A Novel Biallelic LCK Variant Resulting in Profound T-Cell Immune Deficiency and Review of the Literature.

Lymphocyte-specific protein tyrosine kinase (LCK) is an SRC-family kinase critical for initiation and propagation of T-cell antigen receptor (TCR) signaling through phosphorylation of TCR-associated CD3 chains and recruited downstream molecules. Until now, only one case of profound T-cell immune deficiency with complete LCK deficiency [1] caused by a biallelic missense mutation (c.1022T>C, p.L341P) and three cases of incomplete LCK deficiency [2] caused by a biallelic splice site mutation (c.188-2A>G) have been described. Additionally, deregulated LCK expression has been associated with genetically undefined immune deficiencies and hematological malignancies. Here, we describe the second case of complete LCK deficiency in a 6-month-old girl born to consanguineous parents presenting with profound T-cell immune deficiency. Whole exome sequencing (WES) revealed a novel pathogenic biallelic missense mutation in LCK (c.1393T>C, p.C465R), which led to the absence of LCK protein expression and phosphorylation, and a consecutive decrease in proximal TCR signaling. Loss of conventional CD4+ and CD8+ αßT-cells and homeostatic T-cell expansion was accompanied by increased γδT-cell and Treg percentages. Surface CD4 and CD8 co-receptor expression was reduced in the patient T-cells, while the heterozygous mother had impaired CD4 and CD8 surface expression to a lesser extent. We conclude that complete LCK deficiency is characterized by profound T-cell immune deficiency, reduced CD4 and CD8 surface expression, and a characteristic TCR signaling disorder. CD4 and CD8 surface expression may be of value for early detection of mono- and/or biallelic LCK deficiency.

The outcome of 41 Late-Diagnosed Turkish GA-1 Patients: A Candidate for the Turkish NBS.

BACKGROUND: Glutaric aciduria type 1(GA-1) is an inherited cerebral organic aciduria. Untreated patients with GA-1 have a risk of acute encephalopathic crises during the first 6 years of life. In so far as GA-1 desperately does not exist in Turkish newborn screening (NBS) program, most patients in our study were late-diagnosed. METHOD: This study included 41 patients diagnosed with acylcarnitine profile, urinary organic acids, mutation analyses in the symptomatic period. We presented with clinical, neuroradiological, and molecular data of our 41 patients. RESULTS: The mean age at diagnosis was 14.8 ± 13.9 (15 days to 72 months) and, high blood glutaconic acid, glutarylcarnitine and urinary glutaric acid (GA) levels in 41 patients were revealed. Seventeen different mutations in the glutaryl-CoA dehydrogenase gene were identified, five of which were novel. The patients, most of whom were late-diagnosed, had a poor neurological outcome. Treatment strategies made a little improvement in dystonia and the frequency of encephalopathic attacks. CONCLUSION: All GA-1 patients in our study were severely affected since they were late-diagnosed, while others show that GA-1 is a treatable metabolic disorder if it is diagnosed with NBS. This study provides an essential perspective of the severe impact on GA-1 patients unless it is diagnosed with NBS. We immediately advocate GA-1 to be included in the Turkish NBS.

Specific Granule Deficiency Due To Novel Homozygote SMARCD2 Variant.

Background: Specific granule deficiency (SGD) is a rare immunodeficiency associated with CCAT/enhancer-binding protein epsilon (CEBPE) gene variants. It can cause severe recurrent infections and is lethal without successful stem cell transplantation. Few cases with SGD of both type 1 and type 2 have been described in the literature. In this study, we present the first report of a case with a novel homozygous c.511 C > T (p.Gln171Ter) mutation in the SMARCD2 gene of SGD type 2, which was successfully treated with bone marrow transplantation. Case: A male infant presented to our neonatal intensive care unit on the second day of life with an icteric appearance and mild hypotonia. He was evaluated for immunodeficiency as the cause of delayed cord separation and refractory neutropenia. At 6 weeks of age, SGD type 2 with a new variant was diagnosed and successfully treated by bone marrow transplantation. Conclusion: SGD is an immunodeficiency disease that is quite rare. However, we believe that SGD diagnosis and associated new variants can be detected more frequently with the widespread use of all whole-exome sequencing techniques.

