHSD-3 enzyme deficiency due to novel mutations in the HSD17B3 gene diagnosed in a neonate

17-β-Hydroxysteroid dehydrogenase type 3 (17βHSD-3) is present almost exclusively in the testes, and converts androstenedione (A) to testosterone (T). 17βHSD-3 deficiency is rare. The diagnosis can be missed in early childhood as the clinical presentation may be subtle. The most frequent presentation of 17 HSD-3 deficiency is a 46,XY individual with female external genitalia, labial fusion and a blind ending vagina, with or without clitoromegaly. A low testosterone/androstenedion (T/A) ratio is suggestive of 17βHSD-3 deficiency, and such diagnosis can be confirmed with molecular genetic studies. A 12-day newborn was referred to our hospital because of palpable gonads in the labia majora. On physical examination, the baby had female external genitalia and palpable gonads in the labia majora. T/A ratio was 0.26 and the diagnosis was 17βHSD-3 deficiency, which was confirmed by the evidence of compound heterozygousity novel frameshift mutations in exon 9 and 10 of HSD17B3 gene.

A new nonsense mutation in the NF1 gene with neurofibromatosis-Noonan syndrome phenotype

PURPOSE

Neurofibromatosis-Noonan syndrome is a rare autosomal dominant disorder which combines neurofibromatosis type 1 (NF1) features with Noonan syndrome. NF1 gene mutations are reported in the majority of these patients.

METHOD

Sequence analysis of the established genes for Noonan syndrome revealed no mutation; a heterozygous NF1 point mutation c.7549C>T in exon 51, creating a premature stop codon (p.R2517X), had been demonstrated.

RESULT

Neurofibromatosis-Noonan syndrome recently has been considered a subtype of NF1 and caused by different NF1 mutations.

CONCLUSION

We report the case of a 14-year-old boy with neurofibromatosis type 1 with Noonan-like features, who complained of headache with triventricular hydrocephaly and a heterozygous NF1 point mutation c.7549C>T in exon 51.

A case of campomelic dysplasia in whom a new mutation was found in the SOX9 gene

Campomelic dysplasia (CD, OMIM #114290) is a rare autosomal dominant disease characterized with bending and shortness in the long bones of the lower extremities, typical facial features, hypoplastic scapula, costa defect, narrow thorax and pes equinovarus. Campomelic dysplasia occurs with heterozygous mutations in the SOX9 gene in the 17q24 chromosome. The main findings of our four-day old patient included typical facial features, risomelic extremity shortness, angular bending in the long bones of bilateral lower extremities and pes equinovarus. On direct graphies, costa defect and scapula hypoplasia were noted. We showed a missense mutation (c.473C>T [p.A158V]) in the SOX9 gene which had not been reported before in our patient who had the typical clinical findings of CD. The family of the patient was informed about potential future pathologies of this disease and received genetic counseling.

Targeted next-generation sequencing (NGS) analysis of mutations in nonsyndromic tooth agenesis candidate genes : Analysis of a Turkish cohort

PURPOSE

The goal of this study was to assess genes known to be associated with tooth agenesis with next-generation sequencing (NGS) and analyze the relationship between these mutations and tooth agenesis phenotypes.

METHODS

The study included 49 individuals aged between 6 and 13 years. A total of 14 genes related to nonsyndromic tooth agenesis were selected for targeted NGS. Mutations in Msh homeobox 1 (MSX1), Wnt family member 10A (WNT10A), axis inhibition protein 2 (AXIN2), keratin 17 (KRT17), lipoprotein receptor 6 (LRP6), and secreted protein, acidic and rich in cysteine (SPARC)-related modular calcium-binding protein 2 (SMOC2) genes were investigated.

RESULTS

Mutations in six genes were detected in 12 of 49 subjects. Fifteen variants were identified, including the unknown variants c.657G > C in MSX1, c.2029C > T in AXIN2, and c.1603A > T in LRP6. Second premolar tooth agenesis was observed in 43.3% of all tooth agenesis cases with mutations, and it was the predominant phenotype observed for each mutated gene, followed by tooth agenesis of the lateral incisors (20%).

CONCLUSIONS

Variations in MSX1, WNT10A, AXIN2, KRT17, LRP6, and SMOC2 may be a risk factor for hypodontia or oligodontia in the Turkish population.