Vascular endothelial growth factor +405 C/G polymorphism is highly associated with an increased risk of endometriosis in Turkish women.

OBJECTIVE: Endometriosis is a chronic gynecological disease characterized by the growth of hormonally responsive, endometrial tissue outside the uterine cavity. The present study aims to analyze two vascular endothelial growth factor (VEGF) polymorphisms (-460 C/T and +405 C/G) in Turkish women with and without endometriosis. STUDY DESIGN: A case-control study was undertaken at the Infertility Department of Zekai Tahir Burak Women's Health Care Education and Research Hospital. The single nucleotide polymorphisms, -460 C/T and +405 C/G, in the 5'-untranslated region of the VEGF gene were tested in 98 affected women and 94 women with no laparoscopic evidence of disease. Endometriosis was also confirmed histologically. Following genomic extraction of genomic DNA, genotyping of the -460 C/T and +405 C/G polymorphisms of the VEGF gene were performed by polymerase chain reaction and restriction fragment length polymorphism assay. Nominal data were evaluated by Pearson Chi-square or Fisher's Exact test, where applicable. Odds ratios and 95% confidence intervals were also calculated. A P value less than 0.05 was considered statistically significant. RESULTS: Demographic data were similar among groups. The genotype and allele frequencies of the -460 C/T polymorphism did not differ significantly between cases and controls. In contrast, the genotype (P < 0.001) and allele frequencies (P < 0.001) of +405 C/G polymorphism showed a significant difference between cases and controls. Regardless of the early or advanced stage, women with endometriosis showed a higher incidence of the +405 GC genotype and +405G allele when compared with the controls. CONCLUSIONS: These data suggest that VEGF +405 GC genotype and +405G allele may be associated with the risk of developing early and advanced stage endometriosis in the Turkish population.

Isolated congenital diaphragm hernia associated with homozygous SLIT3 gene variant in dizygous twins.

Congenital diaphragmatic hernia (CDH) is a serious life-threatening birth defect characterized by abnormal development in the muscular or tendinous portion of the diaphragm during embryogenesis. Despite its high incidence, the etiology of CDH hasn't been fully understood. Genetic factors are important in pathogenesis; however, few single genes have been definitively implicated in human CDH. SLIT1, SLIT2, and SLIT3 (slit guidance ligand) are three human homologs of the drosophila Slit gene. They interact with roundabout (Robo) homolog receptors to affect cell migration, adhesion, cell motility, and angiogenesis and play important roles in cell signaling pathways including the guidance of axons. In this report, we presented dizygous twin babies with CDH related to the SLIT3 gene variant. Previous studies showed that Slit3 null mice had congenital diaphragmatic hernias on or near the ventral midline portion of the central tendon. This is the first report of homozygous SLIT3 variant associated with CDH in humans.

Familial primary carpal tunnel syndrome with possible skipped generation.

Carpal tunnel syndrome, an entrapment neuropathy of the median nerve, is rarely seen in childhood. Familial carpal tunnel syndrome, an even more exceptional entity, is frequently associated with inherited systemic disorders. Rarely it can be presented as a primary familial form with Mendelian autosomal dominant inheritance. We report the occurrence of carpal tunnel syndrome in two generations of a family in which the index case was a 6-year-old boy with bilateral hand pain and paresthesias. Our report demonstrates an interesting inheritance pattern of carpal tunnel syndrome in a family transmitted by an autosomal dominant gene with variable expressivity and reduced penetrance. To our knowledge, it is the first report of familial bilateral carpal tunnel syndrome in a family with possible skipped generation.

Fabry Disease Screening in Patients With Kidney Transplant: A Single-Center Study in Turkey.

OBJECTIVES: Fabry disease is a rare X-linked multisystemic lysosomal storage disorder of the glycosphingolipid metabolic pathway. Nephropathy is one of the most important complications of Fabry disease, and patients with classical phenotype are at risk of developing endstage kidney disease. In this study, we investigated the use of screening for Fabry disease in kidney transplant recipients at our center. MATERIALS AND METHODS: We screened 301 kidney transplant recipients with functioning grafts. Analyses for α-galactosidase A gene mutation were performed in all female and male kidney transplant recipients. We also measured leukocyte α-galactosidase A enzyme activity in patients with identified GLA mutation. RESULTS: In 301 kidney transplant recipients, mean age was 42.9 ± 12.5 years, and the number of male patients was 180 (60%). Mean time after transplant was 79 ± 56 months, and estimated glomerular filtration rate was 66.8 ± 21 mL/min/1.73 m². One male patient who was diagnosed with Fabry disease before kidney transplant was also evaluated (mutation in the α-galactosidase A gene, c.1093_1101dup [p.Tyr365_lle367dup]). In 2 female patients, p.A143T (c.427G>A) mutation of unknown significance and p.D313Y (c.937G>T) heterozygous mutation were identified; however, leukocyte ?-galactosidase A enzyme activity was normal in these patients (63.7 and 67.3 nmol/h/mg protein). In the patient diagnosed with Fabry disease, family screening revealed 4 additional affected family members. DISCUSSIONS: Although prevalence was shown to be low in our center (1/301 patients; 0.33%), screening studies in kidney transplant recipients may help to detect new patients before they develop life-threatening complications such as renal involvement.

GJB2 and mitochondrial A1555G gene mutations in nonsyndromic profound hearing loss and carrier frequencies in healthy individuals.

This study aimed to assess mutations in GJB2 gene (connexin 26), as well as A1555G mitochondrial mutation in both the patients with profound genetic nonsyndromic hearing loss and healthy controls. Ninety-five patients with profound hearing loss (>90 dB) and 67 healthy controls were included. All patients had genetic nonsyndromic hearing loss. Molecular analyses were performed for connexin 26 (35delG, M34T, L90P, R184P, delE120, 167delT, 235delC and IVS1+1 A-->G) mutations, and for mitochondrial A1555G mutation. Twenty-two connexin 26 mutations were found in 14.7% of the patients, which were 35delG, R184P, del120E and IVS1+1 A-->G. Mitochondrial A1555G mutation was not encountered. The most common GJB2 gene mutation was 35delG, which was followed by del120E, IVS1+1 A-->G and R184P, and 14.3% of the patients segregated with DFNB1. In consanguineous marriages, the most common mutation was 35delG. The carrier frequency for 35delG mutation was 1.4% in the controls. 35delG and del120E populations, seems the most common connexin 26 mutations that cause genetic nonsyndromic hearing loss in this country. Nonsyndromic hearing loss mostly shows DFNB1 form of segregation.

[Autosomal dominant inheritance of congenital dislocation of the hip in 16 members of a family]. / Bir ailenin 16 üyesinde otozomal dominant kalitim gösteren gelisimsel kalça çikigi.

The effect of genetic factors on hip dislocation, acetabular dysplasia, and developmental dysplasia of the hip (DDH) has long been recognized. In this report, we presented a large family that showed single gene inheritance for DDH. Pedigree analysis of a pregnant woman revealed a history of DDH in 16 members of the family. Although the pedigree showed autosomal dominant inheritance with reduced penetrance, the prevalence of DDH was considerably high, almost accounting for one-third of the family members, and skipping only one generation. Of 16 cases, three patients were diagnosed at our center. The remaining 13 patients were diagnosed at other centers. Dislocation was diagnosed very late in most of the family members, while four cases were diagnosed at birth. All family members were informed by a detailed clinical letter and recommended evaluation for DDH at every birth.