Two newborn babies with generalized arterial calcification of infancy, two new mutations

Idiopathic generalized arterial calcification of infancy-1 (GACI-1) is a rare and potentially lethal disease characterized by diffuse calcification of large and medium-sized arteries such as aorta, renal, pulmonary, cerebral and mesenteric arteries. Here we report two new mutations in two newborn babies with GACI-1 treated with bisphosphonates, and their progress in the first year of life.

Microcephaly and developmental delay caused by short-chain acyl-CoA dehydrogenase deficiency

Kılıç M, Şenel S, Karaer K, Ceylaner S. Microcephaly and developmental delay caused by short-chain acyl-CoA dehydrogenase deficiency. Turk J Pediatr 2017; 59: 708-710. We report a four-year-old girl who presented with intrauterine growth retardation, mild dysmorphism, cleft palate, microcephaly, developmental delay, epilepsy and recurrent lower respiratory tract infection and diagnosed short-chain acyl-CoA dehydrogenase deficiency. Metabolic evaluation and molecular analysis confirmed the diagnosis. In spite of many patients already known in literature, this is one of the rarest reports of a Turkish patient. This suggests selective metabolic screening should be done in every patient with unknown etiology of neurological disorder. Furthermore, newborn screening using tandem mass spectrometry may prevent this severe neurological impairment.

A novel mutation in a case of pseudohypoparathyroidism type Ia

Pseudohypoparathyroidism (PHP) type Ia is characterized by multiple hormone resistance; primarily parathyroid hormone (PTH) resistance and Albright's hereditary osteodystrophy (AHO) which involves skeletal and developmental defects. The AHO phenotype alone without hormone resistance is defined as pseudoPHP. A boy was first diagnosed as having both rickets and primary hypothyroidism at 2.5 months of age. His calcium level remained within normal levels after vitamin D treatment, but, elevated PTH and ALP levels and normal-high phosphate levels persisted during his follow-up by age of 2.5 years. He was admitted with hypocalcemic convulsions as well as hyperphosphatemia and elevated PTH levels suggested PTH resistance at 2.5 years of age. He and his mother were obese and had round faces, frontal bossing, small noses, flat nasal bridges, brachydactyly. His mother showed no hormonal resistance. These findings indicated that our patient had PHP type Ia and his mother had pseudoPHP. The same novel heterozygous mutation in the GNAS gene (IVS4+5G > C) was identified in both of patients.

Novel mutation in SUCLA2 identified on sequencing analysis

Succinate-CoA ligase, ADP-forming, beta subunit (SUCLA2)-related mitochondrial DNA depletion syndrome is caused by mutations affecting the ADP-using isoform of the beta subunit in succinyl-CoA synthase, which is involved in the Krebs cycle. The SUCLA2 protein is found mostly in heart, skeletal muscle, and brain tissues. SUCLA2 mutations result in a mitochondrial disorder that manifests as deafness, lesions in the basal ganglia, and encephalomyopathy accompanied by dystonia. Such mutations are generally associated with mildly increased plasma methylmalonic acid, increased plasma lactate, elevated plasma carnitine esters, and the presence of methylmalonic acid in urine. In this case report, we describe a new mutation in a patient with a succinyl-CoA synthase deficiency caused by an SUCLA2 defect.

Vocal cord immobility as a cause of aphonia in a child with 3p13p12 deletion syndrome encompassing FOXP1 gene

Congenital bilateral laryngeal paralysis/immobilization is an uncommon condition and has been described as isolated or accompanying to some recognizable syndromes. Heterozygous mutations in the FOXP1 gene (605515) are related with intellectual disability and, language impairment with or without autistic features. Expressive language is more affected than receptive language and more than half of the patients experience oromotor dysfunction and/or feeding difficulties. Here we report a child with severe developmental, speech delay and aphonia which was considered due to bilaterally abductor vocal cord immobility. Interstitial 8700 kbp deletion encompassing FOXP1 gene was detected on 3p13p12 chromosomal region. Although it is known that FOXP1 defects are related to abnormalities in vocal communication, FOXP1-associated laryngomalacia or vocal cord paralysis/immobilization cases have not been reported yet. The FOXP1 defects are considered to be a cause of delay in speech, and it is suggested that vocal cord evaluation should be conducted in suspicious cases.