Investigation of MKRN3 Mutation in Patients with Familial Central Precocious Puberty

Objective: There have been recent advances in the understanding of the etiology of idiopathic central precocious puberty (iCPP) including new genetic associations. The aim of this clinical study was to determine the frequency of MKRN3 mutation in cases of familial iCPP. Methods: Potential sequence variations in the maternally imprinted MKRN3 gene were evaluated in 19 participants from 10 families using next-generation sequencing analysis. Results: MKRN3 variation was found in only one of the 19 (5.3%) subjects. The male patient, who had a medical history of precocious puberty, had a heterozygous mutation, NM_005664.3:c.630_650delins GCTGGGC (p.P211Lfs*16). The father of this patient also had a history of precocious puberty and had the same mutation. p.P211Lfs*16 is a novel variant and it was identified as probably pathogenic by in silico analysis, consistent with the clinical findings. Conclusion: Given that MKRN3 mutation was detected in only one patient, with a paternal history of precocious puberty, this reinforces the importance of accurate family history taking. The detected incidence of MKRN3 variants in our case series was much lower than reported elsewhere which suggests a need for further studies in Turkish iCPP patients.

Impaired glucose tolerance in Fanconi-Bickel syndrome: Eight patients with two novel mutations.

Seker-Yilmaz B, Kör D, Bulut FD, Yüksel B, Karabay-Bayazit A, Topaloglu AK, Ceylaner G, Önenli-Mungan N. Impaired glucose tolerance in Fanconi-Bickel syndrome: Eight patients with two novel mutations. Turk J Pediatr 2017; 59: 434-441. Fanconi-Bickel syndrome (FBS) is a rare, autosomal recessive disorder of carbohydrate metabolism caused by defects in the facilitative glucose transporter 2 (GLUT2 or SLC2A2) gene. Prominent findings are failure to thrive, renal tubular acidosis, hypoglycemia and postprandial hyperglycemia even mimicking diabetes mellitus. Eight patients from 6 families with FBS were included in this study. c.482_483insC homozygous mutation was detected in six patients from four different families. Mutation analysis of SLC2A2 gene revealed two novel homozygous mutations; c.1069delGinsAATAA and c.575A > G. Standard oral glucose tolerance test with 1.75 g/kg oral glucose was performed in six of the patients who were older than 3-years of age. Impaired glucose tolerance was found in all patients as expected and two of them had overt diabetes. None of the antidiabetic medications were given to them in order to avoid significant hypoglycemia. Beside the conservative treatment, follow up with frequent oral glucose tolerance tests are planned. We report these cases of FBS, as GSD XI is rare, two novel mutations were detected and also to highlight the risk of diabetes mellitus; although there is not a consensus about the treatment.

A case of fetal anticonvulsant syndrome with severe bilateral upper limb defect.

Women with epilepsy have a higher risk of having dysmorphic child. We report on a child exposed prenatally to valproate and carbamazepine presenting with severe bilateral upper limb defect and phenotypic features of fetal valproate syndrome. Anticonvulsant drugs can cause severe birth defects, especially when used in combination.

A novel missense mutation, p.(R102W) in WNT7A causes Al-Awadi Raas-Rothschild syndrome in a fetus.

Al-Awadi-Raas-Rothschild syndrome (AARRS) is a rare autosomal recessive disorder which consists of severe malformations of the upper and lower limbs, abnormal genitalia and underdeveloped pelvis. Here, we present a fetus with severe limbs defects, including bilateral humeroradial synostosis, bilateral oligodactyly in hands, underdeveloped pelvis, short femora and tibiae, absence of fibulae, severely small feet, and absence of uterus. An autosomal recessively inherited novel mutation in WNT7A found in the fetus, c.304C > T, affects an evolutionarily well-conserved amino acid, causing the p.(R102W) missense change at protein level. The findings presented in this fetus are compatible with diagnosis of AARRS, expanding the mutational spectrum of limb malformations arising from defects in WNT7A.

Genotypic and phenotypic features of the cystinosis patients from the South Eastern part of Turkey.

We have conducted this study for the purposes of demonstrating the spectrum of mutations and of identifying their effects on the phenotype, with a particular focus on the clinical course, prognosis and response to treatment. A total of 25 patients from 20 families, who have been treated and followed up after being diagnosed with cystinosis. Nine patients were identified with mutations of homozygous c.451A > G, 7 patients with homozygous c.681G > A, 6 patients with homozygous c.834_842del, 2 patients with homozygous c.18_21delGACT and 1 patient with compound heterozygous for c.451A > G/ c.1015G > A. The c.834_842del mutation identified in six patients from four families has not been previously identified. Progression to renal failure occurred earlier in the patients identified with the new mutation, despite treatment. Larger patient series are required to demonstrate the genotypic properties of the patients with cystinosis and their relationship with the clinical course.

A novel mutation in the lysyl hydroxylase 1 gene causes decreased lysyl hydroxylase activity in an Ehlers-Danlos VIA patient.

The clinical diagnosis of a patient with the phenotype of Ehlers-Danlos syndrome type VI was confirmed biochemically by the severely diminished level of lysyl hydroxylase (LH) activity in the patient's skin fibroblasts. A novel homozygous mutation, a single base change of T(1360)-->G in exon 13 of the LH1 gene, predicted to result in W446G, was identified in the patient's full-length cDNA. This was confirmed in genomic DNA from both the patient and her parents, who were heterozygous for the mutation. This mutation was introduced into an LH1-pAcGP67 baculoviral construct and expressed, in parallel with normal LH1, in an insect cell system. The loss of LH activity in the mutated recombinant construct confirmed the pathogenicity of this mutation. Although not in the major catalytic site, this mutation occurs in a highly conserved region of the LH1 gene and may contribute to loss of activity by interfering with normal folding of the enzyme.

Genetic abnormalities in Turkish women with premature ovarian failure.

OBJECTIVE: To identify the distribution of cytogenetic abnormalities among Turkish women with premature ovarian failure (POF). METHOD: A karyotype analysis was performed at the Medical Genetics Department of Zekai Tahir Burak Women's Hospital, Ankara, Turkey, for 75 women younger than 40years found to have POF over a 5-year period. RESULTS: There were 18 familial cases (24%), 1 of which involving an abnormality of the X chromosome [46,X,del(X)(q22)]. Sixteen patients (21.3%) had chromosomal abnormalities such as Xq and Xp deletions, translocations, and numerical aberrations; 2 had Swyer syndrome; 2 were fragile X premutation carriers; and 1 had galactosemia. CONCLUSION: A genetic cause of POF was identified in 39 (52%) of 75 patients. A thorough genetic evaluation of women with POF should be performed regardless of clinical features suggestive of chromosomal abnormality.

Prenatally diagnosed partial trisomy 3q case with an omphalocele and less severe phenotype.

Trisomy 3q is a very rarely reported chromosomal disorder. Duplication of part of the long arm of human chromosome 3 causes a distinct and severe syndrome that leads to multiple congenital abnormalities. A 27 year-old pregnant woman was admitted to our clinic at 17 weeks of gestation. Prenatal sonography identified a fetus with an omphalocele that contained the liver and bowel, mild ventriculomegaly and polyhydramnios. Amniocentesis revealed the karyotype of 46, XY, der (3) (3qter→3q21: : 3pter→3qter). The pregnancy was subsequently terminated. Postnatally, the proband showed midfacial hypoplasia, micrognathia, hypoplastic 12th ribs, omphalocele and prominent heels. We reported this partial trisomy 3q case because he had less marked malformations compared to other reported cases and also different features such as an omphalocele and hypoplastic 12th rib which have not been described previously in an isolated Trisomy 3q case with this karyotype.