Neurodevelopmental disorder with microcephaly, ataxia, and seizures syndrome: expansion of the clinical spectrum

Neurodevelopmental disorder with microcephaly, ataxia, and seizures (NEDMAS) syndrome is a rare neurodevelopmental disorder characterized by moderate intellectual disability (ID), thin body habitus, microcephaly, seizures, ataxia, muscle weakness, and speech impairment. So far, only two families with NEDMAS have been reported. We report the clinical and molecular characteristics of three unrelated Turkish families with four NEDMAS patients. Whole-exome sequencing was used to search for the disease-causing variant. The main manifestations of the probands are severe developmental delay and ID, thin body habitus, and severe hypotonia. Brain imaging revealed bilateral cerebral and cerebellar diffuse atrophy. Sequencing results showed that both patients carried a novel missense variant c.1196C>T (p.Thr399Met) in the seryl-tRNA synthetase gene. Our findings help expand the variant spectrum of NEDMAS and provide additional information for diagnosing cases with atypical features.

From cataract to syndrome diagnosis: Revaluation of Warburg-Micro syndrome Type 1 patients

Warburg-Micro syndrome (WARBM) is a rare autosomal recessively inherited neuro-ophthalmologic syndrome. Although WARBM shows genetic heterogeneity, the pathogenic variants in RAB3GAP1 were the most common cause of WARBM. In this study, we aimed to evaluate the detailed clinical and dysmorphic features of seven WARBM1 patients and overview the variant spectrum of RAB3GAP1 in comparison with the literature who were referred due to congenital cataracts. A previously reported homozygous variant (c.2187_2188delGAinsCT) was identified in three of these patients, while the other four had three novel variants (c.251_258delAGAA, c.2606+1G>A, and c.2861_2862dupGC). Congenital cataract and corpus callosum hypo/agenesia are pathognomonic for WARBM, which could be distinguished from other similar syndromes with additional typical dysmorphic facial features. Although there is no known phenotype and genotype correlation in any type of WARBM, RAB3GAP1 gene analysis should be previously requested as the first step of genetic diagnosis in clinically suspicious patients when it is not possible to request a multi-gene panel.

NRXN2 Homozygous Variant Identified in a Family with Global Developmental Delay, Severe Intellectual Disability, EEG Abnormalities and Speech Delay: A new Syndrome?

Background. This study aims to characterize the clinical phenotype of a family with two siblings exhibiting neurological manifestations, utilizing whole exome sequencing (WES) to identify potential pathogenic variants within the NRXN2 gene. Methods. A consanguineous family with two affected siblings displaying developmental delay, severe intellectual disability, epilepsy, and speech delay was examined. WES was performed on DNA samples from affected and unaffected family members, followed by a comprehensive bioinformatics analysis. In-silico tools were employed for variant interpretation and structural modeling of the NRXN2 protein. Clinical and genetic data were integrated to elucidate the potential impact of the identified variant. Results. WES revealed a novel homozygous missense variant (c.1475T>G, p.Leu492Arg) in the NRXN2 gene in both affected siblings. This variant was absent in healthy family members and public databases. In-silico analysis predicted a detrimental effect on protein function. Parental segregation confirmed heterozygous carrier status. The variant was classified as 'Likely Pathogenic' based on ACMG/AMP criteria. Conclusion. This study identifies a novel homozygous missense variant in NRXN2 associated with global developmental delay, severe intellectual disability, speech delay and epilepsy. The findings underscore the critical role of NRXN2 in neurodevelopment and highlight the potential implications of genetic variations within this gene in neurodevelopmental disorders. Further research and functional validation are warranted to deepen our understanding of NRXN2-related disorders and explore potential therapeutic interventions.

The case of an infertile male with an uncommon reciprocal X-autosomal translocation: how does this affect male fertility?

Infertility is defined as the inability to conceive after one year of regular unprotected intercourse. Constitutional numerical and/or structural chromosomal aberrations like sex-chromosome aberrations are one of the possible factors involved in fertility problems. Reciprocal translocations between an X-chromosome and an autosome are rarely seen in men. Male carriers of an X-autosome translocation are invariably sterile, regardless of the position of the breakpoint in the X-chromosome. Breakpoints in autosomal chromosomes could also be involved in male infertility. In this paper, we describe a 31-year-old male with azoospermia. GTG banding with high resolution multicolor-banding (MCB) techniques revealed a karyotype 46,Y,t(X;1)(p22.3;q25), and we discuss how the breakpoint of this translocation could affect male infertility. As a conclusion, cytogenetic evaluation of infertile subjects with azoospermia should be considered in the first place before in vitro fertilisation procedures are planned.